JAGT - Qtr 2, 2017

The Journal

of the Association of Genetic Technologists

Volume 43 • Number 2 • Second Quarter 2017

Brain Tickler

Column Editor: Helen Lawce

Brain Tickler

Peripheral blood was received on a 21-year-old female for question of Turner syndrome mosaicism. Fifteen (15) metaphase cells had a 45,X karyotype, and 5 metaphase cells had chromosomes as shown in the photograph below.

Submitted by: Trisha Marsh and Deborah Buckmaster, Oregon Health and Science University, Portland, Oregon.

The answer to this Brain Tickler appears on page 60.

The Journal of the Association of Genetic Technologists Second Quarter 2017 Volume 43, Number 2

Table of Contents

The official journal of the AGT

Brain Tickler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Inside Front Cover Column Editors and Review Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 A Note from the Editor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Editorial Information Editor Mark Terry, BSc Associate Editors Turid Knutsen, MT(ASCP), CLSp(CG) Helen Lawce, BSc, CLSp(CG) Heather E. Williams, MS, CG(ASCP)CM Su Yang, BSc, CLSp(CG) Book Review Editor Helen Lawce, BSc, CLSp(CG) Copyright © 2017 by the AGT. All rights reserved. Contents are not to be reproduced or reprinted without permission of the AGT Editor.

The Journal of the Association of Genetic Technologists is published four times a year and is available to individuals and libraries at a subscription rate of $115 per year. The subscription rate for members of the AGT is included in the annual membership dues.

Back issues can be purchased for members at $25 per issue as long as supplies are available.

Material intended for publication or correspondence concerning editorial matters should be sent to the editor.

JAGT Editor Mark Terry 1264 Keble Lane Oxford, MI 48371 586-805-9407 (cell) Email: markterry@charter.net

Letter to the Editor Mosaic Trisomy 9p in a Patient with Mild Dysmorphic Features and Normal Intelligence Randeep Brar, Donald G. Basel, David P. Bick, LuAnn Weik, Peter vanTuinen, and Jess F. Peterson. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 Brain Tickler Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 Molecular Diagnostics Best Education Practices, Teaching the Next Generation of Technologists NextGeneration Sequencing Michelle Mah. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 Review Cytogenetic Characterization of Myeloid Neoplasms with t(2;3)(p13-25;q25-29): An Analysis of 60 Cases Alexis V. Dowiak and Carlos A. Tirado . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 Continuing Education Opportunities Test Yourself #2, 2017 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 AGT Journal Clubs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 Association Bu siness Association of Genetic Technologists BOD Contacts. . . . . . . . . . . . . . . . . . . . . . . . . . 82 Letter from the President . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 New Membership Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86 Product Order Form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 Scientific Meetings Schedule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Placement service items of less than 150 words and advertisements, requests for back issues, reprint orders, and questions about subscriptions and advertising costs should be sent to the AGT Executive Office at AGT-info@kellencompany.com. Acceptance of advertisements is dependent on approval of the editor-in-chief.

ISSN 1523-7834

The Journal of the Association of Genetic Technologists is indexed in the life sciences database BIOSIS and in the National Library of Medicine’s PubMed. The Journal of the Association of Genetic Technologists 43 (2) 2017

51

The Journal of the Association of Genetic Technologists Staff

Column Editors Abstract Reviews/Genetics in the News Jaime Garcia-Heras, MD, PhD Director of Cytogenetics The Center for Medical Genetics 7400 Fannin, Suite 700 Houston, TX 77054 713-432-1991 713-432-1661 FAX jgarcia@geneticstesting.com Brain Tickler/Book Review Editor Helen Lawce, BSc, CLSp(CG) Clinical Cytogenetics Laboratory Oregon Health Sciences University 3181 SW Sam Jackson Parkway MP-350 Portland, OR 97201 503-494-2790 503-494-6104 FAX lawceh@ohsu.edu

Genetics, Government & Regulation Helen Bixenman, MBA, CLSup, CLSp(CG) San Diego Blood Bank 3636 Gateway Center Avenue, Suite 100 San Diego, CA 92102 619-400-8254 hbixenman@sandiegobloodbank.org Jennifer Crawford-Alvares Cytogenetic Technologist II Section of Hematology/Oncology The University of Chicago Medicine 5841 S. Maryland Ave., Rm. I-304 Chicago, IL jen.crawford34@gmail.com Office: 773-702-9153

Meeting Notices Jun Gu, MD, PhD, CG(ASCP)CM University of Texas MD Anderson Cancer Center School of Health Professions Cytogenetic Technology Program 1515 Holcombe Blvd., Unit 2 Houston, TX 77030 713-563-3094 jungu@mdanderson.org Molecular Diagnostics Michelle Mah, MLT, MB(ASCP)CM Advanced Diagnostics Lab Princess Margaret Cancer Centre University Health Network 610 University Ave., Rm 7-707 Toronto, Ontario Canada M5G 2M9 416-946-4501 ext.5036 michelle.j.mah@gmail.com

Letters to the Editor Mark Terry, JAGT Editor 1264 Keble Lane Oxford, MI 48371 586-805-9407 (cell) markterry@charter.net

Special Interests Turid Knutsen, MT(ASCP), CLSp(CG) 17836 Shotley Bridge Place Olney, MD 20832 301-570-4965 turid.knutsen@verizon.net Test Yourself Sally J. Kochmar, MS, CG(ASCP)CM Magee-Womens Hospital Pittsburgh Cytogenetics Lab 300 Halket St., Room 1233 Pittsburgh, PA 15213 412-641-4882 skochmar@upmc.edu

Profiles & Perspectives Hon Fong Louie Mark, PhD, FACMG President KRAM Corporation 2 Pine Top Road Barrington, RI 02806 401-246-0487 HonFong_Mark@Brown.edu

Review Board Linda Ashworth, BSc, CLSp(CG) (Cytogenetics, Molecular genetics) Helen Bixenman, BSc, CLSp(CG), CLSup (Prenatal diagnosis) Judith Brown, MS, CLSp(CG), CLSp(MB) (Cytogenetics) Kim Bussey, PhD (Cancer genetics, Molecular genetics, Microdissection/PCR/DNA) Mona CantĂş, BSc, CLSp(CG) (Cytogenetics) Anthony Ciminski, CG(ASCP)CM Molecular Genetics, Molecular Cytogenetics Adam Coovadia, CLSpP(CG, MG) (Traditional, Molecular, Regulatory) Philip D. Cotter, PhD, FACMG (Prenatal diagnosis, Chromosome rearrangements, Molecular genetics) Jennifer Costanzo, MS, CLSp(CG) (Cytogenetics, Molecular genetics) Janet Cowan, PhD (Cytogenetics, Cancer genetics, FISH, Solid tumors) Lezlie Densmore, BSc, CLSp(CG) (Cytogenetics, Molecular genetics) Janet Finan, BSc, CLSp(CG) (Hemic neoplasms, Somatic cell hybridization) Lakshan Fonseka, MS (Cytogenetics, Molecular genetics)

Sue Fox, BSc, CLSp(CG) (Bone marrow cytogenetics, Prenatal diagnosis, Supervisory/Management) Jaime Garcia-Heras, MD, PhD (Clinical cytogenetics) Robert Gasparini, MS, CLSp(CG) (Prenatal diagnosis, Cytogenetics) Barbara K. Goodman, PhD, MSc, CLSp(CG) (Molecular cytogenetics)

Hon Fong Louie Mark, PhD, FACMG (Molecular genetics, Somatic cell genetics, Cancer cytogenetics, Breast cancer, Trisomies, Laboratory practices, Regulatory practices, FISH) Jennifer L. McGonigle, BA, CLSp(CG) (Cytogenetics) Karen Dyer Montgomery, PhD, FACMG (Cancer cytogenetics, Cytogenetics, Molecular cytogenetics)

Debra Saxe, PhD (Prenatal diagnosis, Cytogenetics) Jack L. Spurbeck, BSc, CLSp(CG) (Cancer cytogenetics, Molecular genetics) Peggy Stupca, MSc, CLSp(CG) (Cytogenetics, Prenatal diagnosis, Breakage syndromes, FISH, Regulations/ QA)

Nancy Taylor, BSc, CLSp(CG), MT(ASCP) (Cytogenetics, Cancer cytogenetics) Stephen R. Moore, PhD, ABMG Michelle M. Hess, MS, CLSp(CG) (Clinical cytogenetics, radiation biology, (Cytogenetics, Cancer cytogenetics) Thomas Wan, PhD toxicology; clinical molecular genetics) (Cytogenetics, Molecular genetics, Lynn Hoyt, BSc, CLSp(CG), CLSup Cancer genetics) Rodman Morgan, MS, CLSp(CG) (Classical cytogenetics) (Cancer cytogenetics) James Waurin, MSc, CLSp(CG) Peter C. Hu, PhD, MS, MLS(ASCP), CG, MB (Prenatal diagnosis, Counseling) Susan B. Olson, PhD (Cytogenetics, Molecular cytogenetics, (Cancer cytogenetics, Molecular Sara Wechter, BSc Education) genetics, Prenatal diagnosis, OB/GYN, (Cytogenetics, Cancer) Counseling, Cytogenetics) Denise M. Juroske, MSFS, MB(ASCP)CM (Cytogenetics, Molecular, Education) Heather E. Williams, MS, CG(ASCP)CM Jonathan P. Park, PhD (Cytogenetics, Molecular Genetics) (Cytogenetics, Molecular genetics, Julia Kawecki, BSc, CLSp(CG) Cell biology) (Cytogenetics, Molecular genetics) Su Yang, BSc, CLSP(CG) (Education, Traditional Cytogenetics) David Peakman, AIMLT, CLSp(CG) Turid Knutsen, MT(ASCP), CLSp(CG) (Prenatal diagnosis) (Cancer cytogenetics, CGH, SKY) Jason A. Yuhas, BS, CG(ASCP)CM (Cytogenetics, Molecular cytogenetics) Carol Reifsteck, BA Brandon Kubala, BSc, CLSp(CG) (Breakage syndromes, Fanconi’s (Traditional Cytogenetics) James Zabawski, MS, CLSp(CG) anemia, Prenatal diagnosis) (Education, Traditional Cytogenetics) Anita Kulharya, PhD Gavin P. Robertson, PhD (Molecular genetics, Clinical (Cytogenetics, Molecular genetics, cytogenetics) Somatic cell genetics, Tumor suppressor Helen Lawce, BSc, CLSp(CG) genes, Cancer genes) (Prenatal diagnosis, Solid tumors, FISH, Laurel Sakaluk-Moody, MSc, MLT(CG) Chromosome structure, Evolution) (Cytogenetics, Developmental biology, Prenatal cytogenetics)

The Journal of the Association of Genetic Technologists 43 (2) 2017

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A Note from the Editor

Duchenne Muscular Dystrophy, Genetics, the FDA and Drug Pricing When I’m not editing this journal, I am otherwise a freelance writer and editor. The majority of my work these days is focused on the biopharmaceutical industry, covering industry news, career-type articles for graduates in the life sciences, and business-related biopharma materials.

Rather than mention to you the great contents of this issue—it is, go read it—or push you to push your friends and colleagues to join AGT—I’m tired of doing that and you will or you won’t, it’s up to you—I thought I would write on what to me was one of the most interesting topics I covered over the last 18 months. And conveniently, it is genetics related.

“Skipping of the exon 51 enables the truncated production of the dystrophin protein. As a result, a shorter dystrophin protein is produced, which slows the progression of DMD in patients.”

The Circus Begins This story, in its most meaningful way, started for me on January 15, 2016. At that time, there were essentially two companies in a race to get a drug approved for DMD. There are others, but they were the big two. One was Sarepta, the other was San Rafael, California-based BioMarin Pharmaceutical (BMRN). BioMarin’s drug was called Kyndrisa (drisapersen).

In November 2015, the FDA’s Peripheral and Central Nervous System Drugs Advisory Committee got together to discuss Kyndrisa. Of the members, 15 out of 17 voted that they believed the company’s late-stage study lacked statistical significance.

It wasn’t a particularly happy meeting, with the discussions described by The Street’s Adam Feuerstein as “often convoluted and off-target, as if they really didn’t understand the drug or Duchenne muscular dystrophy.”

What happened on January 15, was that the FDA rejected the drug. It should also be noted that the November meeting was a public one, which had numerous patients and their parents testifying about their heartbreaking stories. It’s an awful disease, and one can only feel sympathy and more than a little horror at what it must be like to face it.

At this point, most of the focus—certainly on the part of investors, but also of families of DMD children—shifted to Sarepta. Would the drug be approved? Would it provide, if not a cure, at least some hope for the children and families of DMD children?

Duchenne Muscular Dystrophy (DMD) DMD is a muscle wasting disease. It is caused by mutations in the dystrophin gene which is found on the X chromosome. It has an X-linked recessive inheritance pattern and is passed on by the mother (carrier). It is a progressive disease that usually causes death in early adulthood—often in the 20s, although there have been improvements in treatment, so some patients make it into their 30s and occasionally 40s. In addition to the muscle wasting aspects, serious complications include heart or respiratory-related problems. It mostly affects boys, about 1 in every 3,500 or 5,000 male children.

On September 19, 2016, the FDA approved Sarepta Therapeutics (SRPT)’s eteplirsen, which now goes by the trade name Exondys 51, to treat DMD. It is the first drug to be approved to treat the underlying causes of the disease. [http:// www.biospace.com/News/victory-at-last-sarepta-stock-doublesas-the-fda/432777]

Exondys The dystrophin gene, according to Drug Development Technology, is the largest occurring in nature, and contains 79 exons. The most common mutation in DMD is in exon 51.

Sarepta’s tech platform is known as “exon skipping” or “gene skipping.” Rather than try to explain this myself, I’ll just quote from Drug Development Technology, they did a good job of it: “Exondys 51 is an antisense oligonucleotide produced using Sarepta’s phosphorodiamidate morpholin oligomer (PMO) technology. The drug binds to exon 51 of dystrophin gene to enable exclusion of the exon during expression of the dystrophin gene.

Snowmageddon The FDA hearing on Sarepta’s drug was scheduled for January 22, 2016. On January 21, because of an enormous snowstorm expected to hit the East Coast, the FDA postponed the meeting that was reviewing Sarepta’s New Drug Application (NDA) for eteplirsen. [http://www.biospace.com/News/withsnowmageddon-predicted-for-east-coast-fda/406197] The previous week, at the same time it rejected BioMarin’s drug, an FDA advisory committee did not recommend approval of Sarepta’s drug. But the final decision was to be made on January

AGT Website: www.AGT-info.org Member’s Only area – User Name: First initial, Last initial and AGT ID# (Ex. CR12345) Password: genetics

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A Note from the Editor Duchene Muscular Dystrophy, Genetics, the FDA and Drug Pricing

22, now postponed.

As I wrote on January 21, 2016, “Early evaluation of Sarepta’s eteplirsen have criticized the trial design, efficacy, dystrophin measurement methods, and statistical analysis. In particular, Sarepta’s trial included only 12 patients. ‘It’s a different leap of faith you have to take with Sarepta,’ Ira Loss, an analyst with Washington Analysis, told BloombergBusiness last week. ‘They do have patients who are still walking around after three years.

The risk is you don’t have a lot of patients.’”

The meeting was rescheduled for February 26. Then it was rescheduled for April 25. Officially, it was a meeting of the FDA’s Peripheral and Central Nervous System Advisory Committee.

In the biopharma industry, there is something called the PDUFA date, which stands for Prescription Drug User Fee Act. It’s the date where a decision is made on whether to approve a drug. The advisory committee’s recommendation is taken into consideration, and then a decision is made on whether or not to approve the drug for the market.

did not respond to the drug, was being disregarded by Sarepta, claiming that they weren’t expected to respond to the drug because they were at a later stage of the disease. There were also no real placebo controls to compare the results to. The company used historical data from European studies, arguing that it was unethical to withhold a potentially effective drug from the boys.

The committee voted 6 to 7 against recommending the drug.

The PDUFA date was then scheduled for May 26, 2016.

On May 25, 2016, the FDA and Sarepta announced that the FDA was going to miss the deadline because “they are continuing their review and internal discussions related to our pending NDA for eteplirsen.”

In June, the FDA requested additional information from Sarepta. [http://www.biospace.com/News/sareptas-duchenemuscular-dystrophy-drug/429860] As I wrote in August 18, 2016, in covering a discussion of the placebo effect and the drug, “In short, the FDA seems concerned that Sarepta’s clinical trial and science doesn’t meet the standards other drugs have to meet in order to be approved.

The FDA is not necessarily saying the drug doesn’t work, just that it hasn’t been proven in a way that meets the bar set by the FDA.”

The Circus, Part II: Politics and the Public On March 22, 2016, two co-directors of the Center for Duchenne Muscular Dystrophy at UCLA, M. Carrie Miceli and Stanley Nelson, along with 34 additional doctors and scientists specializing in DMD, wrote a public letter to the FDA. The letter brought up two specific issues. The first: did the patients’ disease progression on eteplirsen substantially deviate from the expected course of the disease in a sufficiently reliable manner? Second: did the drug show “convincing evidence of dystrophin protein induction, the proposed mechanism of action of the drug?”

One of the ways drugs are tested on DMD patients is their ability to walk for six minutes. Although that seems like a relatively objective standard, keep in mind the very real psychological effect, a form of the placebo effect, in being able to walk a specific distance if you think the drug is having an effect. The authors of the letter argued that the three-year data supported accelerated approval by the FDA. They essentially felt the drug should be approved—even if it showed pretty modest effects—and then another four years should be spent on a confirmatory trial, during which patients would be able to receive the drug.

Although I’m sharing this a little out of order, in February 2016, 109 members of Congress also sent a letter to the FDA urging it to accelerate approval of a DMD drug—any DMD drug, apparently, because no specific drug was mentioned in the letter.

A Few Points To Consider Much of my coverage of this story focused on Sarepta. Sarepta is a publicly-traded company, and like many biotech companies, was in an ongoing race between getting the drug approved and what is, by investors, called either the “runway” or the “cash burn.” Both mean that Sarepta had finite funds to work with in order to keep operating, keep its staff working, keep making applications for regulatory approval, keep manufacturing even modest amounts of the drug to be used in clinical trials, etc.

Wall Street was watching closely, and the company’s stock was all over the place. They were literally spending millions of dollars trying to get this drug to market, and they were running out of money.

Although it wasn’t as clear at that point—it became much clearer after September—there were a lot of internal battles going on at the FDA over this drug. [http://www.biospace.com/ News/this-is-why-woodcock-oked-sareptas-dmd-drug/438063] The key players were Janet Woodcock, Director of the FDA’s Center for Drug Evaluation and Research (CDER). Another was Ronald Farkas, clinical team leader, who left the agency shortly before the drug was approved—there’s speculation he left over the controversy, but he hasn’t commented publicly, as far as I know. In addition, two more players were the agency’s acting chief scientist, Luciana Borio, and Ellis Unger, director of the office of drug evaluation.

Farkas, Borio and Unger all were against approval, arguing that Sarepta did not provide substantial evidence of the effectiveness of Exondys 51. It’s important at this point, I think, to note that they weren’t saying the drug was ineffective— they were arguing that Sarepta, with its small trial and lack of placebo controls, did not prove the drug was effective in line with overall FDA guidelines for drug approval.

The Circus, Part III: Welcome Back My Friends…

The FDA held its meeting on April 25, 2016, which lasted 12 hours and included discussions and presentations. There were 52 public commentators at the hearing, including several boys with DMD and their parents. Of those 52 commentators, 51 urged approval.

The primary issue the FDA had with the drug was the size of the study—only 12 boys. The data on two of them, who

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A Note from the Editor Duchene Muscular Dystrophy, Genetics, the FDA and Drug Pricing

P.S.

Ultimately, Woodcock pushed it through, overruling her staff. The final decision then went to Robert Califf, then the FDA’s Commissioner. Among the things Woodcock apparently was taking into consideration was whether Sarepta as a company would survive the rejection financially. There is evidence that Califf had similar reservations as Borio and Unger, but sided with Woodcock.

And before I conclude this rather lengthy Editor’s Note, I want you to remember how one of the U.S. presidential campaign’s hot-button issue was drug pricing. It was helped along by the so-called “Pharma Bro,” Martin Shkreli, thenCEO of Turing Pharmaceuticals, when he bought the license for antiparasitic drug Daraprim and raised its price from $13.50 to $750 per pill.

I think it should be obvious why I found this story interesting.

It has a lot of ramifications for the FDA and drug approval, and it directly connects to genetics and genetics testing. But the story has spun out in other ways, and probably will continue to do so.

On February 10, 2017, I wrote another story [http://www. biospace.com/ News/sarepta-under-pressure-as-marathonpharma-emflazas/446377] about a different biotech company, Marathon Pharmaceuticals. On that day, Marathon announced that the FDA had approved Emflaza (deflazacort) to treat DMD in patients five years or older.

Deflazacort is a corticosteroid that has been on the market in other countries for decades. It is widely used as an antiinflammatory agent, similar to Prednisone. The drug, for example, was available in Canada. And in Canada, it was priced at $1,000 for a year’s worth of the drug.

Marathon initially indicated, for the DMD indication, it was charging $89,000 for a year’s supply of the drug.

I won’t editorialize on that. Feel free.

On March 16, 2017, I wrote yet another article [https:// www.biospace.com/News/ptc-therapeutics-buys-marathonphar ma s/449790/source=TopBreaking], in which PTC Therapeutics (PTCT) was buying the rights to deflazacort from Marathon. Marathon appears to have decided this particular kitchen was too hot and sold the rights for $140 million in cash and stock, in addition to a potential $50 million sales bonus and royalties that could hit low-to-mid 20s. As of that writing, PTC hadn’t indicated how it would price deflazacort.

Lower, would be my guess.

I very much hope that Sarepta or some other company comes up with a completely effective treatment for DMD. I hope that those patients will gain access to it without going bankrupt.

Exondys 51 So, as I mentioned at the beginning of this article, the FDA approved Exondys 51 on September 19, 2016. As part of the approval, Sarepta will have to conduct a two-year, randomized controlled trial to verify the drug’s benefits. Basically, more data is needed to prove that the drug actually improves motor functions. If it fails, FDA approval could be withdrawn.

But the DMD patients do have a drug, which seems to provide at least some benefit, although how much really remains unclear. It also brought up a lot of very important arguments, namely—is the bar the FDA sets for drug safety and efficacy something that is flexible and should the company’s financial status, the lack of other treatments, and public opinion effect where that bar is set?

Exondys 51 has a price tag of $300,000 for a year’s treatment.

I’m going to repeat that, just to make sure everyone caught it. Exondys 51 has a price tag of $300,000 for a year’s treatment. [http://www.biospace.com/News/humana-to-cover-sareptascontroversial-dmd-drug/437013] That number is based on the weight of the patient, with the recommended dose, as set by insurance company Humana, as being 30 mg/kg of body weight. The patients receive the drug once weekly.

To date, insurers, for the most part, are willing to go along with it. Anthem declined, saying that it is “investigational and not medically necessary.”

Humana agreed, but with strings attached. Humana agreed to cover six months of the drug if it’s covered by initial approval.

Humana will cover the next six months if the patient continues to be ambulatory.

Humana’s policy states: “The member must have a diagnosis of Duchenne Muscular Dystrophy with a confirmed mutation of DMD gene that is amenable to exon 51 skipping documented by: Multiplex ligation-dependent probe amplification (MLPA), OR, array comparative genomic hybridization (array CGH), OR, DMD gene sequencing. The member must be ambulatory (e.g. able to walk with assistance, not wheelchair dependent).”

Cheers, Mark Terry, Editor

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Letter to the Editor

Mosaic Trisomy 9p in a Patient with Mild Dysmorphic Features and Normal Intelligence Randeep Brar1, Donald G. Basel1, David P. Bick1,2, LuAnn Weik1, Peter vanTuinen3, and Jess F. Peterson3* *Corresponding authors 1. Department of Pediatrics, Section of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin; 2. The Advanced Genomics Laboratory, Children’s Hospital of Wisconsin, Milwaukee, Wisconsin; 3. Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin

Keywords Trisomy 9p, Mosaicism, Normal Intelligence

To the Editor:

Guilherme et al., 2014; MartĂ­nez-Jacobo et al., 2015; Zhou et al., 2015). Further complicating the predictive 9p duplication Partial and whole duplications of the short arm of chromosome phenotype, unbalanced rearrangements that commonly result 9 have been commonly reported in the literature with in 9p duplications also produce partial monosomies or partial characteristic phenotypic features and intellectual disabilities. trisomies of other chromosomes (Jelin et al., 2010; Bouhjar et The clinical features of 9p duplications are broad and can al., 2011; Guilherme et al., 2014). include growth retardation, developmental delay, intellectual To date, all clinical reports of whole short arm duplications disability, microbrachycephaly, deep set eyes, hypertelorism, of chromosome 9 without additional chromosome imbalances downslanting palpebral fissures, prominent nasal root, bulbous have been associated with characteristic phenotypic features nasal tip, low-set ears, short fingers and toes with hypoplastic and intellectual disability (Guilherme et al., 2014; Zhou et al., nails, and delayed bone age (Bonaglia et al., 2002; Zou et al., 2015). Herein, we report a 13-year-old female with mosaicism for 2009; Guilherme et al., 2014). an extra abnormal chromosome 9 (+add(9)(q13)) with minimal While efforts have been made to delineate the 9p duplication dysmorphic features and without intellectual disability. To our critical region, the clinical phenotype and degree of intellectual knowledge, this is the first clinical report of a patient with disability remains somewhat variable regardless of the duplicated trisomy 9p without additional chromosomal imbalances that 9p chromosomal region (Bonaglia et al., 2002; Zou et al., 2009; presents with mild dysmorphic features and normal intelligence.

Abu-Amero et al., 2010; Jelin et al., 2010; Bouhjar et al., 2011; Our patient is a 13-yearold female who presented to the cleft lip/palate clinic at our institute for velophar y ngeal i nc o m p ete nc e (V PI).

No prior genetic testing or evaluation had been per for med. She has a histor y of oral motor dysfunction and articulation difficulties t h at requi red speech therapy. Birth history was unremarkable. Additional past medical history was significant for a benign h e a r t mu r mu r, m i l d platelet function defect (detected at onset of menses), and borderline to mild high-frequency hearing loss in the right ear. Growth has been normal with no concerns.

Relevant developmental history included delayed walking and crawling and onset of speech, with Figure 1. A, B) Proband at 13-years-old. Note the sloping forehead, low-set ears with simplified speech therapy since she helices, malar flattening, and prominent nasal bridge.

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Letter to the Editor Mosaic Trisomy 9p in a Patient with Mild Dysmorphic Features and Normal Intelligence

was two-years-old. Currently, she is at grade level in all academics a nd pa r ticipates actively i n extracurricular activities.

On clinical evaluation, our patient showed normal growth parameters with normal mental development for age. Her weight was 55.7 kg (76.17% based on CDC 2-20 Years data) and length was 158 cm (41.78% based on CDC 2-20 Years data). Physical exa mi nation wa s sig ni fica nt for unique facial features that included a sloping forehead, lowset ears with simplified helices, malar flattening, and prominent nasal bridge (Figure 1A, B). Family history was remarkable for vocal cord nodules in the father, and a brother with bicuspid aortic valves.

Family histories of consanguinity or other known genetic conditions were not reported.

Array comparative genomic hybridization (aCGH) analysis was performed on purified DNA from Figure 2. A) Array CGH+SNP profiles showing a 68-MB duplication of the 9p24.3-q13 the proband using the CytoScan chromosomal region. B) Representative metaphase cell from a peripheral blood specimen.

Arrows point to both normal copies of chromosome 9 and the extra abnormal chromosome HD microa r r ay (A f f y met r i x, 9. Note the chromatin of undetermined origin attached to the distal long arm of the Santa Clara, CA), and scanned abnormal chromosome 9. C) Sequential FISH analysis of the representative metaphase with a Genechip Scanner 3000 cell (see B) using a locus-specific probe (RP11-318K12) targeting chromosomal region 9q13.

(A f f y m e t r i x). Re s u lt s we r e Positive hybridization (arrows) was observed on both copies of chromosome 9 in addition to displayed by Ch romosome the extra abnormal chromosome 9. However, a tandem duplication of chromosomal region Analysis Suite (ChAS) version 9q10-q21.1 was ruled out on the abnormal chromosome 9. The chromatin of undetermined origin likely represents heterochromatin as no additional gains were observed by whole 2.0 (Affymetrix). The nucleotide genome microarray analysis. coordinates are based on UCSC hg19 (NCBI Build 37, Feb. 2009).

Microarray analysis revealed a chromosomal region (Figure 2C). While duplication of 9q13 68-Mb duplication in the 9p24.3-q13 chromosomal region chromosomal material was not confirmed by FISH (only one (Figure 2A). This duplicated interval contained a total of 608 signal was observed on the abnormal chromosome 9), the genes, including 159 OMIM genes. unidentified chromatin is likely heterochromatin considering Conventional cytogenetic analysis was performed on additional gains were not observed by whole genome microarray phytohemagglutinin (PHA)-stimulated lymphocytes from a analysis. The final karyotype using ISCN 2016 nomenclature peripheral blood specimen. Metaphase image capture was wa s: mo s 47,X X,+add(9)(q13)[16]/46,X X[4].a r r[ h g19] performed using Cytovision software (Leica Biosystems, Buffalo 9p24.3q13(203,861-68,330,127)x3. Abbreviated conventional Grove, IL). A total of 20 metaphase cells were counted and five cytogenetic studies were performed on both parents (five-cell cells were fully analyzed by two ASCP-certified cytogenetic analysis) and revealed normal karyotypes. technologists. Conventional cytogenetic analysis indicated Chromosome 9 is considered highly polymorphic with a high a female with 16 of 20 metaphase cells containing an extra level of both inter- and intra-chromosomal duplications that are abnormal chromosome 9 composed of 9p, the proximal segment thought to predispose and mediate structural rearrangements of 9q, and a questionable tandem duplication of chromosomal (Willatt et al., 2007; Joseph-George et al., 2011; Guilherme et material 9q10-q21.1 (Figure 2B). Four of 20 metaphase cells al., 2014). Whole arm or partial trisomy 9p has been reported indicated a normal female karyotype. in more than 150 patients since first described in 1970 and Fluorescence in situ hybridization (FISH) was performed represents the fourth most common life-compatible autosomal on metaphase cells that contained the questionable 9q10trisomy (Zou et al., 2009; Bouhjar et al., 2011; Guilherme et al., q21.1 tandem duplication using the BAC probe RP11-318K12 2014; MartĂ­nez-Jacobo et al., 2015; Zhou et al., 2015).

(Empire Genomics, Buffalo, NY), located within the 9q13 The Journal of the Association of Genetic Technologists 43 (2) 2017

57

Letter to the Editor Mosaic Trisomy 9p in a Patient with Mild Dysmorphic Features and Normal Intelligence

Although the survivability of patients with 9p duplications has yet to be understood, the relatively gene poor content of 9p has been suggested (Bouhjar et al., 2011; Guilherme et al., 2014).

While the majority of 9p duplication patients have concomitant partial monosomies or trisomies due to inherited unbalanced rearrangements from balanced reciprocal translocation carrier parents, pure 9p duplications have rarely been reported in the literature (Zou et al., 2009). Furthermore, of those patients with reported pure whole arm 9p duplications all presented with characteristic features and intellectual disability.

Adding to the literature, we report a 13-year-old female with mosaicism for a 9pter-q13 duplication with subtle dysmorphic features and normal intelligence. Although the tissue distribution of the extra abnormal chromosome 9 is uncertain, the mild clinical features can certainly be attributed to a normal female cell line. In addition, this case illustrates the limitations of microarray in discriminating mosaicism which could have significant prognostic implications.

Zhou YC, Zhang C, Zhai JS, Li TF, Wu QY, Li WW, Li N, Li XJ, Huang YF, Cui YX, Xia XY. A patient with unusual features and a 69.5 Mb duplication from a de novo extra der (9): a case report. Mol Med Rep. 2015;12: 155-158.

Zou YS, Huang XL, Ito M, Newton S, Milunsky JM. Further delineation of the critical region for the 9p-duplication syndrome. Am J Med Genet A. 2009;149A: 272-276.

*Corresponding Author: Jess F. Peterson, MD Froedtert/MCW Laboratory Building 9200 W Wisconsin Ave Milwaukee, WI 53226 Office: (414) 805-6948 FAX: (414) 805-6980 Email: jepeterson@mcw.edu

Disclosure: The authors have no conflict of interest to declare.

References Abu-Amero KK, Hellani AM, Salih MA, Seidahmed MZ, Elmalik TS, Zidan G, Bosley TM. A de novo marker chromosome derived from 9p in a patient with 9p partial duplication syndrome and autism features: genotype-phenotype correlation. BMC Med Genet. 2010;11: 135.

Bonaglia MC, Giorda R, Carrozzo R, Roncoroni ME, Grasso R, Borgatti R, Zuffardi O. 20-Mb duplication of chromosome 9p in a girl with minimal physical findings and normal IQ: narrowing of the 9p duplication critical region to 6 Mb. Am J Med Genet. 2002;112: 154-159.

Bouhjar IB, Hannachi H, Zerelli SM, Labalme A, Gmidène A, Soyah N, Missaoui S, Sanlaville D, Elghezal H, Saad A. Array-CGH study of partial trisomy 9p without mental retardation. Am J Med Genet A. 2011;155A: 1735-1739.

Guilherme RS, Meloni VA, Perez AB, Pilla AL, de Ramos MA, Dantas AG, Takeno SS, Kulikowski LD, Melaragno MI. Duplication 9p and their implication to phenotype. BMC Med Genet. 2014;15: 142.

Jelin A, Perry H, Hogue J, Oberoi S, Cotter PD, Klein OD. Clefting in trisomy 9p patients: genotype-phenotype correlation using microarray comparative genomic hybridization. J Craniofac Surg. 2010;21: 13761379.

Joseph-George AM, He Y, Marshall CR, Wong RC, MacDonald JR, Fahey CA, Chitayat D, Chun K, Ryan G, Summers AM, Winsor EJ, Scherer SW. Euchromatic 9q13-q21 duplication variants are tandem segmental amplifications of sequence reciprocal to 9q13-q21 deletions. J Med Genet. 2011;48: 317-322.

Martínez-Jacobo L, Ortíz-López R, Rizo-Méndez A, García-Molina V, Santuario-Facio SK, Rivas F, Rojas-Martínez A. Clinical and molecular delineation of duplication 9p24.3q21.11 in a patient with psychotic behavior. Gene. 2015;560: 124-127.

Willatt LR, Barber JC, Clarkson A, Simonic I, Raymond FL, Docherty Z, Ogilvie CM. Novel deletion variants of 9q13-q21.12 and classical euchromatic variants of 9q12/qh involve deletion, duplication and triplication of large tracts of segmentally duplicated pericentromeric euchromatin. Eur J Hum Genet. 2007;15: 45-52.

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Brain Tickler

Brain Tickler Summary (see inside front cover)

45,X[15]/46,X,iso(X)(q10)[5] FISH was performed using a probe set with SHOX (Xp22.33) and the alpha satellite probe for the X chromosome. The isochromosome X did not exhibit a signal for SHOX on the short arm, as expected, as the isochromosome is composed of only long-arm material.

The Journal of the Association of Genetic Technologists 43 (2) 2017

60

Molecular Diagnostics

Column Editor: Michelle Mah, MLT, MB(ASCP)CM

Best Education Practices, Teaching the Next Generation of Technologists Next-Generation Sequencing In the second quarter of last year, I wrote about a nextgeneration sequencing (NGS) analysis workshop I delivered to the students enrolled in the Genetics Technology program at The Michener Institute in Toronto. The Michener Institute is one of two post-secondary institutions offering the Canadian Medical Association accredited Clinical Genetics Technology Programs in the country. Effective in 2015, the competency profile for students included the understanding of NGS— program instructors desired some exposure to the practical application of NGS analysis. We designed a workshop to provide students with the opportunity to work with NGS data as it pertains to the role of a technologist working at the bench.

Students were already familiar with NGS chemistries and platforms; the goal was therefore to demonstrate the importance of supporting the analytical workflow from data generation to variant reporting. The overall reception was very positive from last year’s class. Student feedback reflected their appreciation for learning various NGS data processing steps and the chance to practice basic steps in variant interpretation. In essence, the workshop removed the black box that some have ascribed to the steps that occur after sequencing is complete.

Recently, on the first week of March, my co-worker and I were invited to deliver the same workshop to the current class.

We incorporated constructive feedback for areas to improve on from last year. There were two recurring comments we noted: the first was the need to better present, in a step-by-step fashion, how to analyze a variant list from variant detection to completing proper DNA and protein nomenclature based on the Human Genome Variation Society (HGVS); and second, there was interest from the faculty in divulging the steps performed after variant detection as performed by a technologist. So, generally speaking, what happens to the variant list after a technologist reviews the acceptance criteria for each variant as outlined in Figure 1.

I found the first comment more challenging. As someone

experience using genetic analysis software. There are details associated with all workflows, such as software idiosyncrasies, that can muddle main teaching points. Our goal was not to focus on the use of any specific software, but to present the need for technologists to correctly filter variants and doublecheck variant calls made by NGS software because alignment algorithms do not always interface correctly with variant calling programs.

We tried to simulate real clinical training through the use of a PowerPoint presentation. We were also limited to teaching examples from the workflow we employ at work; hence, a better effort was made to label slides that presented software screenshots, and on directing students to relevant pieces of information, and this meant more image customization and slide editing. The main point of delivery was to direct their attention to how sequence variations can be presented regardless of software choice and how to read sequence alignments, understand the difference between chromosome positions and corresponding positions in coding sequences.

While we improved the delivery of variant calling examples, there is still a learning gap between manual sequence analysis and understanding the use of advanced analytical software.

We would like to better address these topics in the future.

There are many great websites and software to help with HGVS nomenclature for the working technologist, but it is essential for students to understand the fundamentals of DNA directionality, gene direction and the convention for reporting changes at the DNA and protein level using the correct reference sequences. This skill will be increasingly important as technologists handle higher-throughput genetic data.

Because of interest in post variant filtering and detection, the workshop this year added a brief presentation on the process of variant interpretation, report generation and final reporting by laboratory directors. Students and faculty were interested in learning how clinical context is added to generate a meaningful

Figure 1. The general NGS workflow from sequence generation to reporting. Certain responsibilities among different groups can change and overlap as constant communication is maintained to ensure timely and accurate reporting.

report for directors and clinicians. Many individuals who work away from the bench are variant analysts, annotation specialists, genomics specialists, etc., and sometimes genetic counsellors.

Here at the Princess Margaret Cancer Center, they form the

who is not a professional teacher, students’ feedback to explain things more explicitly really did surprise me. But after a year of not working on the material I presented, I can appreciate where the comments were coming from for students without prior

The Journal of the Association of Genetic Technologists 43 (2) 2017

61

Molecular Diagnostics

Column Editor: Michelle Mah, MLT, MB(ASCP)CM

Best Education Practices, Teaching the Next Generation of Technologists Next-Generation Sequencing

variant annotation group responsible for variant interpretation, classification of pathogenicity and report generation.

The annotation team goes through a laboratory published protocol to systematically collect and determine evidence for or against pathogenicity for all filtered variants reviewed by technologists. This includes the use of commercially purchased mutation analysis software and interpreting the resources presented within, or manually accessing external databases like the Exome Sequencing Project, the Catalogue of Somatic Mutations in Cancer, and other locus specific databases.

Literature searches may also be required. Collected information can include population frequencies, histology such as frequent tumour sites recorded in the database, and in silico prediction scores. If there is any relevant published actionable evidence pertaining to care management, information can be applied to the variant under investigation to guide patient care.

This branch of analysis was presented to the class in the form of specialized variant filtering and classification web-based software which incorporates updated information from many credible external resources. In addition, we included laboratory defined classification schemes. The use of variant interpretationtype software assists with the automation of filtering clinically significant variants based on sequencing quality and allele frequencies, and adding clinically relevant information to determine appropriate classification of pathogenicity. Laboratory developed classification schemes may vary slightly from lab to lab, and most follow available guidelines put forth by regulatory bodies such as the American College of Medical Genetics and Genomics.

Finally, variant classifications are reviewed to ensure that information accurately reflects current knowledge. For example, is the variant a pathogenic mutation with known methods of treatment or is it considered a good prognostic indicator?

Conversely, is information insufficient to determine clinical significance at this time? Once clinical context is compiled neatly and checked by different members of the annotation team, report generation is triggered for director sign-out, completing the workflow outlined in Figure 1. As labs around the world generate NGS data and work to contribute and share clinical information associated with variants in specialized areas of disease and management, classification schemes can be refined and better standardized to offer the most informed prognosis, the right diagnosis and the best clinical care. Thank you to the class of 2018 for another great opportunity for continuous learning through teaching.

The Journal of the Association of Genetic Technologists 43 (2) 2017

62

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Review

Cytogenetic Characterization of Myeloid Neoplasms with t(2;3)(p13-25;q25-29): An Analysis of 60 Cases Alexis V. Dowiak1,2 and Carlos A. Tirado1,3 1. The International Circle of Genetic Studies, Los Angeles, CA 90024 2. Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 3. Allina Health, Minneapolis, MN 55401

Abstract Chromosomal translocations involving the short arm of chromosome 2 (p13-25) and the distal part of the long arm of chromosome 3 (q25-29) are rare and still poorly studied to date. These abnormalities are common in myeloid neoplasms and are associated with a poor prognosis. Chromosomal abnormalities within the involved range of bands may contribute to the ectopic expression or formation of fusion genes involving the EVI1 gene, but the exact mechanism by which EVI1 affects leukemogenesis remains unclear. Herein, we report an analysis of 60 patient cases presenting various myeloid malignancies with t(2;3)(p13-25;q25-29) compiled from the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer. In these studies, this translocation has been reported as a sole abnormality or within the context of a complex karyotype. Among the analysis in which molecular cytogenetic analysis was performed in order to assess the involvement of the EVI1 (ecotropic virus integration site 1 proton homolog) locus (n=19), 16 (84%) confirmed its rearrangement. In 37% of studies, the t(2;3) was seen as a sole abnormality (n=22). The t(2;3) was secondary in 11% of cases (n=4), and in 63% of the cases the t(2;3) had additional chromosomal abnormalities (n=38). Monosomy 7, deletion of the 5q arm, and translocations involving (9;22) were most common abnormalities in order of prevalence, occurring in 29% (n=11), 26% (n=10), and 13% (n=5) of case studies, respectively. These observations in the results of the literature on t(2;3), an anomaly not otherwise molecularly characterized, adds to the discussion of this translocation’s approximate incidence in myeloid disease, and specifically in acute myeloid leukemia (AML). The data highlights its nonrandom nature and suggests that it is a part of the myeloid spectrum of disorders. Considering the severe clinical outcome associated with this translocation, this data provides information about a cytogenetic biomarker as well as an understanding of the significance of this set of chromosomal anomalies in the development of myeloid disease.

Introduction Myeloid malignancies are clonal diseases of hematopoietic stem or progenitor cells as a result of genetic and epigenetic alterations. These diseases occur in a variety of ways, impairing the normal physiological process of different blood cell lineages to proliferate, differentiate, or undergo apoptosis.

Chromosomal translocations involving the short arm of chromosome 2 and the distal part of the long arm of chromosome 3 are rare yet recurrent findings, observed in approximately 0.5% of myeloid malignancies at initial diagnosis or during disease progression, and are associated with a poor prognosis (Yamamoto et al., 2013). Such rearrangements can contribute to ectopic expression or formation of fusion genes involving the EVI1 (3q26) (ecotropic virus integration site 1 proton homolog) gene, encoding a stem cell-specific transcription factor essential in the transformation and fate of hematopoietic cells (Hinai et al., 2016). However, the exact mechanism by which EVI1 and such translocations affect leukemogenesis remains unclear. Herein, we present an analysis of 60 cases with t(2;3)(p13-25;q25-29) in various myeloid diseases that were compiled from the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer.

Methods

Figure 1a. Ideograms highlighting the breakpoints most frequently involved in t(2;3)(p13-25;q25-29). Results further quantified in Figure1b.

Relevant cases were identified through a query of the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer. The search included all patients reported up

The Journal of the Association of Genetic Technologists 43 (2) 2017

64

Review Cytogenetic Characterization of Myeloid Neoplasms with t(2;3)(p13-25;q25-29): An Analysis of 60 Cases

nonrandom nature of the chromosomal translocation t(2;3)(p1325;q25-29) and recurrent findings support the assumption that it is involved in this spectrum of disorders.

2p Band

Structural Breaks

3q Band

Structural Breaks

2p25

3

3q25

3

2p24

2

3q26.1

50

Discussion

2p23

26

3q26.2

50

2p22

30

3q26.3

50

2p21

27

3q27

29

2p16

10

3q28

9

2p15

9

3q29

7

2p14

5

2p14

5

2p13

4

2p13

4

This is one of the first large-scale analyses of t(2;3) (p13-25;q25-29), a rare anomaly not extensively molecularly characterized, and provides additional information about the nonrandom incidence of this translocation and its distribution in the spectrum of myeloid neoplasms. Most cases of this translocation present with concomitant abnormalities, the majority of which are recurrent and prognostically relevant in myeloid disease, predominantly monosomy -5q, 7, and t(9;22). -7 and -5q are particularly characteristic of therapy-related AML (tAML) (Breems et al., 2008; Swerdlow et al., 2008; Godley et al., 2010). A total of 90-95% of patients with CML demonstrate t(9;22)(q34;q11.2) resulting in the Ph chromosome (Van Etten, 2016) and this remains consistent with the presence of the abnormality in the included CML cases. However, t(9;22) is also present in two of the t(2;3) cases of AML. This event is more rare, with an incidence of 1% in cases of AML (Westbrook et al., 1992).

Mechanistically, a review of the literature suggests that t(2;3) does not generate an EVI1 chimera, but rather juxtaposes the 5’ region of the EVI1 oncogene next to a transcriptional control element normally located in proximity of the 2p breakpoints,

Figure 1b. Calculated structural aberrations per chromosome band on 2p and 3q within our range of interest. This statistic helps to normalize chromosome banding resolution in conventional cytogenetic characterization

to November 2015, and identified 60 previously published cases of myeloid disorders in which t(2;3)(p13-25;q29) was uncovered via various techniques.

Results Our review focused on myeloid neoplasms with the following disease breakdown: 38 cases of AML, seven cases of CML, and 15 cases of MDS, including two cases of refractory anemia (RA), three cases of refractory anemia with ringed sideroblasts (RARS), six cases of refractory anemia with excess blasts (RAEB), and one case of chronic myelomonocytic leukemia (CMML). t(2;3) existed as the sole abnormality in 22 cases and with concomitant abnormalities in 38 cases (Figure 2).

In the latter group, t(2;3) was a primary abnormality in five of 38 cases (13%), a secondary abnormality in four (11%), and it is significant to note that for the other 29 (76%) of the reviewed complex karyotypes, it could not be determined if t(2;3 was a primary or secondary abnormality. The most common additional abnormalities reported were monosomy 7 (occurring in 29%), deletion of the 5q arm (26%), and translocations involving the Philadelphia chromosome t(9;22) (13%). Ideograms to illustrate the frequencies of observed quantitative and structural aberrations are shown in Figure 3 and Figure 4, respectively. Among the 19 cases in which molecular cytogenetic analysis was performed in order to assess the involvement of the EVI1 locus, 16 (84%) confirmed its rearrangement. In addition, in seven of these cases, EVI1 expression level was assayed by real-time PCR, which confirmed quantitatively aberrant expression relative to normal control samples from healthy donors in all cases. These results and the presented data illustrate the

Figure 2: Secondary abnormalities per chromosome by percentage of cases with secondary abnormalities. Cases with secondary abnormalities were assessed for the number of abnormalities per chromosome. Both structural and numerical abnormalities were included, and were counted on a per chromosome per case basis. Abnormalities on chromosome 2 and 3 presented above were concomitant with the translocation.

In the case of multiple marker chromosomes in one case, it was quantified as one secondary abnormality for the table.

The Journal of the Association of Genetic Technologists 43 (2) 2017

65

Review Cytogenetic Characterization of Myeloid Neoplasms with t(2;3)(p13-25;q25-29): An Analysis of 60 Cases Table 1: Karyotypes of patients with t(2;3) and available EVI1 expression data from the present study Case

Sex

Age

Diagnosis

Karyotype

1

F

53

AML

45,XX,t(2;3)(p15-21;q26-27),del(7)(q11q32),del(12)(p12),21[cp29]/46,XX[1]

Stevens-Kroef et al.

2

F

68

AML

43-45,XX,t(2;3)(p15-21;q26-27),-5,-7,-15,del(17)(q?),-22,+14mar[cp13]/46,XX[7]

Stevens-Kroef et al.

AML

46,XX,del(5q),t(2;3)(p21;q26)

LaStarza et al.

3

EVI1 expression

Reference

4

F

65

AML

47,XX,t(2;3)(p14-16;q25-26),del(9)(q21q31),del(11)(q21),+del(11) (q21)

Peniket et al.

5

F

30

AML

45,XX,t(2;3)(p23;q26),-7

GFCH

6

F

59

AML

46,XX,t(2;3)(p15;q26.2),del(5)(q13q31)[6]/45,sl,der(3)?t(3;13) (p21;q14)t(2;3),)13[1]/45,sl,dic(12;13)(p11.2;p11.2), +9 12dmin[9]/48,sl,)3,der(3)del(3)(p11p25)t(2;3),add(6)(p25), der(6) t(3;6)(p21;p21.3),der(7)t(6;7)(p21.3;p22),+add(8)(p11.2), hsr(11) (p11.2),)12,der(13)t(12;13)(q22;q34),+19,+21,+mar[4]

7

F

66

AML

46,XX,t(2;3)(p21;q27)[28]

8

M

55

AML

46,XX,t(2;3)(p23;q29),del(7)(q31)

AML

47,XX,del(5)(q23q34),+del(21)(q21q22)[4]/46,idem,t(2;3) (p2?2;q2?7)[20]/46,XX[3]

9

+

Bobadilla et al.

Farag et al.

Berger et al. +

Lugthart et al.

10

F

39

AML

46,XX,t(2;3)(p23;q26),t(8;21)(q22;q22)[17]/46,XX,t(2;3),add(6) (q23~q24),del(7)(q22),del(11)(p13),-17,+mar[3]

11

M

17

tAML

46,XY,t(2;3)(p21;q26),del(5)(q?)

+

Yagyu et al.

12

F

63

tAML

48,X,-X,t(2;3)(p13;q28),+4,del(5)(q14q34),-7,+8,-13,-17,add(17) (p13),+3-4mar[cp4]

+

Stevens-Kroef et al.

AML M0

46,XY,t(2;3)(p23;q27)

13

Beyer et al.

Silva et al.

14

M

14

tAML M0

46,XY,t(2;3)(p21;q26),del(5)(q?)[2]/46,XY[3] (Dx) 46,XX (1st CR); 45,XY,der(2)t(2;3)(p21;q26),-3,-7,add(10)(q26),+mar[7]/46,XX[13] (1st relapse); 45,XY,der(2)t(2;3)(p21;q26),-3,-7,add(10) (q26),+mar[18]/46,XX[2] (2nd relapse); 45,XY,der(2)t(2;3) (p21;q26),-3,-7,add(10)(q26),+mar[17]/45,XY,idem,t(9;22) (q34;q11.2),add(17)(q11)[3] (Terminal phase)

15

M

68

tAML M0

46,XY,t(2;3)(p21-23;q26-27)[30]

16

F

30

AML M1

46,XX,t(2;3)(p21-23;q26-27)[4]/46,idem,del(5)(q31)[21]/46,XX[1]

17

F

36

AML M1

46,XX,t(2;3)(p21;q26)[9]/48,XX,idem,+15,+22[11]

AML M2

Dx: 46,XX,t(2;3)(p22;q27)[11]/46,XX[10];Rel: 46,XX,t(2;3)(p22;q27) [4];46,XX,t(2;3)(p22;q27),t(17;17)(p11;q21)[16]

Voskova et al.

18

+*

Yagyu et al.

Stevens-Kroef et al.

Stevens-Kroef et al. +

Trubia et al.

19

F

49

AML M2

45,XX,t(2p;3q)(p21;q27),-7

Barbieri et al.

20

M

56

AML M2

45,XY,t(2;3)(p22 or 23:q27 or 28),-7[29]/46,XY,t(2;3)[2]

Van Lom et al.

21

M

16

AML M2

46,XY,t(2;3)(p13;q26)

Herens et al.

22

M

3

AML M2

45,XY,t(2;3)(p21;q29),-7,del(12)(p12)[15]/45,XY,t(2;3)(p22;q28),7,del(12)(p12)[2]/45,XY,t(2;3)(p22;q28),-7,t(9;22)(q34;q11)[21]

-

Berger et al.

23

F

10

AML M2

46,XX,t(2;3)(p22;q28)[21]/46,XX,t(2;3)(p22;q28),add(5)(p15),del(7) (q22)[cp34]

-

Berger et al.

24

M

74

AML M2

46,XY,t(2;3)(p13;q28)

Berger et al.

25

M

72

AML M2

45,XY,t(2;3)(p23;q26),-7

Levaltier et al.

26

F

37

AML M2

46,XX,t(2;3)(p23;q27),t(8;12)(q23;p13) or t(8;12)(q22;p12),add(9) (p22),+14,-21[23]

Mrozek et al.

The Journal of the Association of Genetic Technologists 43 (2) 2017

66

Review Cytogenetic Characterization of Myeloid Neoplasms with t(2;3)(p13-25;q25-29): An Analysis of 60 Cases

Case

Sex

Age

Diagnosis

Karyotype

27

M

36

AML M2

46,XY,t(2;3)(p21;q27)[20]

28

M

36

AML M2

46,XY,t(2;3)(p21;q27)[9]/45,XY,idem,-7[7]/46,XY[4]

29

F

45

AML M2

46,XX,t(2;3)(p21-23;q26-27)[15]/46,XX[5]

30

M

12

AML M2

46,XY,t(2;3)(p22;q26)[32]/46,XY[2]

31

F

48

AML M2

45,XX,t(2;3)(p16;q26),-7[11]

32

F

60

sAML M2

46,XX,t(2;3)(p22;q26)

+

Poppe et al.

33

F

50

AML M4

46,XX,t(2;3)(p15;q27)[18]

+

Trubia et al.

34

M

59

AML M4

46,XY,t(2;3)(p21;q26)[20]

+

Trubia et al.

35

M

77

AML M4

46,XY,t(2;3)(p22;q26)

GFCH

36

M

51

AML M5

46,XY,t(2;3)(p21-23;q26-27),idic(6)(q12)[30]

Stevens-Kroef et al.

37

M

42

AML M5

46,XY,t(2;3)(p21-23;q26-27),del(5q),del(7q)[2]/46,XY[6]

Stevens-Kroef et al.

38

M

55

AML M5

47,XY,t(2;3)(p22;q27),+13[16]

+

Trubia et al.

MDS

46,XX,t(2;3)(p22-23;q26)[19]

+

Madrigal et al.

39

EVI1 expression

Reference Trubia et al.

+

Trubia et al.

Stevens-Kroef et al.

+

Stevens-Kroef et al.

Stevens-Kroef et al.

40

M

62

MDS

46,XY[27]/46,XY,t(2;3)(p23;q27)[6]

Reilly et al.

41

M

52

tMDS

44,XY,ins(2;3)(p?16;q?21q2?5),der(5;17)(p10;q10),20[14]/44,XY,der(5;17)(p10;q10),dic(7;12)(p10;p13),del(14)(q11q14) [3]/46,XY[13]

Stevens-Kroef et al.

42

F

54

RA

46,XX,del(5)(q14q34)[1]/46,XX,t(2;3)(p14;q26),del(5)(q14q34) [6]/46,XX[5]

43

F

57

RA

46,XX,t(2;3)(p23;q27),del(5)(q22q35),-7 or 7q-

Berger et al.

44

M

53

RARS

46,XY,t(2;3)(p22-23;q26-27)[33]

Stevens-Kroef et al.

45

M

65

RARS

46,XY,t(2;3)(p23;q27)[30]

46

M

37

RARS

46,XY,t(2;3)(p21-23;q27)[19]

+

Stevens-Kroef et al.

47

F

68

RAEB

46,XX,t(2;3)(p22;q26)[9]/46,XX[1]

+

Stevens-Kroef et al.

48

F

48

RAEB

46,XX,t(2;3)(p21;q26),i(14)(q10)

Poppe et al.

49

M

64

RAEB

45,XX,t(2;3)(p21;q27),-7

Berger et al.

50

F

80

RAEB

45,XX,t(2;3)(p14;q26),5q-,-18

51

F

38

RAEB

46,XX,t(2;3)(p16;q26)[10]

52

M

46

RAEBt

46,XY,t(2;3)(p16;q26)[3]/46,idem,add(13)(q34)[2]/46,XY[5]

Stevens-Kroef et al.

53

M

68

CML

46,XY[3]/46,XY,t(2;3)(p21;q26)[26]

Herens et al.

54

F

62

CML

46,XX,t(2;3)(p21;q28)

Dobrovic et al.

55

F

55

CML AP

46,XY,t(9;22)(q34;q11)[6]/46,idem,t(2;3)(p16;q26)[4]

Stevens-Kroef et al.

56

F

28

CML AP

46,XX,t(2;3)(p14;q26),t(6;9;22)(p12;q34;q11)

Bacher et al.

57

M

16

CML BC

46,Y,der(X)t(X;9)(p22;q22),t(2;3)(p13;q26),t(9;22)(q34;q11)

Herens et al.

58

F

30

CML BC

46,XX,t(9;22)(q34;q11)[3]/46,XX,t(2;3)(p13;q26),t(9;22)(q34;q11)

Herens et al.

59

M

77

CML BC

46,XY,t(2;3)(p22;q28),t(9,22)(q34;q11)[10]

Stevens-Kroef et al.

60

M

44

CMML

46,XY,t(2;3)(p22;q26)[26]/46,XY[6]

Stevens-Kroef et al.

-

Stevens-Kroef et al.

Stevens-Kroef et al.

Berger et al. +

Stevens-Kroef et al.

Acute Myeloid Leukemia (AML) subtypes based on the French, American, British (FAB) classification; Chronic Myelogenous Leukemia (CML) phases are based on the World Health Organization (WHO) definitions; MDS = Myelodysplastic Syndrome, RA = Refractory anemia, RARS = Refractory anemia with ringed sideroblasts, RAEB = Refractory anemia with excess blasts, CMML = Chronic myelomonocytic leukemia *=80 to 120-fold higher at initial dx, first recurrence, and terminal phase The Journal of the Association of Genetic Technologists 43 (2) 2017

67

Review Cytogenetic Characterization of Myeloid Neoplasms with t(2;3)(p13-25;q25-29): An Analysis of 60 Cases

Figure 3. Ideograms illustrating the frequency of quantitative aberrations associated with cases of t(2;3) (p13-25;q25-29) translocations. Losses are drawn in red on the left side, gains in green on the right side of chromosomes. Chromosomes 1, 16, and Y ideograms are all omitted from the figure because no abnormalities were reported in our study.

resulting in consequent overexpression of EVI1 (Buonamici et al., 2003; Trubia et al., 2006). Using this suggested model, maturation would become arrested and leukocytes would proliferate, both of which would induce leukemogenesis. This is consistent with the distinct myeloid phenotype and additional clinical characteristics observed across other hematological malignancies that display EVI1 activation or 3q26 rearrangements, including monosomy 7, trilineage dysplasia, thrombocytosis, disturbed megakaryopoiesis, and an unfavorable clinical course. EVI1 can be rearranged with a variety of other partner genes (Haferlach et al., 2012). An evaluation of the literature present little evidence to describe the genes on the 2p arm that may be essential for aberrant expression of EVI1 or affect its overexpression.

Our sample of cases displays a wide and variable range of involved breakpoints on the proximal arm of chromosome 2 from 2p13-2p25. To help narrow in on the breakpoints that are most frequently represented across the cases collected in the present study, and by default, most likely to be involved, ideograms of chromosome 2 in Figure 1a highlight that the region 2p21-2p23 (as opposed to 2p13-2p25) may require the most attention in future investigations, especially those seeking to explain the mechanism that might be involved. Both Trubia et al. and Yamamoto et al. reported involvement of the thyroid adenoma-associated gene (THADA) on 2p21 in 2 (n=6) cases with t(2;3)(p21;q26) (Trubia et al., 2006, Yamamoto et al., 2013). Our results, with the second greatest frequency (27) of breaks on 2p21, are consistent with this hypothesized involvement.

Considering the severe clinical outcome associated with this translocation, further investigation of the molecular mechanisms by which it contributes to carcinogenesis, its interplay with concomitant abnormalities, and its diagnostic and prognostic implications is warranted.

Figure 4. Concomitant structural aberrations overlaying ideograms highlighting the frequency of involved breakpoints

References Bacher U, Kern W, Schnittger S, Hiddemann W, Schoch C, Haferlach T. Blast count and cytogenetics correlate and are useful parameters for the evaluation of different phases in chronic myeloid leukemia. Leuk Lymphoma. 2005 Mar;46(3): 357-66 Barbieri D, Vermaelen K, Van den Berghe H. Preliminary data on the in vitro proliferation pattern and karyotypic characteristics in cells of patients with ANLL. Cancer Genet Cytogenet. 1984 Jan;11(1): 1-9.

Berger R, Flexor M, Le Coniat M, Derré J, Leblanc T. Translocation (2;3) (p22;q28) is associated with myeloid disorders. Cancer Genet Cytogenet.

1995 Feb;79(2): 130-2.

Beyer V, Castagné C, Mühlematter D, Parlier V, Gmür J, Hess U, Kovacsovics T, Meyer-Monard S, Tichelli A, Tobler A, Jacky E, Schanz U, Bargetzi M, Hagemeijer A, de Witte T, van Melle G, Jotterand M. Systematic screening at diagnosis of -5/del(5)(q31), -7, or chromosome 8 aneuploidy by interphase fluorescence in situ hybridization in 110 acute myelocytic leukemia and high-risk myelodysplastic syndrome patients: concordances and discrepancies with conventional cytogenetics. Cancer Genet Cytogenet. 2004 Jul 1;152(1): 29-41.

Bobadilla D, Enriquez EL, Alvarez G, Gaytan P, Smith D, Slovak ML. An interphase fluorescence in situ hybridisation assay for the detection of 3q26.2/EVI1 rearrangements in myeloid malignancies. Br J Haematol.

2007 Mar;136(6): 806-13.

Breems DA, Van Putten WL, De Greef GE, Van Zelderen-Bhola SL, GerssenSchoorl KB, Mellink CH, Nieuwint A, Jotterand M, Hagemeijer A, Berloo HB, Lowenberg B. Monosomal karyotype in acute myeloid leukemia: a better indicator of poor prognosis than a complex karyotype.

J Clin Oncol 2008;26: 4791.

Buonamici S, Chakraborty S, Senyuk V, Nucifora G. The role of EVI1 in normal and leukemic cells. Blood Cells Mol Dis. 2003;31: 206-212.

Dobrovic A, Morley AA, Seshadri R, Januszewicz EH. Molecular diagnosis of Philadelphia negative CML using the polymerase chain reaction and DNA analysis: clinical features and course of M-bcr negative and M-bcr positive CML. Leukemia. 1991 Mar;5(3): 187-90.

Farag SS, Archer KJ, Mrózek K, Ruppert AS, Carroll AJ, Vardiman JW, Pettenati MJ, Baer MR, Qumsiyeh MB, Koduru PR, Ning Y, Mayer RJ,

The Journal of the Association of Genetic Technologists 43 (2) 2017

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Review Cytogenetic Characterization of Myeloid Neoplasms with t(2;3)(p13-25;q25-29): An Analysis of 60 Cases

Silva FP, Morolli B, Storlazzi CT, Anelli L, Wessels H, Bezrookove V, KluinNelemans HC, Giphart-Gassler M. Identification of RUNX1/AML1 as a classical tumor suppressor gene. Oncogene. 2003 Jan 30;22(4): 538-47.

Swerdlow SH, Campo E, Harris NL, et al. (Eds). World Health Organization Classification of Haematopoietic and Lymphoid Tissue, IARC Press, Lyon 2008.

Trubia M, Albano F, Cavazzini F, Cambrin GR, Quarta G, Fabbiano F, Ciambelli F, Magro D, Hernandezo JM, Mancini M, Diverio D, Pelicci PG, Coco FL, Mecucci C, Specchia G, Rocchi M. Liso V, Castoldi G, Cuneo A. Characterization of a recurrent translocation t(2;3)(p15-22;q26) occurring in acute myeloid leukaemia. Leukemia. 2006;20: 48e54.

Van Etten RA. Clinical Manifestations and Diagnosis of Chronic Myeloid Leukemia (Larson RA and Connor RF (Eds). Wolters Kluwer; 26 Apr. 2016. van Lom K, Hagemeijer A, Vandekerckhove F, Smit EM, Löwenberg B. Cytogenetic clonality analysis: typical patterns in myelodysplastic syndrome and acute myeloid leukaemia. Br J Haematol. 1996 Jun;93(3): 594-600.

Voskova D, Schoch C, Schnittger S, Hiddemann W, Haferlach T, Kern W. Stability of leukemia-associated aberrant immunophenotypes in patients with acute myeloid leukemia between diagnosis and relapse: comparison with cytomorphologic, cytogenetic, and molecular genetic findings.

Cytometry B Clin Cytom. 2004 Nov;62(1): 25-38.

Westbrook CA, Hooberman AL, Spino C, Dodge RK, Larson RA, Davey F, Wurster-Hill DH, Sobol RE, Schiffer C, Bloomfield CD. Clinical significance of the BCR-ABL fusion gene in adult acute lymphoblastic leukemia: a Cancer and Leukemia Group B Study (8762). Blood. 1992 Dec 15;80(12): 2983-90.

Yagyu S, Morimoto A, Kakazu N, Tamura S, Fujiki A, Nakase Y, Iehara T, Hosoi H, Kuroda H. Late appearance of a Philadelphia chromosome in a patient with therapy-related acute myeloid leukemia and high expression of EVI1. Cancer Genet Cytogenet. 2008 Jan 15;180(2): 115-20.

Yamamoto K, Okamura A, Sanada Y, Yakushijin K, Matsuoka H, Minami H. Marked thrombocytosis and dysmegakaryopoiesis in acute myeloid leukemia with t(2;3)(p22;q26.2) and EVI1 rearrangement. Ann Hematol.

2013 Dec;92(12): 1713-5.

Stone RM, Larson RA, Bloomfield CD. Pretreatment cytogenetics add to other prognostic factors predicting complete remission and long-term outcome in patients 60 years of age or older with acute myeloid leukemia: results from Cancer and Leukemia Group B 8461. Blood. 2006 Jul 1;108(1): 63-73.

GFCH. Cytogenetic analysis in patients with primary myelodysplastic syndromes in leukaemic transformation. A report on 94 cases. Groupe Français de Cytogénétique Hématologique (GFCH). Hematol Cell Ther.

1996 Apr;38(2): 177-81.

Godley LA, LeBeau MM. Cytogenetics and molecular abnormalities. In: Williams Hematology, 8th ed, Kaushansky K, Lichtman MA, Beutler E, et al. (Eds), McGraw-Hill, Burr Ridge, IL; 2010.

Haferlach C, Bacher U, Grossmann V, Schindela S, Zenger M, Kohlmann A, Kern W, Haferlach T, Schnittger S. Three novel cytogenetically cryptic EVI1 rearrangements associated with increased EVI1 expression and poor prognosis identified in 27 acute myeloid leukemia cases. Genes Chromosomes Cancer. 2012 Dec;51(12): 1079-85.

Herens C, Hermanne JP, Tassin F, Fassotte MF, Thiry A, Jamar M, SchaafLafontaine N, Fillet G, Koulischer L. Translocation (2;3)(p21;q26) as the sole anomaly in a case of primary myelofibrosis. Cancer Genet Cytogenet. 1999 Apr;110(1): 62-4.

Hiller B, Bradtke J, Balz H, Rieder H (2004): “CyDAS Online Analysis Site”, http://www.cydas.org/OnlineAnalysis/ Hinai AA, Valk PJ. Review: Aberrant EVI1 expression in acute myeloid leukaemia. Br J Haematol. 2016 Mar;172(6): 870-8.

La Starza R, Matteucci C, Gorello P, Brandimarte L, Pierini V, Crescenzi B, Nofrini V, Rosati R, Gottardi E, Saglio G, Santucci A, Berchicci L, Arcioni F, Falini B, Martelli MF, Sambani C, Aventin A, Mecucci C. NPM1 deletion is associated with gross chromosomal rearrangements in leukemia. PLoS One. 2010 Sep 21;5(9): e12855.

Levaltier X, Penther D, Bastard C, Troussard X. t(2;3)(p23;q26) in a patient with AML M2. Br J Haematol. 1996 Mar;92(4): 1027.

Lugthart S, van Drunen E, van Norden Y, van Hoven A, Erpelinck CA, Valk PJ, Beverloo HB, Löwenberg B, Delwel R. High EVI1 levels predict adverse outcome in acute myeloid leukemia: prevalence of EVI1 overexpression and chromosome 3q26 abnormalities underestimated.

Blood. 2008 Apr 15;111(8): 4329-37.

Madrigal I, Carrió A, Gómez C, Rozman M, Esteve J, Nomdedeu B, Campo E, Costa D. Fluorescence in situ hybridization studies using BAC clones of the EVI1 locus in hematological malignancies with 3q rearrangements.

Cancer Genet Cytogenet. 2006 Oct 15;170(2): 115-20.

Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer (2016), Mitelman F, Johansson B and Mertens F (Eds.), http://cgap.nci. nih.gov/Chromosomes/Mitelman Mrózek K, Heinonen K, Theil KS, Bloomfield CD. Spectral karyotyping in patients with acute myeloid leukemia and a complex karyotype shows hidden aberrations, including recurrent overrepresentation of 21q, 11q, and 22q. Genes Chromosomes Cancer. 2002 Jun;34(2): 137-53.

Peniket A, Wainscoat J, Side L, Daly S, Kusec R, Buck G, Wheatley K, Walker H, Chatters S, Harrison C, Boultwood J, Goldstone A, Burnett A. Del (9q) AML: clinical and cytological characteristics and prognostic implications. Br J Haematol. 2005 Apr;129(2): 210-20.

Poppe B, Dastugue N, Vandesompele J, Cauwelier B, De Smet B, Yigit N, De Paepe A, Cervera J, Recher C, De Mas V, Hagemeijer A, Speleman F. EVI1 is consistently expressed as principal transcript in common and rare recurrent 3q26 rearrangements. Genes Chromosomes Cancer. 2006 Apr;45(4): 349-56.

Reilly JT, Wilson G, Barnett D, Watmore A, Potter A. Karyotypic and ras gene mutational analysis in idiopathic myelofibrosis. Br J Haematol. 1994 Nov;88(3): 575-81.

Stevens-Kroef, M., B. Poppe, S. Van Zelderen-Bhola, E. Van Den Berg, M. Van Der Blij-Philipsen, A. Guerts Van Kessel, R. Slater, G. Hamers, L. Michaux, F. Speleman, and A. Hagemeijer. Translocation t(2;3)(p1523;q26-27) in Myeloid Malignancies: Report of 21 New Cases, Clinical, Cytogenetic and Molecular Genetic Features. Leukemia. 2004;18.6: 1108114.

Corresponding Author: Carlos A. Tirado, Ph.D. Allina Health, MN University of Minnesota School of Medicine Department of Laboratory Medicine and Pathology Carlos.Tirado@allina.com tirad017@umn.edu

The Journal of the Association of Genetic Technologists 43 (2) 2017

69

Continuing Education Opportunities

Column Editor: Sally J. Kochmar, MS, CG(ASCP)CM

Test Yourself #2, 2017 Readers of The Journal of the Association of Genetic Technologists are invited to participate in this “open book test” as an opportunity to earn Contact Hours. AGT offers 3 Contact Hours for this Test Yourself based on articles in Volume 43, Number 1, First Quarter 2017 of the Journal.

Test Yourself is free to AGT members and $30 for non-members. To take this exam, send a copy of your completed Answer Sheet along with the completed Contact Hours Reporting Form to the AGT Education Committee Representative in your region. The list of representatives can be found on the AGT website.

Non-members should submit a check payable to AGT for $30 with their answer sheet. Entry material must be post-marked on or before September 1, 2017.

Passing score is 86.3% or 18 out of 22 questions answered correctly. Compiled by Doina Ciobanu and Sally Kochmar.

The following questions are from Ghanbarian A et al. Report of a Triploid Fetus Identified in a Pregnancy with Oligohydramnios.

J Assoc Genet Technol. 2017;43(1): 6-8.

1. Fetal triploidy is estimated to occur in……% of all conceptions. a. 18 b. 5 c. 1 d. 10

7. All of the following are true, except: a. There is no difference in survival between t(3;3) and inv(3). b. Median survival for patients with 3q21q26 syndrome is 10.3 months. c. Survival is shorter with del 7q or monosomy 7. d. The prognosis for patients with 3q21q26 syndrome is good.

8. There are at least…..partners involved in MECOM rearrangements. a. 10 b. 12 c. 8 d. 5

2. According to this article, trisomy 21 pregnancies are associated with: I. increased maternal age II. increased maternal serum pregnancy-associated plasma protein A III. increased fetal nuchal translucency IV. increased maternal serum free-human chorionic gonadotrophin

9. Topologically Associated Domains (TAD):

a. I, II and III b. I, III and IV c. I and II only d. All of the above

I. range in size from hundreds of kilobases to one megabase.

II. appear in metaphase.

III. play a role in gene transcription.

IV. disallow interactions between the genes in that TAD and regulatory elements of neighboring genes.

3. Type II triplody is the most common observed.

a. I, II and III b. II, III and IV c. I, III and IV d. All of the above

a. true b. false 4. All of the following are correct, except:

10. AML:

a. The triploid fetus was detected from a fetal scan for anomalies. b. The amniocentesis revealed a 69,XXY karyotype. c. The fetus had an aberrant skull shape. d. There was no consanguinity in this family.

I. is the most common adult acute leukemia.

II. If arising from MDS, AML is refractory to treatment.

III. is classified by WHO into several groups depending on cytogenetic findings.

IV. is characterized by a rapid growth of abnormal white blood cells.

5. What is the incidence of triploidy in liveborns?

a. I, II and III b. II, III and IV c. I and IV only d. All of the above

a. 1:15,000 b. 1:20,000 c. 1:1,000 d. 1:10,000 The following questions are from Lawce H et al. MECOM (EVI1) Rearrangements: A Review and Case Report of Two MDS Patients with Complex 3q Inversions/Deletions. J Assoc Technol. 2017;43(1): 9-14.

The following questions are from Mah M. The Development of NGS Technologies, Looking Back at 2014. J Assoc Genet Technol. 2017;43(1): 17-18.

6. MDS is reclassified as AML when the percentage of blasts increases above……%.

11. The two largest providers of NGS technologies are Illumina and Thermo Fisher Scientific.

a. 5 b. 25 c. 0.5 d. 20

a. true b. false

The Journal of the Association of Genetic Technologists 43 (2) 2017

70

Continuing Education Opportunities

Column Editor: Sally J. Kochmar, MS, CG(ASCP)CM

12. All of the following statements are true except:

18. Why is this case so important?

a. The most relevant NGS platforms in labs are benchtop sequencers. b. Most sequencers are accompanied by same vendor NGStargeted gene panels. c. Illumina uses semiconductor sequencing technology. d. SBS technology is based on the use of DNA polymerase.

I. It highlights the complexity of numerical and structural abnormalities that can be present in MPAL. II. It raises questions about the prognostic impact of their synergistic effect.

III. It is the first report of a CDKN2A/p16 loss in MPAL. IV. It is the first report of an idic(1)(q21) in MPAL. a. I, II and III b. II, III and IV c. I, III and IV d. All of the above

13. The sequencing speed on the Ion Torrent instruments takes about…….hours. a. 24 b. 4 to 6 c. 1 to 2 d. 2 to 4

The following questions are from Coovadia A. Lost in Interpretation: Evidence of Sequence Variant Database Errors.

J Assoc Genet Technol. 2017;43(1): 23-27.

The following questions are from Shabsovich D et al. Novel Cytogenetic Findings in a Case of Mixed Phenotype Acute Leukemia within the Context of a Complex Karyotype. J Assoc Genet Technol. 2017;43(1): 20-22.

19. How many variant databases were listed by the Human Genome Variation Society in 2016? a. 87,000 b. 1,646 c. 183,000 d. 5,125

14. Choose the incorrect statement: a. Mixed phenotype acute leukemia (MPAL) is a rare hematological malignancy. b. MPAL with a complex karyotype is associated with a poor prognosis. c. The most recurrent cytogenetic abnormality of MPAL is del 7q. d. MPAL involves cells of the myeloid, T- and/or B-cell lineages.

20. Which website is recommended by the American College of Medical Genetics as a resource for genomic tools such as reference transcripts?

15. The modal number in this case was……..which is considered…. a. 62, hypodiploid b. 60, hyperdiploid c. 65, hyperdiploid d. 62, hyperdiploid

21. All of the following are true, except: a. The ClinVar website has more than 5,000 hits per day. b. ClinVar has over 137,916 unique variant records. c. ClinVar provides phenotypic data for every variant. d. ClinVar is a public archive.

16. Structural abnormalities involving 1p32 have been observed in about 10% of MPAL cases. a. true b. false

22. According to this article, an estimated………. % of clinical test reports are in significant conflict with clinical reports from other laboratories.

17. Interphase FISH performed in this case revealed extra copies of intact MYC signal in…...nuclei.

a. 12-60 b. 10-50 c. 5-50 d. 12-50

a. 220/300 b. 232/300 c. 117/300 d. 17/300

Answer Sheet 1.____ 2.____ 3.____ 4.____ 5.____ 6.____

7.____ 8.____ 9.____ 10.____ 11.____ 12.____

a. OMIM b. ClinVar c. LSDBs d. HGMD

Please Print Clearly 13.____ 14.____ 15.____ 16.____ 17.____ 18.____

Answers to Test Yourself #1, 2017

19.____ 20.____ 21.____ 22.____

Passing Score: (passing score is 19/22 or 86.3%) 1.d 2.d 3.a 4.c 5.d 6.d

7.b 8.d 9.d 10.a 11.c 12.c

The Journal of the Association of Genetic Technologists 43 (2) 2017

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13.a 14.a 15.d 16.b 17.a 18.c

19.c 20.b 21.a 22.d

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Each successfully completed Journal Club is worth 4.0 Contact Hours. Journal Clubs can be ordered through the AGT Executive Office.

READING LIST 54 – General Content Area: Chromosome Breakage Syndromes–2006 1. Chromosome Breakage Syndromes and Cancer 2. DEB Test for Fanconi Anemia Detection in Patients with Atypical Phenotype 3. Nijmegen Breakage Syndrome: Clinical Manifestation of Defective Response to DNA Doublestrand Breaks

READING LIST 55 – General Content Area: Array Based Prenatal Genetics–2006 1. Array-based Comparative Genomic Hybridization Facilitates Identification of Breakpoints of a Novel der(1)t(1;18) (p36.3;q23)dn in a Child Presenting with Mental Retardation 2. Detection of Cryptic Chromosome Aberrations in a Patient with a Balanced t(1;9)(p34.2;p24) by Array-based Comparative Genomic Hybridization 3. Jumping Translocations in Multiple Myeloma

READING LIST 56 – General Content Area: Leukemia–2007 1. Fluorescence in situ Hybridization Analysis of Minimal Residual Disease and the Relevance of the der(9) Deletion in Imatinib-treated Patients with Chronic Myeloid Leukemia 2. Characterization of the t(17;19) Translocation by Gene-specific Fluorescent in situ Hybridizationbased Cytogenetics and Detection of the E2A-HLF Fusion Transcript and Protein in Patient’s Cells 3. Combination of Broad Molecular Screening and Cytogenetic Analysis for Genetic Risk Assignment and Diagnosis in Patients with Acute Leukemia

READING LIST 57 – General Content Area: Premature Chromosome Condensation–2007 1. Premature Chromosome Condensation in Humans Associated with Microcephaly and Mental Retardation: A Novel Autosomal Recessive Condition 2. Chromosome Condensation: DNA Compaction in Real Time 3. Phosphatase Inhibitors and Premature Chromosome Condensation in Human

Peripheral Lymphocytes at Different CellCycle Phases

READING LIST 58 – General Content Area: Solid Tumor and FISH–2007 1. Methylthioadenosine Phosphorylase Gene Deletions are Frequently Detected

by Fluorescence in situ Hybridization in Conventional Chondrosarcoma 2. Solid Pseudopapillary Neoplasms of the Pancreas are Associated with FLI-1 Expression, but Not with EWS/FLI-1 Translocation 3. High Incidence of Chromosome 1 Abnormalities in a Series of 27 Renal Oncocytomas: Cytogenetic and Fluorescent In Situ Hybridization Studies

READING LIST 59 – General Content Area: Treatment of Prader-Willi Syndrome with Growth Hormone–2008 1. Two Years of Growth Hormone Therapy in Young Children with Prader-Willi Syndrome: Physical and Neurodevelopmental Benefits - American Journal of Medical Genetics Part A, Volume 143A, Issue 5, pages 443-448, 1 March 2007 2. Growth Hormone Therapy and Scoliosis in Patients with Prader-Willi Syndrome 3. Cause of Sudden, Unexpected Death of Prader-Willi Syndrome Patients with or without Growth Hormone Treatment

READING LIST 60 – General Content Area: Generics of Autism–2008 1. 15q11-13 GABAa Receptor Genes are Normally Biallelically Expressed in Brain yet are Subject to Epigenetic Dysregulation in Autism-Spectrum Disorders 2. Characterization of an AutismAssociated Segmental Maternal Heterodisomy of the Chromosome 15q1113 Region 3. 15q Duplication Associated with Autism in a Multiplex Family with a Familial Cryptic Translocation t(14;15)(q11.2;q13.3) Detected Using Array-CGH

READING LIST 61 – General Content Area: Genetics of Nicotine Addiction–2008 1. Fine Mapping of a Linkage Region on Chromosome 17p13 Reveals that

GABARAP and DLG4 are Associated with Vulnerability to Nicotine Dependence in European-Americans 2. Genomewide Linkage Scan for Nicotine Dependence: Identification of a Chromosome 5 Risk Locus 3. Genetic Linkage to Chromosome 22q12 for a Heavy-Smoking Quantitative Trait in Two Independent Samples

READING LIST 62 – General Content Area: Somatic Mutation Detection–2007 1. Inferring Somatic Mutation Rates Using the Stop-Enhanced Green Fluorescent Protein Mouse 2. Paternal Age at Birth is an Important Determinant of Offspring Telomere Length 3. Genome-Wide SNP Assay Reveals Structural Genomic Variation, Extended Homozygosity and Cellline Induced Alterations in Normal Individuals

READING LIST 63 – General Content Area: Polyglutamine Neurodegenerative Disorders–2007 1. CAG- Encoded Polyglutamine Length Polymorphism in the Human Genome 2. Polyglutamine Neurodegenerative Diseases and Regulation of Transcription: Assembling the Puzzle 3. Pathogenesis and Molecular Targeted Therapy of Spinal and Bulbar Muscular Atrophy

READING LIST 64 – General Content Area: Clinical Applications of Noninvasive Diagnostic Testing–2008 1. Digital PCR for the Molecular Detection of Fetal Chromosomal Aneuploidy 2. Noninvasive Testing for Colorectal Cancer: A Review 3. Novel Blood Biomarkers of Human Urinary Bladder Cancer

READING LIST 65 – General Content Area: Diabetes–2010 1. The Development of c-MET Mutation Detection Assay 2. Molecular Mechanisms of Insulin Resistance in Chronic Hepatitis C 3. A Genetic Diagnosis of HNF1A Diabetes Alters Treatment and Improves

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Continuing Education Opportunities Glycaemic Control in the Majority of InsulinTreated Patients

READING LIST 66 – General Content Area: Diabetes–2010 1. Distribution of Human Papillomavirus Genotypes in Invasive Squamous Carcinoma of the Vulva 2. Distribution of HPV Genotypes in 282 Women with Cervical Lesions: Evidence for Three Categories of Intraepithelial Lesions Based on Morphology and HPV Type 3. Evaluation of Linear Array Human Papillomavirus Genotyping Using Automatic Optical Imaging Software

READING LIST 67 – General Content Area: Pancreatic Cancer and its Biomarkers–2010 1. Molecular Profiling of Pancreatic Adenocarcinoma and Chronic Pancreatitis Identifies Multiple Genes Differentially Regulated in Pancreatic Cancer 2. Effect of Recombinant Adenovirus Vector Mediated Human Interleukin-24 Gene Transfection on Pancreatic Carcinoma Growth 3. Highly Expressed Genes in Pancreatic Ductal Adenocarcinomas: A Comprehensive Characterization and Comparison of the Transcription Profiles Obtained from Three Major Technologies

READING LIST 68 – General Content Area: Influenza A(H1N1) Virus–2010 1. Detection of Influenza A(H1N1)v Virus by Real-Time RT-PCR 2. Economic Consequences to Society of Pandemic H1N1 Influenza 2009 – Preliminary Results for Sweden 3. Response after One Dose of a Monovalent Influenza A (H1N1) 2009 Vaccine — Preliminary Report

READING LIST 69 – General Content Area: The Development of c-MET Mutation Detection Assay–2010 1. Somatic Mutations in the Tyrosine Kinase Domain of the MET Proto-Oncogene in Papillary Renal Carcinomas 2. Expression and Mutational Analysis of MET in Human Solid Cancers 3. Role of cMET Expression in Non-Small-Cell Lung Cancer Patients Treated with EGFR Tyrosine Kinase Inhibitors

READING LIST 70 – General Content Area: Molecular Cardiology–2010 1. Identification of a Pleiotropic Locus on Chromosome 7q for a Composite Left Ventricular Wall Thickness Factor and Body Mass Index: The HyperGEN Study 2. Novel Quantitative Trait Locus is Mapped to Chromosome 12p11 for Left Ventricular

Mass in Dominican Families: The Family Study of Stroke Risk and Carotid Atherosclerosis 3. Genome-Wide Association Study Identifies Single-Nucleotide Polymorphism in KCNB1 Associated with Left Ventricular Mass in Humans: The HyperGEN Study

READING LIST 71 – General Content Area: Detection of Clarithromycin Resistance in H. Pylori–2010 1. Rapid Detection of Clarithromycin Resistance in Helicobacter Pylori Using a PCR-based Denaturing HPLC Assay 2. Rapid Screening of Clarithromycin Resistance in Helicobacter Pylori by Pyrosequencing 3. Quadruplex Real-Time PCR Assay Using Allele-Specific Scorpion Primers for Detection of Mutations Conferring Clarithromycin Resistance to Helicobacter pylori

READING LIST 72 – General Content Area: Werner Syndrome Gene–2010 1. Telomeric protein TRF2 protects Holliday junctions with telomeric arms from displacement by the Werner syndrome helicase 2. WRN controls formation of extrachromosomal telomeric circles and is required for TRF2DeltaBmediated telomere shortening 3. Sequence-specific processing of telomeric 3' overhangs by the Werner syndrome protein exonuclease activity

READING LIST 73 – General Content Area: Diagnosis of Melanoma Using Fluorescence in Situ Hybridization–2011 1. Using Fluorescence in situ Hybridization (FISH) as an Ancillary Diagnostic Tool in the Diagnosis of Melanocytic Neoplasms 2. Transcriptomic versus Chromosomal Prognostic Markers and Clinical Outcome in Uveal Melanoma 3. Detection of Copy Number Alterations in Metastatic Melanoma by a DNA Fluorescence In situ Hybridization Probe Panel and Array Comparative Genomic Hybridization: A Southwest Oncology Group Study (S9431)

READING LIST 74 – General Content Area: Role of Short Interfering RNA in Gene Silencing–2011 1. Highly Specific Gene Silencing by Artificial miRNAs in Rice.

2. Gene silencing by RNAi in mouse Sertoli cells.

3. Retrovirus-delivered siRNA.

READING LIST 75 – General Content Area: Multiple Myeloma: Molecular Markers and Tests–2010 1. Multiple Myeloma: Lusting for NF-B 2. Functional Interaction of Plasmacytoid Dendritic Cells with Multiple Myeloma Cells: A Therapeutic Target 3. High-resolution genomic profiles define distinct clinico-pathogenetic subgroups of multiple myeloma patients

READING LIST 76 – General Content Area: Colorectal Cancer and Loss of Imprinting of IGF2–2010 1. Loss of imprinting of IGF2 as an epigenetic marker for the risk of human cancer 2. Temporal stability and age-related prevalence of loss of imprinting of the insulin-like growth factor-2 gene.

3. Epigenetics at the Epicenter of Modern Medicine

READING LIST 77 – General Content Area: Health Effects Associated with Disruption of Circadian Rhythms–2011 1. Circadian Polymorphisms associated with Affective Disorders 2. A new approach to understanding the impact of Circadian Disruption on Human Health 3. Circadian Rhythm and its Role in Malignancy

READING LIST 78 – General Content Area: Role of Hedgehog Signaling Pathway in Diffuse Large BCell Lymphoma–2010 1. Sonic hedgehog signaling proteins and ATP-bindig cassette G2 are aberrantly expressed in diffuse large B-cell lymphoma 2. Sonic Hedgehog Signaling Pathway is Activated in ALK-Positive Anaplastic Large Cell Lymphoma 3. Sonic Hedgehog is Produced by Follicular Dendritic Cells and Protects Germinal Center B Cells from Apoptosis

READING LIST 79 – General Content Area: Whole Genome Amplification & 1986 Chernobyl, Ukraine Nuclear Power Plant Accident–2010 1. BAC-FISH assays delineate complex chromosomal rearrangements in a case of post-Chernobyl childhood thyroid cancer.

2. Whole Genome Amplification Technologies - Eliminating the Concern Over Running Out of DNA Samples Mid Experiment.

3. A break-apart fluorescence in situ hybridization assay for detecting RET translocation in papillary thyroid carcinoma.

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Continuing Education Opportunities READING LIST 80 – General Content Area: Expression of miRNA in Diffuse Large B-Cell Lymphoma–2010 1. Differentiation stage specific expression of microRNAs in B lymphocytes and diffuse large B-cell lymphomas.

2. Coordinated Expression of MicroRNA-155 and Predicted Target Genes in Diffuse Large B-cell Lymphoma.

3. Specific expression of miR-17-5p and miR-127 in testicular and central nervous system diffuse large B-cell lymphoma.

READING LIST 81 – General Content Area: The Genetics of Bipolar Disorder–2010 1. Gene-wide analyses of genomewide association data sets: evidence for multiple common risk alleles for schizophrenia and bipolar disorder and for overlap in genetic risk 2. Subcortical Gray Matter Volume Abnormalities in Healthy Bipolar Offspring: Potential Neuroanatomical Risk Marker for Bipolar Disorder?

3. Genetic and Environmental Influences on Pro-Inflammatory Monocytes in Bipolar Disorder

READING LIST 82 – General Content Area: Role and Detection of Human Endogenous Retroviruses in Rheumatoid Arthritis–2011 1. Increase in Human Endogenous Retrovirus HERV-K(HML-2) Viral Load in Active Rheumatoid Arthritis.

2. A role for human endogenous retrovirus-K (HML-2) in rheumatoid arthritis: investigating mechanisms of pathogenesis 3. Lack of Detection of Human Retrovirus-5 Proviral DNA in Synovial Tissue and Blood Specimens From Individuals With Rheumatoid Arthritis or Osteoarthritis.

READING LIST 83 – General Content Area: Roles of Oncogenes in Breast Cancer–2010 1. The Nuclear Receptor Coactivator Amplified in Breast Cancer-1 Is Required for Neu (ErbB2/HER2) Activation, Signaling, and Mammary Tumorigenesis in Mice.

2. Dysregulated miR-183 inhibits migration in breast cancer cells.

3. Current and emerging biomarkers in breast cancer: prognosis and prediction

READING LIST 84 – General Content Area: Elevated Levels of Human Endogenous Retrovirus-W in Patients With First Episode of Schizophrenia–2010 1. Elevated Levels of Human Endogenous Retrovirus-W Transcripts in Blood Cells From Patients With First Episode Schizophrenia.

2. Endogenous Retrovirus Type W GAG and Envelope Protein Antigenemia in Serum

of Schizophrenic Patients.

3. Reduced Expression of Human Endogenous Retrovirus (HERV)– W GAG Protein in the Cingulate Gyrus and Hippocampus in Schizophrenia, Bipolar Disorder, and Depression.

Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species.

3. Evaluation of next generation sequencing platforms for population targeted sequencing studies.

READING LIST 85 – General Content Area: Esophageal Cancer–2010

READING LIST 91 – General Content Area: Hutchinson-Gilford Progeria Syndrome–2011

1. The Changing Face of Esophageal Cancer 2. Epidermal Growth FactorInduced Esophageal Cancer Cell Proliferation Requires Transactivation of-Adrenoceptors 3. Esophageal cancer risk by type of alcohol drinking and smoking: a casecontrol study in Spain

READING LIST 86 – General Content Area: p53 Family and Its Role In Cancer–2010 1. Telomere dysfunction suppresses spontaneous tumorigenesis in vivo by initiating p53-dependent cellular senescence.

2. Shaping genetic alterations in human cancer: the p53 mutation paradigm.

3. p53 polymorphisms: cancer implications.

READING LIST 87 – General Content Area: Proteins Involved with Chronic Myleloid Leukemia and Other Myleoprolifertive Disorders–2011 1. Gain-of-Function Mutation of JAK2 in Myeloproliferative Disorders.

2. Kinase domain mutants of Bcr enhance Bcr-Abl oncogenic effects.

3. Destabilization of Bcr-Abl/Jak2 Network by a Jak2/Abl Kinase Inhibitor ON044580 Overcomes Drug Resistance in Blast Crisis Chronic Myelogenous Leukemia (CML).

READING LIST 88 – General Content Area: DNA Topology–2010 1. The why and how of DNA unlinking.

2. Bacterial DNA topology and infectious disease.

3. DNA topoisomerase II and its growing repertoire of biological functions.

READING LIST 89 – General Content Area: LPL Waldenstrom Macroglobulinemia–2010 1. Spontaneous splenic rupture in Waldenstrom's macroglobulinemia.

2. How I Treat Waldenstrom's Macroglobulinemia.

3. International prognostic scoring system for Waldenström Macroglobulinemia.

READING LIST 90 – General Content Area: Next Generation Sequencing Platforms–2010 1. Rapid whole-genome mutational profiling using next-generation sequencing technologies.

2. Combining Next-Generation Sequencing

1. Epidermal expression of the truncated prelamin a causing Hutchinson– Gilford progeria syndrome: effects on keratinocytes, hair and skin 2. Defective Lamin A-Rb Signaling in Hutchinson-Gilford Progeria Syndrome and Reversal by Farnesyltransferase Inhibition 3. Increased expression of the Hutchinson– Gilford progeria syndrome truncated lamin a transcript during cell aging.

READING LIST 92 – General Content Area: Severe Combined Immunodeficiency Screening and Patient Studies–2011 1. Long-term Outcome after Hematopoietic Stem Cell Transplantation of a Singlecenter Cohort of 90 Patients with Severe Combined Immunodeficiency.

2. Why Newborn Screening for Severe Combined Immunodeficiency Is Essential: A Case Report.

3. Development of a Routine Newborn Screening Protocol for Severe Combined Immunodeficiency.

READING LIST 93 – General Content Area: Biological and Physical Hazards Encountered in the Laboratory–2011 1. Lab Safety Matters.

2. Virus Transfer from Personal Protective Equipment to Healthcare Employees’ Skin and Clothing. Emerging Infectious Diseases.

3. Prevalence of Hepatitis C Virus Infection Among Health-Care Workers: A 10-Year Survey.

READING LIST 94 – General Content Area: Rapid whole-genome mutational profiling using nextgeneration sequencing technologies–2011 1. Comparison of next generation sequencing technologies for transcriptome characterization.

2. ShortRead: a bioconductor package for input, quality assessment and exploration of highthroughput sequence data.

3. Next-Generation Sequencing: From Basic Research to Diagnostics.

READING LIST 95 – General Content Area: Cell Death–2011 1. Hypoxia induces autophagic cell death in apoptosis-competent cells through a mechanism involving BNIP3.

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Continuing Education Opportunities 2. Truncated forms of BNIP3 act as dominant negatives inhibiting hypoxiainduced cell death.

3. Hypoxia-Induced Autophagy Is Mediated through Hypoxia-Inducible Factor Induction of BNIP3 and BNIP3L via Their BH3 Domains.

3. Evidence for Three Loci Modifying Ageat-Onset of Alzheimer’s Disease in EarlyOnset PSEN2 Families.

READING LIST 96 – General Content Area: Genetic Associations of Cerebral Palsy– 2011

1. A multiplex one-step real-time RT-PCR assay for influenza surveillance.

2. Taking New Tack, PrimeraDx Offers MDx Tech as Open Platform for Test Developers.

3. Comparison of Automated Microarray Detection with Real-Time PCR Assays for Detection of Respiratory Viruses in Specimens Obtained from Children.

1. Mannose-binding lectin haplotypes may be associated with cerebral palsy only after perinatal viral exposure.

2. Methylenetetrahydrofolate Reductase Gene Polymorphisms and Cerebral Palsy in Chinese Infants.

3. Apolipoprotein E genotype and cerebral palsy.

READING LIST 97 – General Content Area: Treatments for HIV/AIDs–2011 1. Early Antiretroviral Therapy Reduces AIDS Progression/Death in Individuals with Acute Opportunistic Infections: A Multicenter Randomized Strategy Trial.

2. Asia can afford universal access for aids prevention and treatment.

3. Trends in reported aids defining illnesses (adis) among participants in a universal antiretroviral therapy program: an observational study.

READING LIST 98 – General Content Area: Myosin Light Chain Kinase (MYLK) Gene Mutation Affect in Smooth Muscle Cells– 2012 1. Myosin light chain kinase is central to smooth muscle contraction and required for gastrointestinal motility in mice.

2. Mutation in myosin light chain kinase cause familial aortic dissections.

3. Chemical genetics of zipper-interacting protein kinase reveal myosin light chain as a bona fide substrate in permeabilized arterial smooth muscle.

READING LIST 99 – General Content Area: Chromosome 6 and Its Associated Diseases–2011 1. Novel Cleft Susceptibility Genes in Chromosome 6q.

2. A susceptibility locus on chromosome 6q greatly increases risk lung cancer risk among light and never smokers.

3. The identification of chromosomal translocation, t(4;6)(q22;q15), in prostate cancer.

READING LIST 100 – General Content Area: Early onset of autosomal dominant Alzheimer disease–2011 1. Genetics of Alzheimer Disease.

2. New mutation in the PSEN1 (E120G) gene associated with early onset Alzheimer’s disease.

READING LIST 101 – General Content Area: Multiplex PCR and Emerging Technologies for the Detection of Respiratory Pathogens–2011

neuronal trigger for inflammation and Alzheimer’s pathology.

3. The inflammasome: a caspase-1activation platform that regulates immune responses and disease pathogenesis.

READING LIST 106 – General Content Area: DNA Barcoding–2011 1. Commercial Teas Highlight Plant DNA Barcode Identification Successes and Obstacles.

2. Mutational Patterns and DNA Barcode for Diagnosing Chikungunya Virus.

3. The Barcode of Life Data Portal: Bridging the Biodiversity Informatics Divide for DNA Barcoding.

READING LIST 102 – General Content Area: Single Nucleotide Polymorphism (SNP) Array Analysis–2011

READING LIST 107 – General Content Area: HERV-K and Its Correlation With Melanoma Cells–2011

1. A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data.

2. SAQC: SNP array quality control.

3. Calibrating the performance of SNP arrays for whole-genome association studies.

1. Expression of human endogenous retrovirus K in melanomas and melanoma cell lines Cancer.

2. Expression of HERV-K correlates with status of MEK-ERK and p16INK4A-CDK4 pathways in melanoma cells cancer.

3. An endogenous retrovirus derived from human melanoma cells.

READING LIST 103 – General Content Area: Research of BRAF Gene Related to Cancer–2011

READING LIST 108 – General Content Area: Refractory Myeloma–2011

1. Kinase-Dead BRAF and Oncogenic RAS Cooperate to Drive Tumor Progression through CRAF. 2. Distinct patterns of DNA copy number alterations associate with BRAF mutations in melanomas and melanoma derived cell lines.

3. Pharmacodynamic Characterization of the Efficacy Signals Due to Selective BRAF Inhibition with PLX4032 in Malignant Melanoma.

READING LIST 104 – General Content Area: Microarray Single Nucleotide Polymorphism (SNP) Troubleshooting–2011 1. Model-based clustering of array CGH data.

2. Application of a target array comparative genomic hybridization to prenatal diagnosis.

3. A model-based circular binary segmentation algorithm for the analysis of array CGH data.

READING LIST 105 – General Content Area: Inflammasome Activation by Proteins–2011 1. Activation of the NLRP3 inflammasome by islet amyloid polypeptide provides a mechanism for enhanced IL-1 2 in type 2 diabetes.

2. ER stress in Alzheimer’s disease: A novel

1. Pomalidomide plus low-dose dexamethasone in myeloma refractory to both bortezomib and lenalidomide: comparison of 2 dosing strategies in dual-refractory disease.

2. Relapse/Refractory Myeloma Patient: Potential Treatment Guidelines.

3. Emerging role of carfilzomib in treatment of relapsed and refractory lymphoid neoplasms and multiple myeloma.

READING LIST 109 – General Content Area: Short Tandem Repeat (STR) Technology in Forensic Community–2011 1. An integrated microdevice for highperformance short tandem repeat genotyping.

2. A comparison of the effects of PCR inhibition in quantitative PCR and forensic STR analysis.

3. Generating STR profile from "Touch DNA".

READING LIST 110 – General Content Area: Methods of Screening and Evaluation of Hepatitis C Virus–2011 1. Hepatitis c virus: prevention, screening, and interpretation of assays.

2. Serial follow-up of repeat voluntary blood donors reactive for anti-hcv elisa.

3. Comparison of fibrotest-actitest with histopathology in demonstrating fibrosis and necroinflammatory activity in chronic hepatitis b and c.

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Continuing Education Opportunities READING LIST 111 – General Content Area: Pharmacogenomics–2011 1. Pharmacogenomic testing: Relevance in medical practice: Why drugs work in some patients but not in others.

2. Clinical assessment incorporating a personal genome.

3. Genomics and drug response.

READING LIST 112 – General Content Area: Adrenoleukodystrophy–2011 1. Novel exon nucleotide deletion causes adrenoleukodystrophy in a Brazilian family.

2. X-linked adrenoleukodystrophy: ABCD1 de novo mutations and mosaicism.

3. Identification of novel SNPs of ABCD1, ABCD2, ABCD3, and ABCD4 genes in patients with Xlinked adrenoleukodystrophy (ALD) based on comprehensive resequencing and association studies with ALD phenotypes.

READING LIST 113 – General Content Area: Quality Assurance and Quality Control of Microarray Comparative Genomic Hybridization–2011 1. Customized oligonucleotide array-based comparative genomic hybridization as a clinical assay for genomic profiling of chronic lymphocytic leukemia.

2. Comparison of familial and sporadic chronic lymphocytic leukaemia using

high resolution array comparative genomic hybridization.

3. Microarray-based comparative genomic hybridization.

READING LIST 114 – General Content Area: mFISH–2012 1. Human interphase chromosomes: a review of available molecular cytogenetic technologies.

2. Establishment of a new human pleomorphic malignant fibrous histiocytoma cell line, FU-MFH-2: molecular cytogenetic characterization by multicolor fluorescence in situ hybridization and comparative genomic hybridization.

3. CD5-negative Blastoid Variant Mantle Cell Lymphoma with Complex CCND1/ IGH and MYC Aberrations.

READING LIST 116 – General Content Area: Autism - 2015 1. Intellectual disability and autism spectrum disorders: Causal genes and molecular mechanisms.

2. Aberrant tryptophan metabolism: the unifying biochemical basis for autism spectrum disorders?

3. Decreased tryptophan metabolism in patients with autism spectrum disorders

READING LIST 115 – General Content Area: Cystic Fibrosis - 2014 1. Rapid Detection of the ACMG/ACOGRecommended 23 CFTR DiseaseCausing Mutations Using Ion Torrent Semiconductor Sequencing 2. Long-Term Evaluation of Genetic Counseling Following False-Positive Newborn Screen for Cystic Fibrosis 3. Rapid Transport of Muco-Inert Nanoparticles in Cystic Fibrosis Sputum Treated with N-acetyl cysteine

Copyright law prohibits AGT from supplying readers with the actual journal articles (electronically or otherwise). Availability of articles online does not imply the service is free.

Some journals require a subscription or impose a fee. The web addresses are included for the convenience of those wishing to obtain the articles in this way.

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Continuing Education Opportunities

AGT Journal Club Question Order Form

To order the AGT Journal Club Questions, please fill in the requested information below. Make check or money order payable to AGT. Copyright law prohibits AGT from supplying readers with the actual journal articles (electronically or otherwise).

Participants must obtain articles themselves.

Discussion and Question Set for Reading List No. (Please enter the number of copies requested next to each Journal Club Number) ____54

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Association Business

AGT, The Organization for Cytogenetic & Molecular Professionals AGT, originally founded in 1975 as the Association of Cytogenetic Technologists, serves to: • promote the scientific and professional development of all areas of genetics; • foster the exchange of information between those interested in genetics; • encourage cooperation between those persons actively or formerly engaged in genetics; and • stimulate interest in genetics as a career.

AGT has approximately 1,000 members. Membership is open to all who are employed or interested in genetics. All regular members are entitled to hold office, vote in elections, attend all AGT meetings, and receive The Journal of the Association of Genetic Technologists and access the AGT International Online Membership Directory.

Board of Directors Officers President Patricia K. Dowling, PhD Pathline Labs 535 E. Crescent Ave. Ramsey, NJ 07446 PDowling@pathlinelabs.com President-Elect Jason A. Yuhas, BS, CG(ASCP)CM Mayo Clinic Division of Laboratory Genetics Cytogenetics Lab 200 First St. SW Rochester, MN 55905 507-538-7634 yuhas.jason@mayo.edu Secretary-Treasurer Denise Juroske Short, MSFS, MB(ASCP)CM 219 Timberland Trail Lane.

Lake City, TN 37769 dmj4565@gmail.com Public Relations Director Ephrem Chin MBA, MB(ASCP)CM, QLC Oxford Gene Technology 520 White Plains Road, Suite 500 Tarrytown, NY 10591 404-579-9995 nzelfman@gmail.com Education Director Sally J. Kochmar, MS, CG(ASCP)CM Magee-Womens Hospital Pittsburgh Cytogenetics Lab 300 Halket St., Room 1233 Pittsburgh, PA 15213 412-641-4882 skochmar@upmc.edu

Annual Meeting Director Jennifer N. Sanmann, PhD, FACMG UNMC Human Genetics Laboratory 985440 NE Med. Center Omaha, NE 68198-5440 402-559-3145 jsanmann@unmc.edu Annual Meeting Co-Director Christina Mendiola, BS, CG(ASCP)CM University of Texas Health Science Center – San Antonio 7703 Floyd Curl Dr. San Antonio, TX 78229 210-567-4050 mendiolac@uthscsa.edu

Council of Representatives Representative to CCCLW Term: 7/14 – 6/20 Hilary E. Blair, BS, MS, CG(ASCP)CM Mayo Clinic 200 First St. SW Rochester, MN 55905 507-255-4385 blair.hilary@mayo.edu Representatives to BOC Term: 10/12 – 9/18 Helen Bixenman, MBA/HCM, CHC, CG(ASCP)CM, DLMCM, QLC San Diego Blood Bank 3636 Gateway Ctr. Ave., Ste. 100 San Diego, CA 92102 619-400-8254 hbixenman@sandiegobloodbank.org Term: 10/11 – 9/16 Amy R. Groszbach, MEd, MLT(ASCP)CM, MBCM Mayo Clinic Molecular Genetics Laboratory – Hilton 920 200 First St. SW Rochester, MN 55905 507-284-1229 groszbach.amy@mayo.edu

Representative to NAACLS Term: 9/12 – 9/16 Peter C. Hu, PhD, MS, MLS(ASCP)CM, CGCM, MBCM University of Texas M.D. Anderson Cancer Center School of Health Sciences 1515 Holcomb Blvd., Box 2 Houston, TX 77030 713-563-3095 pchu@mdanderson.org Representative to Foundation for Genetic Technology Term: 7/10 – 6/16 Patricia LeMay, MT(ASCP), CG(ASCP)CM Monmouth Medical Center Department of Pathology 300 Second Ave. Long Branch, NJ 07740 732-923-7369 plemay1945@aol.com Representative to CAP/ACMG Term: 1/16 – 12/21 Jun Gu, MD, PhD, CG(ASCP)CM University of Texas MD Anderson Cancer Center School of Health Professions Cytogenetic Technology Program 1515 Holcombe Boulevard, Unit 2 Houston, TX 77030 (713) 563-3094 jungu@mdanderson.org

Publications AGT Journal Editor Mark D. Terry 1264 Keble Lane Oxford, MI 48371 586-805-9407 markterry@charter.net

Visit AGT’s Website at www.AGT-info.org The Journal of the Association of Genetic Technologists 43 41 (4) (2) 2015 2017

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Other Contacts Liaison to ASCLS Governmental Affairs Committee Kathryn Sudduth, BA, CG(ASCP)CM, DLMCM 2713 Brookmere Road Charlottesville, VA 22901 434-973-0690 kas3m2@embarqmail.com FGT Board of Trustees President Robin A. Vandergon, CG(ASCP)CM, DLMCM 8767 E. Los Altos Ave. Clovis, CA 93619 559-392-0512 rrink@quixnet.net

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Association Business

Letter from the President Greetings, All You Genetic Technology Professionals!

I bet you thought you got rid of me! Not so fast! I want to make sure all of you have heard that the 4th Edition of the AGT Technical Manual is now available for purchase!!!! Hallelujah and Mazel Tov!!!! It was a decade in the making, but it was definitely worth the wait. I can’t wait to touch it! If you think I am anxious to get my hands on it, how do you think the editors feel? That wasn’t thunder you heard last week. That was a collective sigh of relief, from sea to shining sea, and even from heaven!!

One of the editors, Helen Lawce, wrote a history of the AGT manual, from her point of view, and shared it on Facebook. It’s too good not to include in this journal. I place it here, for your reading pleasure.

AGT Manual history from my view, by Helen Lawce.

Today, Wiley will have the 4th edition of the AGT Laboratory Manual available for purchase and delivery. It has been a long road to travel, and I think back on the ten-years-plus that it took to produce, I feel many emotions: wonder, gratitude to the dozens of people who helped without compensation, awe that it is finally final, pride, that it is the resource we wanted it to be, and love, both for the people I worked with and the work itself.

My coworker Judy Canham at UCSF had an idea when we worked there together in the 1970s that we should start an organization for cytogenetic technologists and create a book of laboratory methods. She was in disbelief that the techniques we used in our lab were not published all together in one place, and as she was being trained, she became acutely aware of the need for a reference. She and a handful of other like-minded techs from Northern California made the dream of an organization come true, and Judy became the first president of the new Association of Cytogenetic Technologists (ACT, now AGT). Marilyn Arsham of New York and I undertook the project of the book, the ACT Technical Manual (now AGT Cytogenetics Laboratory Manual).

The first edition was an adventure, a self-published, manually-typed manuscript bound in a loose-leafed binder.

Marilyn compiled the laboratory methods, and we along with other volunteers, wrote the chapters. It was meant to be both a training resource and a laboratory reference. In the introduction we likened it to Donald Duck's nephews' *Junior Woodchuck Guide, which was such a wonderful resource that one could look up any question, including the safest ship passage through the Straits of Doomgurgle in a storm. I typed most of it myself on a snazzy rented IBM Selectric typewriter. We used 12-by-17-inch paper and had the printer copy it on 8.5-by-11-inch paper to reduce the font size and make the book smaller and cheaper. I remember my husband and I were racing horses in Mexico, when I wrote the Microscopy chapter in Juarez, in a tackroom, with a pen and yellow pad, while we were waiting to go to post or for an exercise rider to show up.

The book cost members $20, about the price of a pair of running shoes back in the 1980s, and Denise Sivhonen and I wrapped, addressed, and mailed them out ourselves. At the time we used my personal mailing address to collect the money, and later the California Franchise Tax Board tried to ask me to pay income taxes on the sales.

Luckily, ACT had a lawyer by then who was able to explain to the tax board that I did not make any money from the sales.

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Association Business The second edition was edited by Margaret Barch, and we actually used word processing computers to write our chapters, and a real publisher did a hardbound book for us. The computer I did my chapters on was a hand-medown TRS-80 that my dad gave me when he got a better one. The publisher received my floppy discs with the chapters, but the TRS-80 code did not work for them, and they had me print everything so they could scan it into their software program. This resulted in some pretty funny typos, such as hypnotic solution instead of hypotonic solution, and I received a number of letters to point this out. I tried to laugh, but some jokes are funnier for the person who was not simultaneously writing, learning computerese, and struggling with a Tandy Radio Shack Tinkertoy computer that the publisher could not even use.

The third edition, edited by Margaret Barch, Turid Knutsen, and the great Jack Spurbeck, was again a computergenerated, professionally-produced book, but the illustrations were all still made by photographic means. We added the Overview chapter, covering a sort of "day in the lab" description of what a cytogenetics technologist does with samples that come through the door from receipt to completion of the different tests. This chapter was well received by students and pathology residents, for whom cytogenetics appeared as some kind of occult magic performed by people too busy to share their secrets except in small sub-sections that did not intuitively connect with the other bits. We also added a chapter on FISH, and like many things scientific, it was outdated before the book even went to the publisher. This third edition has been the only available manual since it was published in 1995.

In 2005, AGT announced that they would be doing the 4th edition, and Marilyn Arsham (1st edition editor), Margaret Barch (2nd and 3rd edition editor), and I (1st edition co-editor), dubbed the triumvirate by Pat Dowling, volunteered. Little did we dream in our wildest imaginations that the book would take more than a decade to be published. That it would take three years of battling to get permission to use the ISCN diagrams. That we would have authors retract chapters that we ended up rewriting ourselves, that children would be born to some authors and grow most of the way up, or that contributors, including one of us, would pass away before it was in print.

Since it had been several computer iterations since the third edition, we could not just edit what we had on those floppy discs, as the world had moved on to other data storage methods and there was no longer hardware that could read the discs. For many chapters, I used a line-by-line scanner to copy the text into Word from a copy of the book. Many more humorous typos were made, and hopefully found and corrected by many proofreaders' eyes.

We scanned the illustrations that were scannable to make tifs. We sent the text to volunteers who made many great suggestions, rewrote, and repeated. A wonderful bio illustrator, Gret Boyd, helped us make new illustrations for three chapters, and was invaluable for the chromosome identification chapter, a new addition to the book.

So we hope that the fourth edition is all we meant it to be, and that it inspires many in the field, and many others in related fields. We know that parts of it are already outdated. The microarray field may have to make a dedicated, updatable volume. More and more automation and robotics will be introduced, and perhaps robots will even make our slides and stain them for us.

If you read this note before the meeting, I sincerely hope that I will see many of you in person at the AGT annual conference at the Union Station Hotel in St. Louis, MO from June 15 -17. If you came to the meeting and are reading this after, it was a pleasure seeing you in St. Louis! If you didn’t come to the meeting and are reading this after June 17, you missed a good time!!! Good luck, Jason!!!

Pat Dowling, AGT President The Journal of the Association of Genetic Technologists 43 (2) 2017

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Association Business

How does AGT membership benefit you?

TAY INFORMED

AGT’s publications, educational offerings and research reports deliver the news and information most relevant to your role so you’re prepared to tackle any challenge

AKE CHARGE

CCESS TO PEOPLE

Increase your value to your organization. AGT’s directories of members and labs, educational offerings, research reports and our flagship Journal can help you realize greater success.

Connect with thousands of cytogenetics, molecular and biochemical genetics professionals. Become a leadership volunteer, contribute content or participate in committees.

EACH NEW HEIGHTS

Between our in-person and online education opportunities (many free to members!) and online resources, we will help get you there. Learn from industry leaders and colleagues alike.

Are you ready to be a S.T.A.R? Join today!

How does AGT membership benefit your organization?

GROW YOUR ORGANIZATION As a member, you’ll access the resources and tools you need to help innovate and inspire your organization. AGT also promotes the interests of geneticists and genetic technologists on a National scale, with representation on organizations such as NAACLS, BOC, CCCLW, CAP/ACMG and others.

MAXIMIZE EFFICIENCY Realize efficiencies and implement improved methodologies at your organization by seeing how others have met similar challenges.

BE PREPARED All organizations look different, but the challenges they face are often the same.

We can help you prepare to meet any organizational challenge with the right knowledge and solutions by providing you an easy way to meet your CE needs.

www.agt-info.org

The Journal of the Association of Genetic Technologists 43 (2) 2017

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THREE EASY WAYS TO JOIN: Online: http://www.agtinfo.org/Pages/joinagt.aspx Mail: Return the application to the address listed With an Event: Sign up for membership at the same time you register for one of our events. It’s that easy!

Regular Members. Regular membership shall be available to persons who are professionally interested in the field of genetics.

New Membership Application Please check the appropriate membership category. If you are applying for a collaborative membership, please indicate the related organization and your member ID number:

 Regular Membership  Student Membership  Emeritus Membership

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Student Members. Student membership shall be available to persons who are pursuing a full or part-time course of study at an educational institution or school and who are interested in pursuing a career in the field of genetics.

Emeritus Members. Emeritus membership shall be available to persons who are retired from or inactive in the field of genetics.

Collaborative Members. Collaborative membership shall be available to persons who currently hold membership in any other health-related national organization and who have never been members of ACT/AGT.

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[NOTE: Submission and acceptance of this membership application authorizes the AGT Executive Office the right and privilege to email you as a member. AGT does not sell or distribute in any other manner its member email address list.]

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Referred By_____________________________________________________________________ Membership # ___________________________ Did you use a different name last year:

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Position: (check one)

 Director  Head (Lead, Core) Technologist

 Supervisor  Technologist  Tissue Culture Tech.  Education Coordinator

 Lab Manager  Other

 Biochemical  Cytogenetics  Molecular  Other Appropriate years experience in Genetics:  under 2  2-4  5-7  8-10  11-15  16-20  21-30 Principal area of Genetics: (check one)

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Journal Hard Copy Order: Although The Journal of Genetic Technologists is available online to ALL MEMBERS, only North American members can elect to receive a hard copy via regular mail for an additional fee of $100. This fee covers four issues. If you are a North American resident and would like a hard copy of the Journal, please remit the additional fee with your membership application by checking the box and adding the amount to your total payment.  $100 Please note: AGT does not accept purchase orders and does not bill/invoice for services.

Mail application form and appropriate fee for membership in correct U.S currency. Money order or check in U.S. funds drawn on a U.S. bank only. CHECKS DRAWN ON INTERNATIONAL BANKS WILL NOT BE ACCEPTED. Make checks payable to Association of Genetic Technologists. For your convenience, you may pay by credit card. Applications received after September 15 are applied toward the next membership year. NOTE: Membership expires on December 31 of each year.

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The AGT Cytogenetics Laboratory Manual, 4th Edition

[Please note: Note: The 4th Edition of AGT's Cytogenetics Laboratory Manual is currently in production.

Preorder publication now through the publisher (available April 2017)

The Cytogenetics Symposia, 2nd Edition

The AGT Molecular Biology Techniques Review Guide Select method of delivery:

 Dropbox (no shipping cost)  Secure Document Hyperlink (no shipping cost) The Dynamics of Chromosome Spreading Video – CD featuring Jack Spurbeck

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AGT Executive Office, 4400 College Boulevard, Suite 220, Overland Park, KS 66211 Fax (913) 222-8606  Email: agt-info@kellencompany.com  Website: www.agt-info.org

Please allow 2-4 weeks for shipping.

Association Business

2017-2018 Scientific Meetings Schedule If you know of a relevant meeting, please send information to Ephrem Chin, Public Relations Director at nzelfman@gmail.com.

Meeting

Location

Dates

Website

American Society of Clinical Oncology (ASCO) Annual Meeting

Chicago, IL

June 2-6, 2017

www.asco.org

American Society for Mass Spectrometry (ASMS) Annual Conference

Indianapolis, IN

June 4-8, 2017

www.asms.org

Cambridge Healthtech Institute (CHI) World Preclinical Congress

Boston, MA

June 13-15, 2017

www.healthtech.com

International Aids Society (IAS) Conference

Paris France

July 2017

www.iasociety.org

European Society of Human Reproduction & Embryology (ESHRE) Annual Meeting

Geneva, Switzerland

July 2-5, 2017

www.eshre.com

American Association for Clinical Chemistry (AACC)’s San Diego, CA Annual Meeting

July 30 – August 3, 2017

www.aacc.org

American Society of Clinical Laboratory Science (ASCLS) Annual Meeting

San Diego, CA

July 30 – August 4, 2017

www.ascls.org

Society for Inherited Metabolic Disorders (SIMD) Annual Meeting

Rio de Janeiro, Brazil

September 5-8, 2017

www.simd.org

International Congress of Pediatric Laboratory Medicine (ICPLM)

Durban, South Africa

October 20-22, 2017

www.icplm2017.org

American Chemical Society (ACS) National Meeting & Exposition

New Orleans, LA

March 18-22, 2018 portal.acs.org

American Association for Cancer Research (AACR) Annual Meeting

Chicago, IL

April 14-18, 2018

www.aacr.org

International Union of Basic and Clinical Kyoto, Japan Pharmacology (IUPHAR) World Congress of Basic and Clinical Pharmacology

July TBD, 2018

www.iuphar.org

American Chemical Society (ACS) National Meeting & Exposition

Boston, MA

August 19-23, 2018

portal.acs.org

American Association of Blood Banks (AABB) Annual Meeting & CTTXPO

Boston, MA

October 13-16, 2018

www.aabb.org

American Society of Human Genetics (ASHG) Annual Meeting

San Diego, CA

October 16-20, 2018

www.ashg.org

2018

Job placement ads are online at http://www.AGT-info.org

AGT accepts classified job advertising for: x x x x

Posting on Jobline page of the web site; Online postings are also included in the monthly e-news blast to members.

E-blast to AGT members For publication in JAGT (Journal of the Association of Genetic Technologists) For publication in AGT e-news only - monthly blast to members

Advertisements submitted for posting on the website or as an e-blast are generally completed within approximately 48 hours of acknowledged receipt. If logos are to be used on the posting, they must be submitted in GIF. or JPG. format. Logos and text must be submitted via e-mail.

Advertisements submitted for publication in the Journal of the Association of Genetic Technologists (JAGT) must be submitted by the deadline date for the requested issue and adhere to the mechanical requirements outlined on the insertion order form.

To place your order for advertising, please complete the appropriate form and submit to the AGT Executive Office via email agt-info@kellencompany.com.

Forms can be found on the AGT website here: http://www.agt-info.org/Pages/pricing.aspx

Association Business

Foundation for Genetic Technology 2016-2017 Board of Trustees Voting Members President Robin Vandergon NeoGenomics 30 E River Park Place West, Ste. 400 Fresno, CA 93720 559-392-0512 cell 559-433-6601 Fax rvandergon@neogenomics.com Vice President, AGT Representative, Grants Committee Chair Patricia LeMay 301-22 Spring Street Red Bank, NJ 07701 plemay1945@aol.com Secretary DeNesha Criswell NeoGenomics 618 Grassmere Park Drive, Unit 20 Nashville, TN 37211

Treasurer, Chair Capital Management Committee Tara Ellingham MUSC-Children’s Hospital Cytogenetics Lab 165 Ashley Ave., Suite 309 Charleston, SC 29425 843-792-6873 ellingha@musc.edu tellingham@hotmail.com

Public Member, Corporate Compliance Officer Bob Gasparini Consultant 12701 Commonwealth Dr. Ft. Myers, FL 33913 239-357-4237 bgasparini@neogenomics.com

Non Voting Members

AGT Representative, Awards & Scholarship Chair Denise Juroske Short 219 Timberland Trail Ln. Lake City, TN 37769 832-878-6119 dmj4565@gmail.com

Advisor, AGT President Patricia K. Dowling Pathline Labs 535 E. Crescent Ave. Ramsey, NJ 07446 PDowling@pathlinelabs.com

Public Member, Chair FGT Fundraising Jeff Sanford MetaSystems Group, Inc. 70 Bridge St., Ste. 100 Newton, MA 02458 617-924-9950 jsanford@metasystems.org

Ex-Officio, AGT Education Director Sally J. Kochmar Magee-Womens Hospital Pittsburgh Cytogenetics Lab 300 Halket St., Room 1233 Pittsburgh, PA 15213 412-641-4882 skochmar@upmc.edu

The Journal of the Association of Genetic Technologists The Journal of the Association of Genetic Technologists is a peer-reviewed journal, and scientific materials for publication containing original research will be reviewed by independent referees. Manuscripts that require revision or that contain major editorial changes will be returned to the senior author of the article. Materials submitted will not be retained following publication nor will photographs, disks, or hard copies of manuscripts be returned to authors. Rejected manuscripts will not normally be returned, although an effort will be made to return original photographs and prints.

Manuscript content is the responsibility of the author(s). All articles published, including editorials, letters, book reviews, invited articles, Brain Ticklers, columns, and reviews, represent the opinions of the authors and do not reflect the official policy of AGT or the institution with which the author is affiliated unless specified by the author. AGT, its members, and the editor of The Journal of the Association of Genetic Technologists make no warranty and assume no liability with respect to the information contained herein.

Information For Authors The Journal of the Association of Genetic Technologists is pleased to consider manuscripts that describe experience with cytogenetics, molecular genetics, or biochemical genetics and the application of these disciplines.

Submitted manuscripts must be typed, preferably double-spaced, using a 12 point font and 1” margins. In addition to the original, three copies of the manuscript and camera-ready illustrations must be submitted to the editor-in-chief. Items to be italicized or enhanced (bold, underlined) should be clearly indicated. The conversion factor for print equivalency is as follows: two double-spaced typed pages equal approximately a one-half typeset page.

Authors may supply the material on a 3½” disk, preferably in Microsoft Word, WordPerfect, or ASCII format, along with the hard copy. Macintosh disks are also acceptable, but conversion costs will be assessed accordingly to AGT and a delay in processing may occur. Materials may alternatively be supplied to the editor via email at the address shown on inside front cover. Email submission is preferred.

Illustrations must be original photographs, computer-generated digitized files (preferably saved as a .tif, .eps, or .bmp file), or black and white line drawings, professionally prepared. The cost of separating and printing color photographs or illustrations will be charged to the author. Photographs must be properly identified on the back, including the author’s name, title of article, and top direction. A ball point pen should not be used for labeling. The affixing of a typewritten label to the illustration or table will prevent damage.

Notation & References Authors’ titles must be accompanied by a position description of less than 15 words, which will be printed with the article.

Textual citations to the referenced literature should be parenthetically noted by author’s surname followed by year of publication, and arranged chronologically and then alphabetically, as demonstrated in the following example: (Lese and Ledbetter, 1998; Reilly, 1998a; Morgan et al., 1999).

In situations with more than two authors, the first author’s surname should be followed with et al. When references are made to more than one paper published in the same year by the same author, a lower case a, b, etc. should be appended to the date of publication and should be included in both textual citations and the reference list.

References should be listed completely at the end of the paper in alphabetical order by surname of first author, and then by year of publication.

When more than one publication appears with the same first author, listings will be alphabetized by the first varying co-author. Irrespective of the number of authors, et al. should not be used in the reference list. Journal titles should be abbreviated according to Index Medicus and book titles should be italicized. Use the following format for references: Journal Article Brothman AR, Zhu XL, Maxell T, Cui J, Derbler DA. Advances in the cytogenetics of prostate cancer. J Assoc Genet Technol. 1999;25(1):1-6.

Book Chapter Barch MJ and Lawce HJ. The cell and cell division. In: Barch MJ, Knutsen T, Spurbeck JL (eds). The AGT Cytogenetics Laboratory Manual, 3rd ed. Philadelphia: Lippincott-Raven; 1997:1-18.

Book Mark HFL. Medical Cytogenetics. New York: Marcel Dekker; 2000.

All references should be complete. Accuracy is the responsibility of the authors. Only published articles and those in press may be included in the reference list. If necessary, unpublished data and submitted manuscripts should be cited parenthetically within the text.

Reprint Orders Reprints of articles can be purchased by authors at cost within two years after publication. On the order request, specify the journal’s volume and issue numbers, year of publication, page numbers, article title, author(s), and quantity requested. Include the contact name(s), address(es) and phone number(s) to be used for either shipping purposes or related questions. Payment should accompany the order. Checks must be made payable to AGT. Minimum order is 50 copies.

Reprints are produced on 60# white offset paper, saddle-stitched (unless under four pages), and will appear exactly as they do in the journal.

Price is based on article length, quantity ordered, and color requirements. Orders are not processed until payment is received. Once payment is received, allow four weeks for printing and shipping. Prices quoted include shipping by UPS ground; expedited shipping is available at an additional charge. Journal copies can be purchased by AGT members for $25/each, if copies are available.

Please forward reprint orders or questions regarding price quotations to the AGT Executive Office (see inside front cover for address).

ISSN 1523-7834