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Hematologic Diseases ALCL

ALL

AML

CLL

CML

MM

MDS

NHL

Solid Tumors Breast

Cervical

Colorectal

Lung

EXCELLENCE IN ONCOLOGY

DNA-FISH Probe Catalog

www.cancergeneticsitalia.com contact@cancergeneticsitalia.com

2013


Visit our website, www.cancergeneticsitalia.com,

and keep abreast of our latest product releases, access complete information about our product portfolio, and learn about our R&D pipeline.

EXCELLENCE IN ONCOLOGY


Table of Contents

4

About CGI Italia

5

Our Commitment to Quality

6

What is FISH?

8

DNA-FISH Probe Portfolio

28

Appendix 28 29

33

Scoring Guidance and Signal Interpretation Filter Specifications Troubleshooting

Ordering Products 33

Ordering Information

34

Product Index by Disease

36

Product Index by Name

37

Product Index by Chromosome Number


About CGI Italia

Mission Statement

Cancer Genetics Italia S.r.l. (CGI Italia) was founded in 2009 and is headquartered in Milan, Italy. CGI Italia is a wholly owned subsidiary of Cancer Genetics Inc. (CGI), which was founded in 1999 by world-renowned human geneticist R.S.K. Chaganti, Ph.D. CGI’s affiliation with major cancer centers along with the firm’s foundation in world-class scientific knowledge has enabled CGI to develop strong intellectual properties (IP) in solid and blood-borne cancers.

Our mission is to provide professionals with robustly designed DNA-FISH Probes that are highly specific, easy to interpret, and possess strong signal quality, for the clinical management of cancer patients.

It is from this foundation that CGI Italia draws its ability to design and manufacture proprietary DNA-FISH Probes. Our DNAFISH Probes detect a range of genetic aberrations, such as translocations and copy number changes, in several cancer types and are protected by the following patents: §§ U. S. Patent (#7,585,964, Publication: pending) & CAN Patent (2,447,320, Published: 21 November 2002) entitled Methods of Analyzing Chromosomal Translocations using Fluorescence in situ Hybridization (FISH). §§ U. S. Patent (#11/932,422, Publication: 30 April 2009) & EU PCT Patent (#08844570.5, Published: 07 May 2009) entitled Panel for the Detection and Differentiation of Renal Cortical Neoplasms. §§ U. S. Patent (#13/227,027, Publication: pending & PCT/US2011/050681, Published: 15 March 2012) entitled Methods for Detecting Human Papilloma Virus-Associated Cancers.

Our products are marketed globally and are provided in a ready-to-use format as CE marked or Research Use Only (RUO).

Milestones 2009

• CGI Italia is founded

2010 • 12 CE products are launched

2012 • Portfolio expands to 31 CE products • Release of FHACTTM (FISH based HPV-Associated Cancer Test)

2013 • Release of D13S319

LittleFISH Program Through its LittleFISH Program, CGI Italia sponsors academic efforts involving FISH technology. This program provides undergraduate, graduate, and training physician students with discounted FISH Probes, and aims to encompass research projects as well as training and certification programs teaching the FISH technique. Laboratory reagents can represent an expense that may be difficult for academic laboratories and training programs to manage. By giving students a “Little” help, CGI Italia hopes to support research and promote FISH technology in the management of cancer around the globe. For further information, contact CGI Italia at contact@cancergeneticsitalia.com.

Academic Sponsorship Program

Page 4


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

A New Standard for FISH Probes: Our Commitment to Quality “The results of our comparison study demonstrate that CGI Italia Probes are user-friendly, robust and produce signals that are easy to score. The signals are very specific, bright and balanced in intensity, and have low levels of background noise. CGI Italia is a great choice for DNA-FISH Probes.” Sankar Mohan, Ph.D., OncoMDx Laboratories

CGI Italia takes great care in developing FISH Probes, and ensuring that every lot of Probe meets a quality standard. • Optimal concentration of each probe is rigourously determined to ensure balance of signal intensity among the 2-4 color probes, as well as minimized background noise. • Enumeration Probes are paired with a control locus to give the end-user a more complete picture of the gain/deletion of interest. Accurate screening of Enumeration Probes is generally not complete without control loci. Signal patterns of the locus of interest and control locus make it possible to gauge the likelihood of a whole chromosome deletion versus a localized deletion, which, in many cases, is important to distinguish. • During the validation and manufacture stages, the FISH probes are tested on normal peripheral blood, intended tissue (bone marrow, formalin-fixed paraffin embedded tissue, or liquid cervical specimen) to ensure sensitivity, specificity, and reproducibility of results. Break Apart & Fusion Probes are also tested on positive cell lines to ensure fusion signals are well-balanced. • With regards to CE versus RUO classification, RUO Probes are subject to the same QA/ QC standard as CE-marked Probes as part of CGI Italia’s commitment to providing high quality products. • Finally, some customers may request cut-off values for positive versus negative FISH results. It should be noted that CGI Italia does not provide cut-off values as it is recommended that each laboratory determine its own cut-offs based on testing of normal specimens. This is generally a requirement for most clinical laboratories. • CGI Italia FISH Probes have been designed with the intention of providing robust products that outperform competition. For more information about our comparison study conducted by OncoMDx, please contact us at contact@cancergeneticsitalia.com.

Page 5


What is FISH? Fluorescence in situ hybridization (FISH) is a sensitive and accurate technique that enables the detection of chromosomal aberrations and is complementary to conventional cytogenetic analysis. The method entails the hybridization of a single-stranded fluorescently labeled nucleic acid sequence (probe), which is complementary to a target genomic sequence that is present in metaphase chromosomes as well as interphase nuclei. Once the hybridization is complete, the excess FISH probe is washed off from the slide, which allows signal localization and enumeration. The primary advantage of the FISH technique is its applicability to non-dividing cells and a variety of specimen types. The technique allows the detection of a given genomic abnormality such as translocation, gain, or loss. FISH is also a preferred method for diagnosis, prognosis, treatment response, and minimal residual disease detection in a variety of hematopoietic neoplasms and solid tumors.

Page 6


DNA-FISH Probe Portfolio


Disease Legend ALCL

Page 8

Anaplastic Large Cell Lymphoma

ALL

Acute Lymphoblastic Leukemia

AML

Acute Myeloid Leukemia

CLL

Chronic Lymphocytic Leukemia

CML

Chronic Myeloid Leukemia

MM

Multiple Myeloma

MDS

Myelodysplastic Syndrome

NHL

Non-Hodgkin’s Lymphoma


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

Table of Contents 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

5p15, 9q34, 15q24 • Hyperdiploidy 5, 9, 15 • Ref: 16-003

MM

A20/PRDM1/SHGC-79576 • del(6q23),del(6q21)/6p12 • Ref: 19-001

ALL

NHL

ABL1/BCR • t(9;22) • Ref: 10-001

ALL

CML

ALK Break Apart • t(2p23) • Ref: 21-002

ALCL Solid Tumor

ALK/NPM1 • t(2;5) • Ref: 21-001

ALCL

AML1/ETO • t(8;21) • Ref: 12-005

AML

API2/MALT1 • t(11;18) • Ref: 17-001

NHL

ATM/D11S1251 • del(11q22)/11p15 • Ref: 14-018

CLL

BCL6 Break Apart • t(3q27) • Ref: 18-010

NHL

CCND1/IGH • t(11;14) • Ref: 14-006

MM

D7S486/Cen7 • del(7q31)/Cen7 • Ref: 11-007

AML MDS

D13S25/D13S1009 • del(13q14)/13q34 • Ref: 14-009

CLL

D20S108/8q11 • del(20q12) & trisomy 8 • Ref: 11-001

AML MDS

EGFR/Cen7 • EGFR Amplification • Ref: 22-007

Solid Tumor

EGR1/5p15 • del(5q31)/5p15 • Ref: 11-004

AML MDS

ERBB2/Cen17 • ERBB2 Amplification • Ref: 22-003

Solid Tumor

FGFR3/IGH • t(4;14) • Ref: 16-005

MM

FHACTTM • 3q26/5p15/20q13/Cen7 • Ref: 25-002

Solid Tumor

IGH/BCL2 • t(14;18) • Ref: 18-001

ALL

NHL

IGH Break Apart • t(14q32) • Ref: 13-014

ALL

MM

IGH/MAF • t(14;16) • Ref: 16-010

MM

IGH/MALT1 • t(14;18) • Ref: 17-004

NHL

MDM2/D12S1837 • 12q15/12p11 • Ref: 14-017

CLL

NHL

MLL Break Apart • t(11q23) • Ref: 11-002

ALL

AML

MYB/SHGC-79576 • 6q23/6p12 • Ref: 14-016

ALL

CLL

MYC Break Apart • t(8q24) • Ref: 13-008

ALL

CLL

MYC/IGH • t(8;14) • Ref: 13-004

ALL

NHL

MYH11/CBFB • inv(16) • Ref: 12-010

AML CML MDS

PBX1/E2A • t(1;19) • Ref: 13-001

ALL

PML/RARA • t(15;17) • Ref: 12-008

AML CML

RB1/D13S1009 • del(13q14)/13q34 • Ref: 27-014

AML

CLL

MDS

MM

TP53/RARA • del(17p13)/17q21 • Ref: 14-015

AML

CLL

MDS

Solid Tumor

NHL

NHL

MM

NHL

NHL

NHL

Page 9


5p15, 9q34, 15q24

5p15, 9q34, 15q24

Three Color, Enumeration Probe Ref: 16-003

MM

The 5p15, 9q34, 15q24 DNA-FISH Probe is designed to detect changes in copy number of chromosome(s) 5, 9, and 15 by fluorescence in situ hybridization (FISH). Hyperdiploidy is characterized by increased copy numbers of chromosomes such that the modal chromosomal number is 47-57. It is observed in 30-50% of multiple myeloma (MM) cases where the most common trisomies involve chromosomes 3, 5, 7, 9, 11, 15, 19, and 21.[1] In a diagnostic setting, gain of at least two of the three chromosomes 5, 9, or 15 in MM is considered an indicator for hyperdiploidy.[2] When assessed by G-banded karyotype and in the absence of other aberrations such as IGH translocations or deletion of chromosome 13, hyperdiploidy in MM is associated with a good prognosis.[3-5] 9

5 AFMA055ZD9 5p15

telomere

centromere

9q34

centromere

D9S64

telomere ~468 kb

~554 kb

15 15q24

centromere

D15S169

telomere

References

1. Liebisch, P., Döhner, H. Eur J Cancer, 2006. 42(11): p. 1520-9. 2. Chen, L., et al. Exp Oncol, 2007. 29(2): p. 116-20. 3. Chng, W. J., et al. Leukemia, 2006. 20(5): p. 807-13. 4. Boyd KD, et al. NCRI Haematology Oncology Studies Group. Leukemia. 2012 26(2): p 349-55. 5. Kumar S, et al. Blood, 2012. 119(9): p 2100-5.

~269 kb

A20/PRDM1/SHGC-79576 A20/PRDM1/SHGC-79576

Three Color, Enumeration Probe Ref: 19-001

The A20 (also called TNFAIP3)/PRDM1/SHGC-79576 DNA-FISH Probe is designed to detect deletion of the A20 gene located on 6q23 and the PRDM1 gene located on 6q21 relative to the control locus SHGC-79576 on 6p12, using fluorescence in situ hybridization (FISH). Deletion of 6q is observed in all types of B-cell malignancies, where two commonly deleted regions map to the A20 and PRDM1 gene region.[1,2] Loss of the A20 gene has been observed in ~20% of non-Hodgkin lymphoma (NHL) cases, ~20% of mucosa-associated lymphoid tissue (MALT) lymphoma cases[3] and in nonsplenic marginal zone lymphomas (MZLs) cases.[4] The loss of the A20 gene has been observed most frequently in mantle cell lymphoma (MCL) and diffuse large B-cell lymphoma (DLBCL) cases with a frequency rate of 31% and 38%, respectively.[5] In DLBCL, inactivation of A20 is seen more frequently in the activated B-cell (ABC) subtype of DLBCL (50%) versus the germinal center B-cell (GCB) subtype (22%).[3,5,6] DLBCL cases exhibit a variety of complex 6q deletions, which encompasse either A20 or PRDM1 alone or together as part of a larger deletion.[2] Additionally, the deletion of the PRDM1 gene has been observed in 53% of primary central nervous system lymphomas (PCNSLs).[7,8] 6 SHgC-79576

telomere

~494 kb

Page 10

PRDM1

5’

3’

~774 kb

A20

5’ 3’ ~772 kb

telomere

ALL

References

NHL

1. Offit, K., et al. Blood, 1993. 82(7)L p. 1781-7. 2. Thelander, E. F., et al. Leuk Lymphoma, 2008. 49(3): p.477-87. 3. Kato, M., et al. Nature, 2009. 459(7247): p.712-6. 4. Novak, U., et al. Blood, 2009. 113(20): p.4918-21. 5. Compagno, M., et al., Nature, 2009. 459(7247): p. 717-21. 6. Lenz, G., et al. PNAS, 2008. 105(36): p.13520-5. 7. Schwindt, H., et al. Leukemia, 2009. 23(10): p.1875-84. 8. Pasqualucci, L. et al., J Exp Med 2003 (2): p 311-7.


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

ABL1/BCR

Two Color, Two Fusion Translocation Probe Ref: 10-001

ALL

CML

9q34

centromere

ASS

5’

ABL1

References 3’

telomere

~285 kb

~390 kb

22 22q11

centromere

5’

ABL1/BCR

The ABL1/BCR DNA-FISH Probe is designed to detect the translocation between the ABL1 gene on chromosome 9q34 and the BCR gene on chromosome 22q11 by fluorescence in situ hybridization (FISH). This reciprocal translocation results in the Philadelphia chromosome (Ph), the der(22), and is the hallmark of chronic myeloid leukemia (CML). Approximately 90-95% of CML and up to 5% of pediatric and 20% of adult acute lymphocytic leukemia (ALL) are Ph positive.[1-3] ABL1/BCR FISH is used in diagnosis, prognosis, and monitoring of t(9;22) in CML and ALL patients.[4] A subset of CML (~10%) and ALL (~5%) cases exhibit large deletions adjacent to the breakpoints on chromosomes der(9) and der(22).[4-5] Such submicroscopic losses carry a poor prognosis[6] and can be detected by the Cancer Genetics Italia DNAFISH Probe. 9

BCR

telomere

3’

~350 kb

1. Huret, J. L. t(9;22)(q34;q11) in CML, Dec. 1997 www.AtlasGeneticsOncology.org. 2. Huret, J. L. t(9;22)(q34;q11) in ALL, Sep 1997 www.AtlasGeneticsOncology.org. 3. Nashed, A. L., et al. J Mol Diagn, 2003. 5:63-72. 4. Landstrom, A.P., Tefferi, A. Leuk Lymphoma, 2006. 47(3): 397-402. 5. Gorusu, M., et al. Cancer Genet Cytogenet, 2007. 173:97-106. 6. Huntly, B.J. et al. Blood, 2003. 120(4): 1160-8.

~390 kb

ALK Break Apart

ALCL

The ALK Break Apart DNA-FISH Probe is designed to detect the translocation between the ALK gene located at 2p23 and one of at least 14 known translocation partner loci using fluorescence in situ hybridization (FISH).[1] Translocation of the ALK gene occurs in ~50% of anaplastic large cell lymphoma (ALCL) cases with a form of t(2;5)(p23;q35), as determined by conventional cytogenetics; in such cases, the presence of the t(2;5)(p23;q35) form carries a better overall prognosis for ALCL patients.[2] ALK translocation has been observed in vesical inflammatory myofibroblastic tumors (IMT) of the bladder (>66%)[3] and serves as a diagnostic biomarker for differential diagnosis of IMT from sarcomatous lesions.[3] ALK translocation is observed in ~5% - 16% of non-small cell lung cancer (NSCLC) cases in the form of inv(2)(p21p23), as determined by FISH,[4] and serves as a biomarker for therapy response.[4,5] The presence of the ALK translocation in NSCLC patients is correlated with a marked sensitivity to pemetrexed and crizotinib treatment.[6] 2

2p23

ALK

telomere

3’ ~541 kb

5’

centromere

References

Lung

1. Chiarle, R., et al. Nat Rev Cancer, 2008. 8(1): 11-23. 2. Drexler, H. G., et al. Leukemia, 2000. 14(9): p.153359. 3. Sukov, W. R., et al. Mod Pathol, 2007. 20(5): p.592603. 4. Kwak, E.L., et al. N Eng J Med, 2010. 363(18): p. 1693-703. 5. Gerber, D. E., et al. Cancer Cell, 2010. 18(6): p.54851. 6. Camidge, D. R., et al. J Thorac Oncol, 2011. 6(4):p.774-80.

ALK Break Apart

Two Color, Break Apart Probe Ref: 21-002

~556 kb

Page 11


ALK/NPM1

ALK/NPM1

Two Color, Two Fusion Translocation Probe Ref: 21-001

ALCL

The ALK/NPM1 DNA-FISH Probe is designed to detect the translocation between the ALK gene located at 2p23 and the NPM1 gene located at 5q35, using fluorescence in situ hybridization (FISH); the translocation between the ALK and NPM1 gene is designated as t(2;5)(p23;q35). By conventional cytogenetics, the translocation occurs in up to 50% of anaplastic large cell lymphoma (ALCL) cases.[1] As assessed by immunohistochemistry, expression of the fusion protein ALK/NPM1 that is generated by t(2;5), occurs more frequently in childhood ALCL with an occurrence rate of 83% versus adult ALCL which has an occurrence rate of 31%.[1,2] The presence of t(2;5) (p23;q35) carries a better overall prognosis for ALCL patients.[1] 2

2p23

ALK

3’

telomere ~541 kb

5’

References

centromere

1. Drexler, H.G., et al. Leukemia, 2000. 14(9): p.1533-59. 2. Weitzman, S., et al. Curr Oncol Rep, 2002. 4(2): p.107-13.

~556 kb

5 5q35

NPM1

5’ 3’

centromere

telomere

~552 kb

~502 kb

AML1/ETO

AML1/ETO

Two Color, Two Fusion Translocation Probe Ref: 12-005 The AML1/ETO (also named RUNX1/RUNX1T1) DNA-FISH Probe is designed to detect the translocation involving the AML1 (RUNX1) gene on chromosome 21q22 and the ETO (RUNX1T1/ MTG8) gene on chromosome 8q22 by fluorescence in situ hybridization (FISH). This translocation generates an AML1-ETO fusion protein and is detected in 12% of de novo AML cases and in up to 46% of cases in the AML subtype M2.[1,2] The detection of the t(8;21) is clinically relevant because it is generally associated with a favorable prognosis and particularly with high-dose cytorabine-based consolidation chemotherapy.[3]

8 ETO 8q22

3’

centromere

telomere

5’

~635 kb

21q22

centromere ~570 kb

AML1 3’

telomere

5’ ~630 kb

References

1. Nucifora, G., Rowley, J.D. Blood (Review), 1995. 86(1):1-14. 2. Peterson, L. F., Zhang, D.E. Oncogene, 2004. 23(24):4255-62. 3. Dohner, H., et al. Blood, 2010. 15(3): 453-74.

~472 kb

21

Page 12

AML


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

API2/MALT1

Two Color, Two Fusion Translocation Probe Ref: 17-001

NHL

API2/MALT1

The API2/MALT1 DNA-FISH probe is designed to detect the translocation between the API2 gene located at 11q21 and the MALT1 gene located at 18q21 using fluorescence in situ hybridization (FISH).[1] The translocation between the API2 and MALT1 gene, designated as t(11;18)(q21;q21), can be detected in around 15% of mucosa-associated lymphoid tissue (MALT) lymphomas, but varies in frequency based on primary tumor site.[2] In pulmonal and gastric MALT, t(11;18) is found more frequently (38-53% and 22-24%, respectively) and in these cases is almost always the only detected chromosomal abnormality.[2] When observed in gastric MALT lymphoma, t(11;18) is highly associated with a lack of response to antibiotic H. pylori eradication treatment.[3,4] 11 References

API2 11q21

5’

centromere

3’

telomere

~498 kb

~645 kb

18 MALT1 18q21

centromere ~641 kb

5’

3’

1. Dierlamm, J., et al., Blood, 2000. 96(6): 2215-18. 2. Heim, S., and Mitelman, F. (Ed) Cancer Cytogenetics, 2009 (3rd Edition), Wiley-Blackwell, New Jersey. p. 317-320. 3. Nakamura, T., et al. J Gastroenterol, 2003. 38(10): p.921-9. 4. Toracchio, S., et al. Cancer Sci, 2009. 100(5): p.8881-7.

telomere ~738 kb

ATM/D11S1251

CLL

NHL

The ATM/D11S1251 DNA-FISH Probe is designed to detect the deletion of the ATM gene located on 11q22 relative to the control locus D11S1251 located on 11p15 by fluorescence in situ hybridization (FISH). ATM deletions are frequently seen in several types of hematologic malignancies. The deletion of the ATM gene is detected in ~65% of T-cell prolymphocytic leukemia (T-PLL) cases[1], ~50% of mantle cell lymphoma (MCL) cases[1,2], and ~20% of chronic lymphocytic leukemia (CLL) cases.[3] Deletion of 11q in CLL patients is associated with extensive lymphadenopathy, disease progression, and shorter median survival.[3,4] Significantly improved clinical outcomes in previously untreated CLL patients with ATM loss have been observed using alkylating agent-based chemo-immunotherapy regimens.[5] 11

References

D11S1251

5’

telomere ~423 kb

ATM

3’

~399 kb

telomere

1. Monni, O., Knuutila, S. Leuk Lymphoma, 2001. 40(3-4): p. 259-66. 2. Stilgenbauer, S., et al., Blood, 1999. 94(9): p. 3262-4. 3. Dohner, H., et al. N Engl J Med, 2000. 343(26): p. 1910-6. 4. Stilgenbauer, S., et al., Leukemia, 2002. 16((6): p. 993-1007. 5. Tsimberidou, A.M., et al. Cancer, 2009. 115(2): p. 373-80.

ATM/D11S1251

Two Color, Enumeration Probe Ref: 14-018

Page 13


BCL6 Break Apart

BCL6 Break Apart

Two Color, Break Apart Probe Ref: 18-010

NHL

The BCL6 Break Apart DNA-FISH Probe is designed to detect the translocations between the BCL6 gene located on 3q27 and one of at least 20 known translocation partner loci as detected by fluorescence in situ hybridization (FISH). Translocation of the BCL6 gene occurs in 6-26% of follicular lymphoma (FL)[1] with higher incidence (44%) in grade 3 cases negative for t(14;18) (q32;q21).[2] Rearrangement of the BCL6 gene is observed at a frequency of 15~40% in diffuse large B-cell lymphomas (DLBCL).[1-3] 3 BCL6 3q27

3’

centromere

5’

telomere

~471 kb

~756 kb

References

1. Chaganti, R.S., et al. Semin Hematol, 2000. 37(4): p. 396-411. 2. Gu, K., et al. Mod Pathol, 2009. 22(9): p. 1251-7. 3. Lo Coco, F., et al., Blood, 1994. 183(7): p. 1757-9.

CCND1/IGH

CCND1/IGH

Two Color, Two Fusion Translocation Probe Ref: 14-006

NHL

The CCND1/IGH DNA-FISH Probe is designed to detect the translocation between the CCND1 gene located on 11q13 and the IGH gene located on 14q32 by fluorescence in situ hybridization (FISH). The translocation between the CCND1 and IGH gene is designated as t(11;14)(q13;q32) and is the cytogenetic hallmark of mantle cell lymphoma (MCL), which distinguishes it from other non-Hodgkin lymphomas.[1,2] The t(11;14) also has been detected in light chain amyloidosis, monoclonal gammopathy of undetermined significance (MGUS), and multiple myeloma (MM) cases.[3,4] The presence of t(11;14)(q13;q32) in MM patients is associated with an improved survival.[5]

11

References

CCND1 11q13

5’

centromere

3’

~513 kb

telomere ~511 kb

C segments

14q32

centromere

J segments D segments

14 IGH

V segments

3’ ~561 kb

Page 14

MM

5’ ~420 kb

telomere

1. Heim, S., Mitelman, F. (Ed). Cancer Cytogenetics, 2009 (3rd Edition). Wiley-Blackwell, New Jersey. p. 313-315. 2. Bentz, J.S., et al. Cancer, 2004. 102(2): p.124-31. 3. Barille-Nion, S., et al. Hematology Am Soc Hematol Educ Program, 2003. p.248-78. 4. Liebisch, P., et al. Eur J Cancer, 2006. 42(11): p.1520-9. 5. Fonseca, R., et al. Leukemia, 2009. 23(12): p.221021.


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

D7S486/Cen7

AML

MDS

The D7S486/Cen7 DNA-FISH Probe is designed to detect the deletion of the D7S486 locus located on 7q31 relative to the centromere 7 control locus, using fluorescence in situ hybridization (FISH). Deletions of chromosome 7 are frequently seen in many types of myeloid neoplasms. Loss of the D7S486 locus is detected in ~5% of adults with de novo myelodysplastic syndrome (MDS) and in ~50% of children with de novo MDS.[1] Additionally, loss of the D7S486 locus is observed in 5% of de novo acute myeloid leukemia (AML) patients and in 30 - 40% of therapy related MDS (t-MDS)/AML (t-AML) patients.[1,2] Deletion of the D7S486 locus or monosomy of chromosome 7 is associated with a poor prognosis in adults and children diagnosed with MDS and/or AML.[1,3] Cen7

References

7q31

D7S486

centromere

1. Heim, S., Mitelman, F. (Ed). Cancer Cytogenetics, 2009 (3rd Edition). Wiley-Blackwell, New Jersey. p. 141-178. 2. Shali, W., et al., Cancer Genet Cytogenet, 2006. 168(2): p. 133-145. 3. Haase, D. Ann Hematol, 2008. 87(7): p.515-26.

telomere

~230 kb

D13S25/D13S1009

CLL

Two Color, Enumeration Probe Ref: 14-009

MM

NHL

The D13S25/D13S1009 DNA-FISH Probe is designed to detect loss of the D13S25 locus on chromosome 13q14 relative to the control marker D13S1009 on chromosome 13q34 by fluorescence in situ hybridization (FISH). The deletion of D13S25, a locus distal to the RB1 gene, has been detected in B-cell chronic lymphocytic leukemia (B-CLL),[1] in multiple myeloma (MM),[2,3] and rarely in a variety of non-Hodgkin lymphomas (NHL).[4] Deletion of 13q14 has a strong prognostic value correlating with slower disease progression and better prognosis in B-CLL patients,[5] whereas in MM patients it is associated with a higher stage of disease and shorter survival.[6]

References

13 D13S25

D13S1009

centromere

telomere ~186 kb

~321 kb

1. Nelson, B. P., et al. Am J Clin Pathol, 2007. 128(2): 323-32. 2. Chen, L., et al. Exp Oncol, 2007. 29(2):116-20. 3. Terpos, E., et al. Leuk Lymphoma, 2006. 47(5):80314. 4. Dierlamm, J., et al. Cancer Genet Cytogenet, 2000. 1;120(1):1-5. 5. Dal Bo, M., et al., Genes Chromosomes Cancer, 2011. 50(8): p. 633-43. 6. Kroger, N., et al., Blood, 2004. 103(11): p.4056-61.

D13S25/D13S1009

7

D7S486/Cen7

Two Color, Enumeration Probe Ref: 11-007

Page 15


D20S108/8q11

D20S108/8q11

Two Color, Enumeration Probe Ref: 11-001

AML

The D20S108/8q11 DNA-FISH Probe is designed to detect the deletion of the D20S108 locus on 20q12 and the gain of chromosome 8 using fluorescence in situ hybridization (FISH). Genomic copy number changes are frequent in myeloid disorders such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML).[1-3] Deletion of the D20S108 locus is observed in 0.6 - 5% of de novo MDS patients and in less than 2% of de novo AML patients. [1,2] In MDS patients, deletion of the D20S108 locus is associated with a good prognosis[3] whereas in AML patients it is a marker of either an intermediate or an unfavorable outcome.[2] The trisomy of chromosome 8 is observed as a sole abnormality in ~5% of MDS patients or as part of a complex karyotype in >15% of such patients and is generally associated with an intermediate prognosis.[2,3] Additionally, trisomy 8 can be observed as a sole aberration in 5% of de novo AML patients or simultaneously with other aberrations in 15% in such patients.[2] However, trisomy 8 is more common in de novo AML cases than in therapy related AML (t-AML) with an occurrence of 7.4% vs. 3.3%, respectively[4,5] and has been associated with an intermediate prognosis.[2,3] 8q11

8 20 20q12

D20S108

centromere

MDS

References

1. Sole, F., et al. Haematologica, 2005. 90(9): p.1168-78. 2. Heim, S., Mitelman, F. (Ed) Cancer Cytogenetics, 2009 (3rd Edition). Wiley-Blackwell, New Jersey. p. 45-178. 3. Haase, D. Ann Hematol, 2008. 87(7):p.515-26. 4. Qian, Z., et al. Chem Biol Interact, 2010. 184(12): p.50-7. 5. Mauritzson, N., et al. Leukemia, 2002. 16(12): p.2366-78.

telomere

~302 kb

EGFR/Cen7

Breast

EGFR/Cen7

Two Color, Enumeration Probe Ref: 22-007

Lung

The EGFR/Cen7 DNA-FISH Probe is designed to detect an increase in copy number of the EGFR gene on 7p11 (previously assigned to band 7p12) relative to the control Cen7 probe using fluorescence in situ hybridization (FISH) in formalin-fixed, paraffin-embedded (FPPE) tissues.[1] The EGFR gene encodes a transmembrane protein involved in cell proliferation.[2,3] Increased copy number of the EGFR gene has been reported in non-small cell lung cancer (NSCLC) cases and some other carcinomas such as colorectal, head and neck, and breast cancer cases.[3-6] An increased EGFR copy number is predictive of response to anti-EGFR therapies.[1-5] Cen7

7

EGFR

telomere 7p11

5’

3’

centromere ~ 495 kb

Page 16

Colorectal

References

1. Varella-Garcia, M. et al. J Clin Pathol, 2009. 62:970977. 2. Toschi, L., and Cappuzzo, F. The Oncologist, 2007. 12:211-220. 3. Bhargava, R. et al. Modern Patholy,2005. 18: 1027-1033. 4. Hirsch, F.R. et al. J Clin Oncol, 2008. 26(20):33513357. 5. Personeni, M. et al. Clin Cancer Res, 2008. 14(18):5869-5876. 6. Zimmermann, M., et al. Radiation Oncology, 2006. 1:11.


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

EGR1/5p15

Two Color, Enumeration Probe Ref: 11-004

AML

MDS

EGR1/5p15

The EGR1/5p15 DNA-FISH Probe is designed to detect the deletion of the EGR1 gene located on 5q31 relative to the control locus 5p15 by fluorescence in situ hybridization (FISH). The deletion of the EGR1 gene is detected in 10-15% of de novo myelodyplastic syndrome (MDS) and acute myeloid leukemia (AML) patients, and in 35-42% of therapy-related MDS (t-MDS) and therapy-related AML (t-AML) patients.[1, 2] When observed as the sole chromosomal aberration in cases of MDS (also called 5q-syndrome), deletion of the EGR1 gene is associated with a favorable prognosis and good response to lenalidomide treatment.[3] In cases of MDS/AML and t-MDS/tAML, deletion of EGR1 as part of a complex karyotype is associated with a worse prognosis and unfavorable outcome.[3,4] 5 References 5p15

EGR1

5’

telomere

3’

telomere

~222 kb

~554 kb

1. Herry, A., et al. Eur J Haematol, 2007. 78(6): p. 457-67. 2. Schoch, C., et al. Genes Chromosomes Cancer, 2002. 35(1): p. 20-9. 3. List, A., et al. N Engl J Med, 2006. 355(14): p. 1456-65. 4. Haase, D. Ann Hematol, 2008. 87(7): p. 515-26.

ERBB2/Cen17

Two Color, Enumeration Probe Ref: 22-003 The ERBB2/Cen17 DNA-FISH Probe is designed to detect the amplification of the ERBB2 gene (also named HER2/neu) on chromosome 17q12 relative to the control Cen17 using fluorescence in situ hybridization (FISH) in formalin-fixed, paraffin-embedded (FFPE) breast cancer tissues. Overexpression of the ERBB2 gene occurs in 25-30% of human breast carcinomas, and ~90-95% of these cases result directly from gene amplification.[1] Patients showing such an amplification are at high-risk for relapse and lower overall survival.[1-3] Amplification of the ERBB2 gene predicts a favorable response to certain chemotherapy regimens and selective monoclonal antibody therapy with trastuzumab.[1-5] ERBB2 amplification is also seen in other solid tumors such as gastric, esophageal, gynecologic, bladder, and non-small cell lung cancer and correlates with a poor prognosis.[6]

17 17q12

centromere

Cen17

5’

References

ERBB2

3’

~ 160 kb

telomere

1. Pauletti, G., et al. J Clin Oncol, 2000. 18(21):3651-64. 2. Harries, M., et al. Endocr Relat Cancer, 2002. 9(2):75-85. 3. Kallioniemi, O. P., et al. Proc Natl Acad Sci USA, 1992. 89(12):5321-5. 4. Slamon, D. J., et al. Science, 1987. 235(4785):17782. 5. Wolff, et al. J Clin Oncol, 2007. (1):118-145. 6. Mano, M. S., et al. Cancer Treat Rev, 2007. 33(1):64-77.

ERBB2/Cen17

Breast

Page 17


FGFR3/IGH

FGFR3/IGH

Two Color, Two Fusion Translocation Probe Ref: 16-005

MM

The IGH/FGFR3 translocation probe is designed to detect the translocation between the FGFR3 gene located on 4p16 and the IGH gene located on 14q32 using fluorescence in situ hybridization (FISH). Rearrangement of the FGFR3 and IGH genes is designated as t(4;14) and it has been observed in ~15% of multiple myeloma (MM) patients. Detection of the t(4;14) translocation is clinically relevant because it confers an aggressive phenotype with a poor prognosis and a rapid relapse after high-dose chemotherapy.[1-3] 4 4p16

telomere

5’

FGFR3

3’

centromere

~593 kb

~644 kb

14

14q32

centromere 3’

C segments

J segments D segments

References IGH

V segments

5’

~561 kb

1. Chen, L., et al. Exp Oncol, 2007. 29(2):116-20. 2. Moreau, P., et al. Blood, 2002. 100(5):1579-83. 3. Avet-Loiseau, H., et al. J Clin Oncol, 2012. 30(16): 1949-52.

telomere

~420 kb

FHACTTM

FHACTTM

Four Color, Enumeration Probe Ref: 25-002

Cervical

The FISH-based HPV-Associated Cancer Test (FHACT TM) DNA-FISH Probe is designed to detect changes in copy number of the TERC gene located on 3q26, the D5S2095 locus located on 5p15, the D20S911 locus located on 20q13, and the Cen7 region by fluorescence in situ hybridization (FISH). Increased copy number of these genomic regions have been observed in cervical carcinoma and their precursor lesions.[1-4] This probe may be useful in identifying high-risk dysplastic lesions that progress to invasive cervical cancer.[3,4] 5

3 3q26 centromere

TERC

telomere

5p15

telomere

~904 kb

7

D5S2095

~601 kb

Cen7

References

20 20q13

centromere

D20S911

~493 kb

Page 18

centromere

telomere

1. Andersson, S., et al. Br J Cancer, 2006. 95(3):331-8. 2. Rao, P.H., et al. BMC Cancer, 2004. 4:5-14. 3. Narayan, G., et al. Genes Chrom Cancer, 2007. 46(4):373-84. 4. Scotto, L., et al. Mol Cancer, 2008. 7:58.


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

IGH/BCL2

Two Color, Two Fusion Translocation Probe Ref: 18-001

ALL

NHL

References

C segments

J segments D segments

14

14q32

IGH/BCL2

The IGH/BCL2 DNA-FISH Probe is designed to detect the translocation between the IGH gene located on 14q32 and the BCL2 gene located on 18q21, using fluorescence in situ hybridization (FISH). The translocation between the IGH and BCL2 gene is designated as t(14;18)(q32;q21) and is the hallmark of follicular lymphoma (FL). The t(14;18) translocation is more frequent in lower FL grades, such as FL grades 1 and 2 (88%), than in higher grades, such as FL 3b (4-13%).[1] The translocation is also detected in 30% of diffuse large B-cell lymphoma (DLBCL) cases, but is less frequently detected in other non-Hodgkin lymphomas.[1,2] By conventional cytogenetics, the t(14;18) (q32;q21) translocation that involves the IGH and BCL2 genes is indistinguishable from the t(14;18)(q32;q21) translocation that involves the IGH and MALT1 genes. Such translocations can be distinguished by using the respective DNA-FISH probes.[1]

IGH

1. Heim, S., Mitelman, F. (Ed). Cancer Cytogenetics, 2009 (3rd Edition). Wiley-Blackwell, New Jersey. P. 297-358. 2. Fan, Y.S., Rizkalla, K. Cancer Genet Cytogenet, 2003. 143(1): p. 73-9.

V segments

3’

centromere

5’

~561 kb

telomere

~420 kb

18 3’

centromere

BCL2

5’

~441 kb

telomere ~575 kb

IGH Break Apart

ALL

Two Color, Break Apart Probe Ref: 13-014

MM

NHL

The IGH Break Apart DNA-FISH Probe is designed to detect the translocation involving the immunoglobulin heavy chain (IGH) locus on chromosome 14q32 using fluorescence in situ hybridization (FISH). At least 40 translocation gene partners to the IGH locus have been identified.[1] Rearrangements involving the IGH locus and specific partners are mainly found in multiple myeloma (MM)[2,3] and non-Hodgkin’s lymphoma (NHL) subtypes.[1,4] The prognosis is dependent upon the translocation partner and the type of malignancy. The design of the IGH Break Apart DNA-FISH Probe allows the visualization of a break between the constant C domain (red) and the variable V domain (green) of the IGH locus and the resulting translocation.

centromere 3’ 14q32

C segments

~561 kb

J segments D segments

14 IGH

References V segments

5’ ~420 kb

telomere

1. Bernicot, L., et al. Cytogenet Genome Res, 2007. 118(2-4):345-52. 2. Moreau, P., et al. Blood, 2002. 100(5):1579-83. 3. Avet-Loiseau, H., et al. Blood, 2002. 99(6):2185-91. 4. Haferlach, C., et al. Leukemia, 2007. 21(12):2442-51.

IGH Break Apart

18q21

Page 19


IGH/MAF

MM

The IGH/MAF DNA-FISH Probe is designed to detect the translocation between the IGH gene located on 14q32 and the MAF gene located on 16q23 by fluorescence in situ hybridization (FISH).[1] The translocation between the IGH and MAF gene, designated as t(14;16)(q32;q23), is found in 2-10% of multiple myeloma (MM) cases and is associated with a more aggressive disease along with an unfavorable prognosis and outcome.[2,3]

14 C segments

14q32

J segments D segments

IGH/MAF

Two Color, Two Fusion Translocation Probe Ref: 16-010

IGH

V segments

3’

centromere

5’

~561 kb

telomere

References

~420 kb

1. Chesi, M., et al., Blood, 1998. 91(2): p. 4457-63. 2. Kapoor, P., et al. Mayo Clin Proc, 2010. 85(6): p. 532-7. 3. Boyd, K.D., et al., Leukemia, 2012. 26: p. 349-55.

16

16q23

MAF

3’

centromere

5’

telomere

~655 kb

IGH/MALT1

14 C segmentsV

14q32

centromere

References IGH

segments

3’

5’

~561 kb

~420 kb

18 MALT1 18q21

centromere

5’ ~641 kb

Page 20

NHL

The IGH/MALT1 DNA-FISH probe is designed to detect the translocation between the IGH gene located at 14q32 and the MALT1 gene located at 18q21 by fluorescence in situ hybridization (FISH), designated as t(14;18) (q32;q21). The rearrangement of IGH/MALT1 has been observed in 10-20% of mucosa-associated lymphoid tissue (MALT) lymphoma, predominantly occurring in liver, skin, and ocular adnexa.[1-3] By conventional cytogenetics, t(14;18)(q32;q21) involving the IGH and MALT1 genes is indistinguishable from the t(14;18)(q32;q21) involving the IGH and BCL2 genes (the hallmark of follicular lymphoma). These translocations can be distinguished by FISH, using the respective DNA-FISH probes.

J segments D segments

IGH/MALT1

Two Color, Two Fusion Translocation Probe Ref: 17-004

telomere

3’ ~738 kb

telomere

1. Streubel, B., et al. Blood, 2003. 101(6): p.2335-9. 2. Streubel, B., et al. Leukemia, 2004. 18(10): p.1722-6. 3. Murga Penas, E.M, et al., Leukemia, 2003. 17(11): p. 2225-9


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

MDM2/D12S1837

CLL

The MDM2/D12S1837 DNA-FISH Probe is designed to detect both the polyploidy of chromosome 12 and the amplification of the MDM2 gene located on 12q14.3-q15 relative to the control locus D12S1837 located on 12p11 by fluorescence in situ hybridization (FISH). MDM2 is frequently amplified in many solid tumor, including soft tissue tumors. Well-differentiated liposarcomas has been found by molecular and cytogenetic studies to contain amplification of the 12q13-15 region, including the MDM2 gene.[1,2] Precise recognition of benign lipoma and well-differentiated liposarcoma by core needle biopsy can facilitate appropriate clinical management.[3] Trisomy of chromosome 12 (+12) is a commonly observed numerical aberration in non-Hodgkin lymphomas (NHL) cases. It has been observed in ~15-50% chronic lymphocytic leukemia (CLL) cases.[4] In CLL, trisomy 12, when observed as a sole abnormality, appears to have limited prognostic implications and is often associated with an atypical morphology, although it is only observed in a subset of tumor cells.[5]

12 D12S1837

MDM2

5’

telomere ~304 kb

3’

telomere

NHL

References

1. Weaver, J., et al. Modern Pathol, 2008. 21(8): p. 943-9. 2. Dal Cin, P., et al. Cancer Genetics and Cytogenetics, 1993. 68(2): p. 85-90. 3. Weaver, J., et al., Modern Pathol, 2010. 23(10): p. 85-90. 4. Heim, S., Mitelman F. (Ed) Cancer Cytogenetics, 2009 (3rd Edition). Wiley-Blackwell, New Jersey. P. 310. 5. Dohner, H., et al. J Mol Med, 1999. 77(2):p.266-81.

MDM2/D12S1837

Two Color, Enumeration Probe Ref: 14-017

~289 kb

MLL Break Apart

ALL

The MLL Break Apart probe is designed to detect the translocation involving the MLL gene on chromosome 11q23 using fluorescence in situ hybridization (FISH). At least 104 translocation partner genes have been identified. [1] Translocation of MLL is found in ~3-10% of acute lymphoblastic leukemia (ALL) cases, and in ~8-10% of acute myeloid leukemia (AML) cases, and is prognostically relevant in these leukemias.[2,3] However, the prognostic implication is dependent on the age and phenotype of the leukemia. MLL rearrangement has been observed in ~80% of infant ALL cases and is associated with a high risk in such cases and requires aggressive treatment. In AML, the prognosis is intermediate regardless of age. MLL translocations are also found in ~25% of patients with therapy-related leukemias, particularly following treatment with DNA topoisomerase II inhibitors and the prognosis in such patients is poor.[2,3] In addition to translocations, deletions of 3’ MLL and amplification of MLL also occurs in a subset of ALL and AML cases.[4,5]

11 MLL 11q23

5’

centromere ~770 kb

3’

References

AML

1. Meyer, C., et al., Leukemia, 2009. 23: 1490-9. 2. Coenen, E.A., et al., Blood, 2011. 117(26): 7102-11. 3. Chowdhury, T., et al. Blood Cells Mol Dis, 2008. 40:192-199. 4. Barber, K. E, et al. Genes Chromosomes Cancer, 2001. 41:226-271. 5. Andersen, M. K, et al. Genes Chromosomes Cancer, 2001. 31:33-41.

MLL Break Apart

Two Color, Break Apart Probe Ref: 11-002

telomere ~820 kb

Page 21


MYB/SHGC-79576

MYB/SHGC-79576

Two Color, Enumeration Probe Ref: 14-016

ALL

The MYB/SHGC-79576 DNA-FISH Probe is designed to detect copy number changes of the MYB locus located on 6q23 relative to a 6p12 control locus, using fluorescence in situ hybridization (FISH).[1] MYB gene is involved in duplications, translocation, and deletions in a variety of cancer types. Loss of MYB has been observed in ~5% of chronic lymphocytic leukemia (CLL) cases[2] and has been associated with a poor prognosis in CLL cases.[2] In breast tumors, the gain of the MYB gene has been observed in ~ 30% of hereditary BRCA1 positive breast tumors.[3]

6 SHGC-79576

MYB

5’

telomere

3’

telomere

~777kb

~494kb

MYC Break Apart

MYC Break Apart

8 MYC

5’

centromere ~647 kb

1. Barletta, C., et al., Science, 1987. 235(4792): p. 1064-7. 2. Reddy, K. S. Br J Haematol, 2006. 132(6): p.705-22. 3. Kauraniemi, P., et al. Cancer Res, 2000. 60(19): p.5323-8.

CLL

The MYC Break Apart DNA-FISH Probe is designed to detect the translocation between the MYC gene located at 8q24 and one of 11 known translocation partner loci using fluorescence in situ hybridization (FISH). The most common translocation, t(8;14)(q24;q32), is found in 75-85% of Burkitt lymphoma (BL) cases and is the cytogenetic hallmark of BL.[1,2] The t(8;14) (q24;q32) in BL is associated with an aggressive clinical course that responds well to high-intensity, brief-duration drug regimens with an overall favorable outcome.[2,3] Translocation of MYC is often detected as a secondary genomic abnormality at low frequencies in high-grade B-cell lymphomas, such as diffuse large B-cell lymphoma (DLBCL) (5-16%) and chronic lymphocytic leukemia (CLL) (0.1-2%).[1,3-5] In DLBCL, the presence of the MYC translocation is associated with an aggressive disease with a poor prognosis and an unfavorable outcome.[4] MYC translocation has also been observed in 4-6% of acute lymphoblastic leukemia (ALL).[6]

8q24

References

ALL

Two Color, Break Apart Probe Ref: 13-008

Page 22

CLL

3’

telomere ~594 kb

References

NHL

1. Heim, S., Mitelman, F. (Ed) Cancer Cytogenetics, 2009 (3rd Edition). Wilwy-Blackwell, New Jersey. p. 326-328. 2. Blum, K. A., et al. Blood, 2004. 104(10): p. 3009-20. 3. Lones, M. A., et al. J Pediatr Hematol Oncol, 2004. 26(3): p. 169-78. 4. Snuderl, M., et al. Am J Surg Pathol, 2010. 34(3): p. 327-40. 5. Aukema, S.M., et al., Blood, 2011. 17(8): p. 2319-31. 6. Moorman, A. V., et al. Blood, 2010. 115(2): p. 206-14.


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

MYC/IGH

Two Color, Two Fusion Translocation Probe Ref: 13-004

ALL

NHL

8

References MYC

5’

centromere

3’

~647 kb

telomere ~594 kb

C segments

centromere

J segments D segments

14

1. Blum, K. A., et al. Blood, 2004. 104(10): p.3009-20. 2. Lones, M. A., et al. J Pediatr Hematol Oncol, 2004. 26(3): p.169-78. 3. Heim, S., et al. Cancer Cytogenetics, 2009 (3rd Edition). 4. Akasaka, T., et al. J Clin Oncol, 2000. 18(3): p.510-18. 5. Moorman, A. V., et al. Blood, 2010. 115(2): p.206-14.

IGH V segments

3’

5’

~561 kb

telomere

~420 kb

MYH11/CBFB

AML

Two Color, Two Fusion Translocation Probe Ref: 12-010

CML

MDS

The MYH11/CBFB DNA-FISH Probe is designed to detect the pericentric inversion of chromosome 16 inv(16)(p13q22) and t(16;16)(p13;q22) involving the MYH11 gene on 16p13 and the CBFB gene on 16q22 using fluorescence in situ hybridization (FISH). The rearrangement of the MYH11 and CBFB gene results in a fusion of both genes. The inv(16) abnormality is found in ~5 - 8% of all of de novo acute myeloid leukemia (AML) cases and is associated with AML-M4eo subtype (based on FAB classification).[1,2] Inv(16) and t(16;16) has also been observed in therapy related myelodysplastic syndrome (t-MDS) cases and in eosinophilic blast crisis of chronic myelogenous leukemia (CML) cases.[2] Whether alone or as part of a complex patient karyotype, inv(16) is indicative of a good prognosis in AML cases.[3] CBFB 16q22

5’

centromere

3’

~444 kb

telomere ~472 kb

16 16p13

3’

telomere ~472 kb

MYH11

5’

References

1. LeBeau, M.M., et al., N Eng J Med, 1983. 309(11): 630-6. 2. Huret, J. L. inv(16)(p13q22),t(16;16)(p13;q22), del(16)(q22). www.AtlasGeneticsOncology.org. 3. Mrozek K, et al. Blood Rev, 2004. 18:115-136.

MYH11/CBFB

8q24

14q32

MYC/IGH

The MYC/IGH DNA-FISH Probe is designed to detect the translocation between the MYC gene located at 8q24 and the IGH gene located at 14q32, using fluorescence in situ hybridization (FISH). The translocation between the MYC and IGH gene is designated as t(8;14)(q24;q32) and is the cytogenetic hallmark of Burkitt lymphoma (BL), which is found in 75-85% of patients.[1] In BL, t(8;14)(q24;q32) is associated with an aggressive clinical course that responds well to high-intensity, brief-duration drug regimens with an overall favorable outcome.[1,2] This rearrangement has been observed at lower frequencies in other non-Hodgkin lymphomas (NHLs), such as diffuse large B-cell lymphoma (DLBCL) (<10%).[3,4] This translocation also occurs less frequently in acute lymphoblastic leukemia (ALL) where it has been associated with an unfavorable outcome.[3,5]

centromere ~233 kb

Page 23


PBX1/E2A

PBX1/E2A

Two Color, Two Fusion Translocation Probe Ref: 13-001 The PBX1/E2A (also named TCF3/PBX1) DNA-FISH Probe is designed to detect the translocation between the PBX1 gene located on 1q23 and the E2A gene located on 19p13, using fluorescence in situ hybridization (FISH). The translocation between the PBX1 and E2A gene is designated as t(1;19) (q23;p13) and occurs in ~ 6% of pediatric and adult acute lymphoblastic leukemia (ALL) cases; as determined by conventional cytogenetics and reverse transcription-polymerase chain reaction.[1] In both pediatric and adult ALL, the translocation is correlated with a negative prognosis.[2,3] It may occur as a balanced translocation, t(1;19)(q23;p13), or as an unbalanced translocation, der(19)t(1;19)(q23;p13), where only the derivative chromosome 19 is present.[2] The unbalanced translocation, der(19), is the most common form and accounts for 75% of all PBX1/E2A rearrangements.[2] Both balanced and unbalanced translocations are sometimes observed in the same patient as separate clones.[2]

1

1q23

centromere

PBX1

5’

~255 kb

3’

telomere

ALL

References

1. Hunger, S.P., et al., Blood, 1991. 77(4): p. 687-93. 2. Shearer, B. M., et al. Br J Haematol, 2005. 129(1): p.45-52. 3. Anderson, M.K., et al., Br J Haematol, 2011: 155(2): p. 235-43.

~326 kb

19 19p13

telomere

E2A

3’

5’

~275kb

centromere ~307 kb

PML/RARA

PML/RARA

Two Color, Two Fusion Translocation Probe Ref: 12-008

CML

The PML/RARA DNA-FISH Probe is designed to detect the translocation between the PML gene on chromosome 15q24 (previously assigned to band 15q22) and the RARA gene on chromosome 17q21, using fluorescence in situ hybridization (FISH). The t(15;17) translocation is the diagnostic hallmark of acute promyelocytic leukemia (APL), a sub-group of acute myelogenous leukemia (AML), and results in the fusion of the PML and RARA genes.[1] The presence of a PML-RARA fusion predicts a favorable response to differentiation therapy with all-trans retinoic acid (ATRA) and is currently the most curable subtype of acute myeloid leukemia (AML).[1-3] The t(15;17) translocation has also been identified in chronic myeloid leukemia (CML) cases with promyelocytic blast crisis.

15 References

PML 15q24

centromere

5’

telomere

3’

~270 kb

~350 kb

17 RARA 17q21

centromere

5’ ~570 kb

Page 24

AML

telomere

3’ ~510 kb

1. Kakizuka, a., et al., Cell, 1991. 66: 663-74. 2. Brockman, S. R, et al. Cancer Genet Cytogenet, 2003. 145:144-15. 3. Mistry, A.R., et al., Blood Rev., 2003. 17(2): 71-97.


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

RB1/D13S1009

Two Color, Enumeration Probe Ref: 27-014

AML

CLL

MDS

MM

13

References

5’

1. Lee, W.-H., et al., Science, 1987. 235: 1394-99. 2. Steigenbauer, S., et al., Blood, 1993. 81(8): 2118-24. 3. Dao, D.D., et al., Leukemia, 1994. 8(8): 1280-4.

D13S1009

RB1

centromere

RB1/D13S1009

The RB1/D13S1009 DNA-FISH Probe is designed to detect loss of the RB1 gene on chromosome 13q14 relative to the control marker, D13S1009 on chromosome 13q34, using fluorescence in situ hybridization (FISH). The RB1 gene is a well characterized tumor-suppressor gene and bi-allelic inactivation of the gene due to mutations and/or deletions is causal for the development of Retinoblastoma (RB). Deletion of the RB1 gene is also common in a wide variety of solid tumors and hematologic malignancies such as chronic lymphocytic leukemia (CLL), multiple myeloma (MM), acute myelocytic leukemia (AML), myelodysplastic syndrome (MDS), and chronic myeloproliferative disorders.[1-3] The RB1 gene is proximal to the D13S25 locus at 13q14, which is often co-deleted with the RB1 gene in some B-cell hematologic malignancies.

telomere

3’ ~305 kb

~368 kb

Breast

Two Color, Enumeration Probe Ref: 14-015

Colorectal

AML

Lung

CLL

MDS

The TP53/RARA DNA-FISH Probe is designed to detect the deletion of the TP53 gene located on 17p13, relative to the control marker gene RARA located on 17q21, using fluorescence in situ hybridization (FISH). The TP53 gene is a known tumor suppressor gene and is frequently deleted in a wide variety of solid tumors [1, 2] and hematologic malignancies such as mature Bcell neoplasms,[3] myeloid disorders such as acute myeloid leukemia (AML),[4] and myelodysplastic syndrome (MDS).[5] Deletion of the TP53 gene has been associated with advanced stage, shortened survival, and resistance to treatment in several malignancies and solid tumors.[3,6] The loss of TP53 is also found in chronic lymphocytic leukemia (CLL) cases and is associated with a very poor clinical outcome.[7,8]

17

References RARA

TP53

telomere

5’

5’

3’ ~226 kb

~233 kb

3’ ~472 kb

telomere

TP53/RARA

TP53/RARA

1. Bertheau, P., et al. Pathobiology, 2008 (Review). 75(2):132-9. 2. Doak, S. H, et al. Br J Cancer, 2003. 89(9): 1729-35. 3. Döhner, H., et al. J Mol Med, 1999 (Review). 77(2): 266-81. 4. Seifert, H., et al. Leukemia, 2009. 23(4): 656-63. 5. Silveira, C. G., et al. Leuk Res, 2009. 33(1): 19-27. 6. Hof, J., et al. J Clin Oncol, 2011. 29(23): 3185-93. 7. Dal Bo, M., et al. Genes Chromosomes Cancer, 2011. 50(8): 633-43. 8. Boyd, K.D., et al., Leukemia, 2012. 26: 349-55.

Page 25


Appendix


Scoring Guidance & Signal Interpretation

Signal interpretation depends on the DNA-FISH Probe type and should be made with the full knowledge of the product design. The following table divides the DNA-FISH Probe into two types: translocation and enumeration probes.

Count As (R = Red, G = Green, F = Fusion)

Scoring Guidance

Translocation Probes

The boundary of each nucleus is clear; for each nucleus count as 2R2G signals.

Count as 2R2G signals; the green signal is a split.

Count as 1R2G1F signals.

Count as 1R1G2F signals, depending on the probe this pattern could be indicative of a reciprocal translocation.

Count as 2F signals. Depending on the overlap, the red and green signal overlap can appear as yellow.

Count as 2F signals; the distance between the red and green signals is less than one signal width apart.

Enumeration Probes

The boundary of each nucleus is clear; for each nucleus count as 2R2G signals.

Count as 2R2G signals; the green signal is a split.

Count as 2R2G signals; the green signal is stringy or dispersed.**

Count as 2R2G signals, depending on the nuclear organization, the red and green signal can overlap and appear as yellow.

Count as 2R2G signals; the red and green signals are less than one signal width apart. When overlapping occurs, the signal appears as yellow.

Count as 1R2G signals; the pattern is indicative of the deletion of the red locus.

Count as 1R1G signals; the pattern is indicative of the loss of an entire chromosome.

Count as >6R2G signals; one red signal is focally amplified.

Characteristic of certain probes that target a highly transcribed region (i.e. IGH).

Do Not Count

**

Page 28

Nucleus is physically damaged and nuclei overlap prevents distinction of which signals belong to which nucleus.

The true green signal and the green artifact are indistinguishable. The green artifact or fluorescent debris is so bright, it interferes with a proper evaluation.

The signals are indistinguishable from the background.

The irregular red signal and the green signal on the periphery could be artifacts.


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

The following table shows the filter requirements for Cancer Genetics Italia DNA-FISH Probes. Fluorophore Green

Excitationmax

Emissionmax

496 nm

520 nm

Red 580 nm 603 nm 1

Red2

593 nm

612 nm

Gold

525 nm

551 nm

Aqua

431 nm

480 nm

1.

Applies to all the CGI Italia DNA-FISH Probes.

2. Preferably used for three or more color DNA- DAPI 360 nm 460 nm FISH Probes.

Filter Maintenance Recommendation Filters age with use and should be regularly examined for dirt and/or imperfections which may occur over time. Heat from the high intensity transmitted light can etch and damage frequently used filters (such as the DAPI filter), resulting in dimmer images and unevenly illuminated areas. Such filters should be replaced. Handle filters according to manufacturers recommendations.

Filter Specifications

Filter Specifications

Troubleshooting Weak signals may be observed due to: • Use of an old mercury lamp (run time >200 hours); replace the mercury lamp after 200 hours of run time. • Use of unsuitable immersion oil; use immersion oil with no auto-fluorescence in the UV range. • Use of unsuitable filters; use the appropriate filter sets. Also, check that the excitation and emission of the dyes fall within the range claimed by the filter manufacturer. The filter specifications table (see table above) identifies the filter requirements for Cancer Genetics Italia DNA-FISH Probes. Also, be sure the filters are well maintained and have no visible damage. • Inadequate denaturation of the DNA-FISH Probe; increase the denaturation temperature and/or duration. Optionally, the specimen may be treated with pepsin prior to denaturation. • Insufficient pretreatment of the specimen (visible cytoplasm on the specimen appearing as a green or yellow haze). In such cases it may be beneficial to perform the optional pretreatment steps outlined in the Instructions for Use (IFU). • Baking or aging the slide for too long; check the temperature of the hot plate or oven that is used to age the slide. The time and temperature routinely used to artificially age the slide varies among specimen types and laboratories. Adjust conditions according to laboratory SOPs.

2. Why do I see areas without signals? Areas without signals indicate a lack of hybridization in those areas. This may be due to: • Presence of air bubbles during hybridization, or application of an insufficient volume of Probe. • Before adding the coverslip, gently remove all air bubbles with a pipette tip or needle. After adding the coverslip, gently remove any air bubbles by rolling a pencil eraser evenly across the coverslip. Also, ensure there is sufficient Probe volume (10 μl Probe/22×22mm target area). Increase or decrease the volume of Probe and size of coverslip proportionally with any increase or decrease in the size of the target area. • Low permeability of the specimen to the Probe, which results in resistance to hybridization. Optionally, the specimen may be treated with pepsin prior to denaturation (protocol is provided in the IFU).

Troubleshooting

1. I am observing weak signals. How can I correct this?

Page 29


3. Why do the signals appear to be fading? The signals may be fading due to: • Photobleaching of the slide; always close the microscope shutter when not observing the specimen. It is important that hybridized slides are stored at 4°C and protected from light. Fluorescently labeled probes are readily photobleached by exposure to light, both before and after hybridization. To minimize photobleaching, handle Probes and hybridized specimens in reduced light as much as possible. • Use of immersion oil with auto-fluorescence in the UV range. Be sure to use immersion oil with no autofluorescence in the UV range. • Use of expired or oxidized Antifade/DAPI, which will appear deep purple/brown in color. Verify the expiration date of the Antifade used. • Image acquisition. Some photobleaching will occur from extended exposure to the UV source during image acquisition.

Troubleshooting

4. Why do I see no signals on my hybridized slide? Seeing no signals on a hybridized slide indicates a lack of hybridization. This may be due to: • Application of an insufficient Probe volume and/or lack of cells in target area. It is good practice to check the slide under a phase contrast microscope, prior to hybridization, to select appropriate areas for hybridization. • Inappropriate denaturing/incubation conditions. Check the temperature of the controlled hot plate prior to use and ensure that the hot plate is calibrated regularly. Make sure to respect the recommended time and temperature for denaturation/incubation, and ensure that the incubation chamber is humidified, as recommended in the IFU (provided with the product and available at www.cancergeneticsitalia.com). • Too much cytoplasm present (appears as a green or yellow haze), which impedes the Probe from hybridizing to the target DNA. Optionally, the specimen may be treated with pepsin prior to denaturation (protocol is provided in the IFU). • Specimen quality not optimal for FISH. Occasionally a specimen will not lend itself to be processed for FISH. This may be the case in a subset of formalin-fixed paraffin embedded (FFPE) specimens when a variety of involved tissues (such as bone) may inhibit processing of the slide, and yield poor FISH signals, or no signals at all.

5. Why is the nuclear morphology compromised? The nuclear morphology may be compromised due to: • Over-denaturation of the specimen; reduce the duration and/or temperature of denaturation. It is important to check the temperature of the hot plate or oven used to age the slide. • Excessive pretreatment of the specimen, which leads to chromatin loss; reduce the pepsin concentration and/or incubation time during pretreatment, or eliminate this optional step altogether.

6. Why do I see a high level of background noise? A high level of background noise may be due to: • Use of an unclean slide during specimen preparation; clean slide with 70% ethanol and wipe with a lint free cloth prior to dropping the specimen on the slide. • Presence of cellular debris in the specimen; wash the specimen pellet in fresh fixative prior to dropping. Allow residual debris to settle to bottom of tube before drawing up the specimen. • Allowing the slide to dry during hybridization or post-hybridization washes; when placing coverslip over target area, ensure proper sealing with rubber cement to prevent the Probe from drying. Also, do not allow slide to dry after removing coverslip for post-hybridization washes, or in between the washes. • Inadequate post-hybridization washing; ensure the wash buffers have reached the optimal temperature recommended in the IFU prior to starting the washes. Also be sure to wash the slide for the duration recommended in the IFU.

7. Why do I see a high level of nuclear background noise? A high level of nuclear background noise may be caused by: • Inadequate post-hybridization washing; although rarely observed, a high level of nuclear background noise may be reduced by increasing the washing stringency and/or duration.

Page 30


Ordering products


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

Ordering Information CGI Italiaâ&#x20AC;&#x2122;s DNA-FISH Probes are available in a ready to use, 10 tests per vial format. To place an order, please contact your local authorized distributor. To locate your local authorized distributor please visit our website at www.cancergeneticsitalia.com; if a distributor is not located within your region, please contact us at purchase@cancergeneticsitalia.com.

Ordering Information

We are dedicated to providing professionals the most clinically relevant products and are constantly developing new reagents. If you would like more information about our pipeline or if you have specific inquiries, please contact us at contact@cancergeneticsitalia.com.

If you are interested in distributing our DNA-FISH Probes or would like more information, please contact us at contact@cancergeneticsitalia.com.

Page 33


Product Index By Disease Disease

Probe Name

Reference Number

Page

ALK Break Apart

21-002

11

ALK/NPM1

21-001

12

A20/PRDM1/SHGC-79576

19-001

10

ABL1/BCR

10-001

11

IGH/BCL2

18-001

19

IGH Break Apart

13-014

19

MLL Break Apart

11-002

21

MYB/SHGC-79576

14-016

22

MYC Break Apart

13-008

22

MYC/IGH

13-004

23

PBX1/E2A

13-001

24

AML1/ETO

12-005

12

D7S486/Cen7

11-007

15

D20S108/8q11

11-001

16

EGR1/5p15

11-004

17

MLL Break Apart

11-002

21

MYH11/CBFB

12-010

23

PML/RARA

12-008

24

RB1/D13S1009

27-014

25

TP53/RARA

14-015

25

ATM/D11S1251

14-018

13

D13S25/D13S1009

14-009

15

MDM2/D12S1837

14-017

21

MYB/SHGC-79576

14-016

22

MYC Break Apart

13-008

22

RB1/D13S1009

27-014

25

TP53/RARA

14-015

25

ABL1/BCR

10-001

11

MYH11/CBFB

12-010

23

PML/RARA

12-008

24

5p15, 9q34, 15q24

16-003

10

CCND1/IGH

14-006

14

HEMATOLOGIC PROBES ALCL

Product Index By Disease

ALL

AML

CLL

CML

MM

Page 34


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

Disease MM

MDS

NHL

Probe Name

Reference Number

Page

D13S25/D13S1009

14-009

15

FGFR3/IGH

16-005

18

IGH Break Apart

13-014

19

IGH/MAF

16-010

20

RB1/D13S1009

27-014

25

D7S486/Cen7

11-007

15

D20S108/8q11

11-001

16

EGR1/5p15

11-004

17

MYH11/CBFB

12-010

23

RB1/D13S1009

27-014

25

TP53/RARA

14-015

25

A20/PRDM1/SHGC-79576

19-001

10

API2/MALT1

17-001

13

ATM/D11S1251

14-018

13

BCL6 Break Apart

18-010

14

CCND1/IGH

14-006

14

D13S25/D13S1009

14-009

15

IGH/BCL2

18-001

19

IGH Break Apart

13-014

19

IGH/MALT1

17-004

20

MDM2/D12S1837

14-017

21

MYC Break Apart

13-008

22

MYC/IGH

13-004

23

EGFR/Cen7

22-007

16

ERBB2/Cen17

22-003

17

TP53/RARA

14-015

25

EGFR/Cen7

22-007

16

TP53/RARA

14-015

25

FHACTTM

25-002

18

ALK Break Apart

21-002

11

EGFR/Cen7

22-007

16

TP53/RARA

14-015

25

Product Index By Disease

Product Index By Disease

SOLID TUMOR PROBES Breast

Colorectal

Cervical Lung

Page 35


Product Index By Name

Product Index By Name

vProbe Name

Page 36

Reference #

Aberration

5p15, 9q34, 15q24

16-003

Hyperdiploidy 5, 9, 15

A20/PRDM1/SHGC-79576

19-001

del(6q23),del(6q21)/6p12

ABL1/BCR

10-001

t(9;22)

ALK Break Apart

21-002

t(2p23)

ALK/NPM1

21-001

t(2;5)

AML1/ETO

12-005

t(8;21)

API2/MALT1

17-001

t(11;18)

ATM/D11S1251

14-018

del(11q22)/11p15

BCL6 Break Apart

18-010

t(3q27)

CCND1/IGH

14-006

t(11;14)

D7S486/Cen7

11-007

del(7q31)/Cen7

D13S25/D13S1009

14-009

del(13q14)/13q34

D20S108/8q11

11-001

del(20q12) & trisomy 8

EGFR/Cen7

22-007

EGFR Amplification

EGR1/5p15

11-004

del(5q31)/5p15

ERBB2/Cen17

22-003

ERBB2 Amplification

FGFR3/IGH

16-005

t(4;14)

FHACTTM

25-002

3q26/5p15/20q13/Cen7

IGH/BCL2

18-001

t(14;18)

IGH Break Apart

13-014

t(14q32)

IGH/MAF

16-010

t(14;16)

IGH/MALT1

17-004

t(14;18)

MDM2/D12S1837

14-017

12q15/12p11

MLL Break Apart

11-002

t(11q23)

MYB/SHGC-79576

14-016

6q23/6p12

MYC Break Apart

13-008

t(8q24)

MYC/IGH

13-004

t(8;14)

MYH11/CBFB

12-010

inv(16)

PBX1/E2A

13-001

t(1;19)

PML/RARA

12-008

t(15;17)

RB1/D13S1009

27-014

del(13q14)/13q34

TP53/RARA

14-015

del(17p13)/17q21

Page 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25


Cancer Genetics Italia 2013 DNA-FISH Probe Catalog www.cancergeneticsitalia.com

Chromosome

Probe Name

Reference Number

Page

1;19

PBX1/E2A

13-001

24

2

ALK Break Apart

21-002

11

2;5

ALK/NPM1

21-001

12

3

BCL6 Break Apart

18-010

14

3, 5, 7, 20

FHACTTM

25-002

18

4;14

FGFR3/IGH

16-005

18

5

EGR1/5p15

11-004

17

5, 9, 15

5p15, 9q34, 15q24

16-003

10

6

A20/PRDM1/SHGC-79576

19-001

10

6

MYB/SHGC-79576

14-016

22

7

D7S486/Cen7

11-007

15

7

EGFR/Cen7

22-007

16

8

MYC Break Apart

13-008

22

8;14

MYC/IGH

13-004

23

8, 20

D20S108/8q11

11-001

16

8;21

AML1/ETO

12-005

12

9;22

ABL1/BCR

10-001

11

11

ATM/D11S1251

14-018

13

11

MLL Break Apart

11-002

21

11;14

CCND1/IGH

14-006

14

11;18

API2/MALT1

17-001

13

12

MDM2/D12S1837

14-017

21

13

D13S25/D13S1009

14-009

15

13

RB1/D13S1009

27-014

25

14

IGH Break Apart

13-014

19

14;16

IGH/MAF

16-010

20

14;18

IGH/BCL2

18-001

19

14;18

IGH/MALT1

17-004

20

15;17

PML/RARA

12-008

24

16

MYH11/CBFB

12-010

23

17

ERBB2/Cen17

22-003

17

17

TP53/RARA

14-015

25

Product Index By Number

Product Index By Chromosome Number

Page 37


Notes


Notes


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CGI Italia: DNA-FISH Probe Catalog