Far left: Postdoctoral researcher Marie-Stanislas Remigereau and third-year molecular biology doctoral student Pei Zhang discuss Arabidopsis thaliana that are cultivated in two growth chambers in the basement of Ray R. Irani Hall. Middle: Professor of Biological Sciences John Tower uses a stereo microscope to score genetic markers in Drosophila melanogaster (fruit fly).
S. NUZHDIN LAB PHOTO BY MAX S. GERBER; MAP PROGRAM PHOTO BY LAURIE MOORE
Left: Professor of Biological Sciences Sergey Nuzhdin (center) and members of his lab — Bradley Main, Margaret Sherriffs, Yu Huang (of Associate Professor of Biological Sciences Magnus Nordborg’s lab), Julia Saltz, Courtney Fjeldsted, and Maren Friesen — investigate genetic variation.
Next, quantitative analyses of the resulting data will be performed by Associate Professor of Biological Sciences and Computer Science Ting Chen, Assistant Professor of Biological Sciences Liang Chen, Assistant Professor of Biological Sciences Andrew Smith, Professor of Biological Sciences Fengzhu Sun, and Associate Professor of Biological Sciences Xianghong Jasmine Zhou. Together this team of computational biologists will develop novel, efficient algorithms that will allow them to scan enormous amounts of sequencing data generated through the Epigenome Center and better identify the possible SNPs or genetic variant sets that are responsible for the phenotypic expressions observed in Arabidopsis and Drosophila. “One of the biggest challenges we face is improving and enforcing statistical methods of quality control such as accounting for false positives,” Liang Chen said. “In an effort to best enforce quality control, we consider intermediate phenotypes, which although not directly related provide extra information about the path from genotype to phenotype.” Once these new methods for understanding the genotype-to-phenotype map have been developed in the first three years of the grant, Tavaré and his USC College colleagues will partner with preventive medicine faculty members at the Keck School to investigate how these techniques might be applied to existing human cancer studies. Keck School’s Paul Marjoram, Kimberly Siegmund and David Conti point out that while phenotypes might be different across organisms, they are often measured on the same scale, so techniques developed for one organism’s phenotype can be applied to the analysis of another. “There is the real prospect that using the model systems in CEGS will help us refine and verify methods we develop for analyzing human data,” Marjoram said. “This gives us the experience we need to more successfully apply them to human data and more accurately interpret these new results when looking at colon cancer data, for example.” Marjoram and his colleagues plan to begin by applying their findings to the Colon Cancer Family Registry, which is supported by National Cancer Institute and to date includes data and biospecimens for more than 30,000 subjects from multiple institutes. “The answers to many questions are written in our DNA,” he said. “Our hope is to develop methods that allow us to uncover as many of these answers as we can, as quickly as we can.” ■
VIEW THE
Steven Finkel, deputy director of the Center of Excellence in Genomic Science at USC and director of its Minority Action Plan, with molecular and computational biology doctoral students Lorraine Provencio and Eduardo Ayala
THE CENTER OF EXCELLENCE IN GENOMIC SCIENCE
MINORITY ACTION PLAN
@ USC
ot only does the Center of Excellence in Genomic Science (CEGS) at USC carry out its research mission, it also administers an National Institutes of Health-funded Minority Action Plan (MAP), which provides education and training about basic research in the life sciences to under-represented minorities. “Many students don’t know what it’s like to be a scientist,” said Steven Finkel, associate professor of biological sciences as well as deputy director of the CEGS at USC and director of its MAP program. “So the goal of our program is to give, particularly undergraduates, the opportunity to conduct high-quality research under the mentorship of a faculty member as well as guide students through their educational and career transitions.” The CEGS at USC, which initially began in 2003, runs three programs: an academic-year research program for undergrads called the Genomics Research Experience for Undergraduates (GREU); a summer version of GREU, which includes a journal club and seminar series; and the Genomics Graduate Scholars (GGS) program, which provides stipends for minority graduate students working in laboratories in the biological sciences. Approximately $1.5 million of the CEGS grant renewal is directed to the MAP program at USC. This generous funding currently supports the highest number of participants yet: 19 undergrads and seven doctoral students.
N
NLINE VIDEO at college.usc.edu/cegsrenewal Spring/Summer 2010 | 53