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USC receives $18.7 million grant for study of genes that cause disease

by Eva Emerson and Usha Sutliff

The National Human Genome Research Institute (NHGRI) has awarded USC $18.7 million to establish a center that will develop faster ways to identify genes that cause disease.

The USC Center of Excellence in Genomic Science will unite scientists from the USC College of Letters, Arts & Sciences with colleagues at the Keck School of Medicine in an international effort to catalog human genetic variations.

“We will focus on developing and testing new experimental and computational techniques that will increase our ability to find disease-related genes and extract other useful knowledge from the human genome,” said computational biologist Michael Waterman, a University Professor, holder of the USC Associates Chair in Natural Sciences and professor of biological sciences, computer science and mathematics. Waterman is the center’s principal investigator.

The co-director is Norman Arnheim, USC Distinguished Professor and holder of the Ester Dornsife Chair in Biological Sciences.

The NHGRI, one of the National Institutes of Health (NIH), will spread the $18.7 million over five years. USC, one of only seven universities to receive such a grant, will have the only center of its kind in Southern California.

Research at the new center will tie into a study called the International HapMap Project—also funded in part by the NIH—that is working to find DNA landmarks that will provide shortcuts to identifying disease-causing genes.

The human genome, often referred to as the “Book of Life,” comprises roughly 3 billion pairs of DNA—genetic material made up of chemicals, or ‘nucleotides,’ identified by the letters A, T, C and G.

While most people share identical DNA sequences, much of human variation stems from genetic differences in as little as one DNA letter. Some of these ‘spelling’ changes—called single nucleotide polymorphisms, or SNPs—are thought to cause or contribute to disease.

While researchers have discovered millions of SNPs in the genome, figuring out a way to identify the variations important in common diseases has been challenging.

They hope to simplify this search by breaking the human genome into segments, called haplotype blocks, that are shared by many people. Researchers will be able to go directly to those blocks to search for genes linked to cancer, diabetes and other common diseases.

As part of the international project, researchers from five nations are investigating these patterns of genetic variation by collecting samples from about 300 people, including Han Chinese, Yorubas in Nigeria, Japanese and U.S. residents of northern and western European descent.

They hope to identify the SNPs that can be used to quickly tag entire blocks. In the end, they want to characterize just 500,000 SNP tags out of the 10 million estimated to be in the genome. The USC group will analyze data collected in the HapMap Project and conduct original research.

As part of the center’s research, the team will test and refine any new computational methods they develop using real cancer genetics data collected by team members from the epidemiology group in the Keck School.

Keck researchers, led by Duncan Thomas, professor of preventive medicine and the Verna K. Richter Chair in Cancer Research, and Malcolm Pike, professor of preventive medicine, hope their work will quicken the pace of their search for genes involved in breast and prostate cancer.

The researchers are studying 35 candidate genes in thousands of samples. For each gene, they must identify one SNP in every 2,000 to 5,000 DNA bases.

Pike said, “What appeals to me about figuring out a way to use the block structure is that if there are 10 SNPs in a gene under study, you might be able to look at only three and get the same information.”

Other USC projects will include:

• developing a way to determine which SNPs should be used as tags;

• investigating the quality of human genetic variation data;

• improving the reliability of techniques used to find SNPs; and • studying the biological processes that created the block structure.

A $3-million portion of the grant will go toward a training program in the USC College designed to recruit and support minority undergraduates, graduate students and postdoctoral fellows pursing careers in genomics, bioinformatics and computational biology.

“This NIH grant ratifies USC’s decision to begin supporting in the 1980s what was then an obscure field—computational biology,” said Joseph Aoun, dean of USC College and holder of the Anna H. Bing Dean’s Chair.

“We were among the first to focus on this field, and Mike Waterman’s pioneering work here at USC laid the foundation for one of modern science’s most significant achievements—the sequencing of the human genome. Now this USC research provides a blueprint for attacking complex, pernicious diseases while advancing the development of a new kind of personalized medicine.”

In addition to Thomas and Pike, Keck researchers who are part of the new center’s team include Daniel Stram, associate professor of preventive medicine, Paul Marjoram, research assistant professor of preventive medicine, and Joseph Hacia, assistant professor of biochemistry and molecular biology.

USC receives $18.7 million grant for study of genes that cause disease

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