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1,000 Genomes ProjectLooking for the Differencesby Ruth SoRelle, M.P.H. We are more alike than we are different—if we are considering our genomes. However, an international research consortium of public-private scientific groups is looking for the differences that make us big or small, strong or weak, well and eventually sick. They call it the 1,000 Genomes Project because eventually, they expect to sequence the genomes—the genetic blueprints—of at least 1,000 people from around the world. Baylor College of Medicine, already a leader in genome sequencing, is at the heart of shaping the project into a form that will provide the most information. The project receives major support from the Wellcome Trust Sanger Institute in Hinxton, England, the Beijing Genomics Institute, Shenzhen (BGI Shenzhen) in China and the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH). The body contains trillions of cells. Within each of these cells are 23 pairs of chromosomes. The chromosomes are made up of an estimated 25,000 genes. These genes and the other DNA or genetic material in the cell are our genomes. The genome defines the biology of who we are. The instruction book is more than 99 percent the same for all of us. Where it differs is where we differ. The 1,000 Genomes Project seeks to find that 1 percent or less difference. Variations—single changes in one of those (A)denine, (T)hymine, (G)uanine, (C)ytosine letters that spell the genetic code, deletions or duplications of parts of it or switches that change the order—can affect a person's physical or mental abilities and his or her risk of disease. Science has looked at human variation before, but not in such detail. "This comes out of the HapMap project, which also sought to define human variation," said Richard Gibbs, Ph.D., Director of the Baylor Human Genome Sequencing Center and a Professor of Molecular and Human Genetics at BCM. "HapMap defined the common variants." HapMap was the logical progeny of the Human Genome Sequencing Project, the 13-year international project that sought to identify all the genes in human DNA and determine the sequence of the 3 billion chemical base pairs that make up human DNA. "The genome project was like an aerial map of the continental United States... Gibbs compares the project to a series of maps that include more and more detail. "The genome project was like an aerial map of the continental United States," he said. It identified the big markers but left out most of the detail. "The HapMap was like a map with posts every 10 miles," he said. "The 1,000 genomes project will fill in the detail to mileposts." Five years ago, he said, experts hoped that the common variations in the genetic picture would be the most likely to contribute to disease. "We knew that all classes of variations were a part, but now we have more appreciations that it is the rare variations that are important in disease," he said. This project promises to find the areas of the genome that have biomedical relevance, he said. How to achieve that goal is a matter under debate. For example, Gibbs thinks they should determine the sequences of exons—those portions of genes that contain the actual code for proteins. "We feel we ought to look at the exons for a variety of reasons, one of which is that we can do more than 1,000 people that way," he said. Other experts propose sequencing the genomes of fewer people but in great depth and with great precision—which means sequencing over and over. Still others think the project should concentrate on filling in the gaps left in the HapMap. Right now, the program is involved in a pilot project, testing each method to determine which one provides the most and best information. Then there is the matter of which technology is best for the project. Currently, three companies have signed on—454 Life Sciences, a Roche company, Branford, Conn.; Applied Biosystems, an Applera Corp. business, Foster City, Calif.; and Illumina Inc., San Diego. Each makes sequencing equipment that has some advantages and disadvantages for the project. "An unambiguous comparison of the different platforms will emerge from this," said Gibbs. The BCM Center is a strong participant in the pilot project, focusing on sequencing the exons. Whichever method wins out, the goal is the same, said Gibbs. "We want to complete our knowledge of all classes of human variation," he said. The pilot project is slated to finish in 2008. Then the experts will get together to plot their next step. Are 1,000 genomes enough or too many? How best can they achieve their purposes? Those are questions that remain to be answered before the most important one can even be posed. What makes us different? How do these differences really affect our health and our health risks? |
FeaturesBaylor College of Medicine in Houston: 65 years of Excellence BCM Looks to the Future on the McNair Campus Legacy of Leadership: BCM Icons Set Foundation for the Future 1,000 Genomes Project: Looking for the Differences NewsO'Malley Receives National Medal of Science Robert Todd Named to Lead BCM's Department of Medicine Roy Huffington Remembered as Bold and Generous SpotlightFollowing his Passion—One Physician's Journey When Two Degrees are Better Than One: M.D. - M.P.H. Thomas Street—The Road to Health Perceiving—A new Look at Brain and Behavior BriefsGenetics Used to Personalize Heart Disease Treatment First Drug for Huntington's Disease Eye Problems from Pain Free Migraines Genetic Insights into Deadly Brain Tumor Made-to-Order Weapon in the Fight Against Childhood Cancer BCM Joins Largest Children's Study Development/AlumniGifts Help Restore Sight to Patients with Corneal Damage Alums Start Careers, Life Together at BCM Development BriefsCharitable Gifts Lead to National Recognition Trustee Chuck Watson Makes Unique Gift
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Volume 4, Issue 3, Winter 2008 |
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| Last modified: December 23, 2008 |