Human Genome – first map of cultural variations

A nationwide team of researchers, funded in part by the National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), has produced the first sequence-based map of large-scale structural variation across the human genome.

Recently created maps such as the HapMap have catalogued the patterns of small-scale variations in the genome that involve single DNA letters, or bases.  A sequence-based map provides much finer resolution and location information.

Researchers constructed the structural variation map by partially sequencing the genomes of eight people: four people of African descent, two of Asian descent and two of European descent. Sequence data were collected from each end of roughly 1 million random small pieces of DNA from each individual’s genome.

These end sequences were compared to the reference sequence of the human genome completed in 2003. Where precise matches did not occur, the scientists inferred that there was a structural difference between the volunteer’s sample and the reference sequence of the human genome.

In addition to revealing new variations, the map also provides a more detailed look at the locations of nearly 1,700 structural variations – half of which had not been previously described . About half of the structural variations were found in at least two of the eight genomes analyzed. The work also uncovered 525 new regions of large-scale structural variation in the human genome. The large-scale differences came in many forms, including deletions and out-of-place insertions of long stretches of DNA. Almost half of the new variations consist of differences in how many copies individuals have of a certain gene, which researchers refer to as a copy number variant.

“The structural variation map will give us a much better picture of genetic variation between each individual, and help us better understand these areas of the genome that are prone to large-scale changes over time,”said Evan Eichler, Ph.D., of the University of Washington, who led the research.

Sequence data from the structural variation map are publicly available through the NIH’s National Center for Biotechnology Information Trace Archive, www.ncbi.nlm.nih.gov/Traces. Mapping data are also freely available from the University of Washington, http://hgsv.washington.edu.

Elaine Warburton  www.geneticsandhealth.com