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Eight New Human Genome Projects Offer Large-scale Picture Of Genetic Difference

ScienceDaily (May 2, 2008) — A nationwide consortium led by the University of 
Washington in Seattle has completed the first sequence-based map of structural 
variations in the human genome, giving scientists an overall picture of the 
large-scale differences in DNA between individuals. The project gives 
researchers a guide for further research into these structural differences, 
which are believed to play an important role in human health and disease. The 
results appear in the May 1 issue of the journal Nature.

The project involved sequencing the genomes of eight people from a diverse set 
of ethnic backgrounds: four individuals of African descent, two of Asian 
descent, and two of European background. The researchers created what's called 
a clone map, taking multiple copies of each of the eight genomes and breaking 
them into numerous segments of about 40,000 base pairs, which they then fit 
back together based on the human reference genome. They searched for structural 
differences that ranged in size from a few thousand to a few million base 
pairs. Base pairs are one of the basic units of information on the human genome.

Most previous studies of the genome have focused on small genetic variations 
called SNPs (pronounced "snips"), or single-nucleotide polymorphisms -- changes 
on the scale of a single base pair. More recent research on the human genome 
has shown, however, that larger-scale differences may account for a great deal 
of genetic variation among individuals. Structural variation in the human 
genome has already been linked to individual differences in susceptibility to 
conditions like coronary heart disease, HIV, schizophrenia, autism, and mental 

In addition to millions of smaller differences, the researchers identified 1695 
regions of structural variation in the genome. They also provided a detailed 
look at the sequence for 261 regions of the genome, revealing an unprecedented 
view of the complexity of the genetic differences among different humans. The 
large-scale differences that the researchers were looking for can come in many 
forms, such as the deletion of a large swath of DNA, or the insertion of an 
out-of-place string of genetic code. Others simply appear as a different number 
of copies of a gene or DNA sequence.

Until now, there has not been a comprehensive study to sequence these 
variations systematically in multiple individuals. As part of their study, the 
authors also discovered 525 segments of DNA that were previously unknown to the 
human genetics community.

"There is a perception that the human genome is essentially completely 
understood," explained the project's leader, Dr. Evan Eichler, UW associate 
professor of genome sciences and an investigator for the Howard Hughes Medical 
Institute. "The sequences we have identified range in size from a few thousand 
to hundreds of thousands of base pairs, and are not part of the published human 
genome reference sequence. We found that many of these are highly variable in 
copy and content between individuals. This represents uncharted territory that 
can now be examined in more detail to determine the function of these new 
segments of the human genome with respect to disease and gene activity."

Eichler expects that the structural variation map will give scientists a much 
better picture of genetic variations, and help them better understand these 
areas of the genome that are prone to large-scale changes over time. Even more 
research is needed on structural variations, the scientists argue in the 
article, to help get a more accurate picture of the human genome than what we 
already have in the reference genome constructed by the Human Genome Project.

"The important point here is that we could not have found these differences 
without sequencing more human genomes from individuals of diverse ancestry to a 
high-quality standard," Eichler added.

The project will also serve as a sound resource for the science community, said 
Eichler, since the researchers have preserved the many segments of DNA used for 
the project. As new genomes are studied, someone might find a new sequence or 
new area of variation, and the researchers can revisit that particular segment 
of DNA to study it more closely.

In addition to Eichler, several UW researchers in the UW Departments of Genome 
Sciences and Medicine worked on the project, including Jeffrey Kidd, a graduate 
student in genome sciences, and Maynard Olson, professor of medicine and genome 
sciences and director of the UW Genome Center. The project also included 
researchers at Agencourt Bioscience Corp. in Beverly, Mass.; Agilent 
Technologies in Santa Clara, Calif.; Washington University School of Medicine 
in St. Louis; the National Human Genome Research Institute in Bethesda, Md.; 
the University of Wisconsin, in Madison; the Broad Institute of MIT and 
Harvard, in Cambridge, Mass.; and Illumina, Inc. in San Diego. The researchers 
were supported by the National Science Foundation, the Jane Coffin Childs 
Memorial Fund, Merck, and the National Human Genome Research Institute, part of 
the National Institutes of Health.
Adapted from materials provided by University of Washington, via EurekAlert!, a 
service of AAAS.
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University of Washington (2008, May 2). Eight New Human Genome Projects Offer 
Large-scale Picture Of Genetic Difference. ScienceDaily. Retrieved February 13, 
2009, from http://www.sciencedaily.com­ /releases/2008/04/080430134251.htm

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