First individual genome sequence...(ns (indels) copy number variants block s...)

Date:9/3/2007

ns (indels), copy number variants, block substitutions, and segmental duplications. While the SNPs outnumbered the non-SNP types of variants, the non-SNP variants involved a larger portion of the genome. This suggests that human-to-human variation is much greater than previously thought. The researchers suggest that much more research needs to be done on these non-SNP variants to better understand their role in individual genomics.

According to Sam Levy, Ph.D., lead author and senior scientist at JCVI, The ability to use unbiased, high throughput sequencing methods, coupled with advance computational analytic methods, enables us to characterize more comprehensively the wide variety of individual genetic variation. This offers us an unprecedented opportunity to study the prevalence and impact of these DNA variants on traits and diseases in human populations.

Another important feature that is made possible by having an individual, diploid genome is the ability to begin to do better and more informed haplotype assemblies. Haplotypes are groups of linked variants. Through the government-sponsored HapMap project, many common haplotypes have been identified; however, these are based on averages of large ethnogeographic populations rather than individuals. Having individual haplotypes would enable researchers to understand and find more rare or individual variants that would explain and help predict diseases in that particular persona truly personalized, individualized genomics paradigm. In the HuRef analysis, the team used the 4.1 million variant set and new algorithms to build haplotype assemblies that, when compared to the HapMap project, represented longer and more complete linkages. The JCVI researchers expect this number to improve significantly as additional sequence coverage is added to HuRef using a variety of new seque ncing technologies.

Long-range haplotype linkages will enable much more complete analysis of human variation and the
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Contact: Natalie Bouaravong press@plos.org 415-568-3445 Public Library of Science Source:Eurekalert

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