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Genomics In The Journals: Aug 18, 2011

NEW YORK (GenomeWeb News) – Through a genome-wide association study involving thousands of Han Chinese individuals, members of the China Consortium for the Genetics of Autoimmune Thyroid Disease found two new risk loci for an autoimmune condition called Graves' disease. The researchers genotyped 1,536 cases and 1,516 controls for the discovery phase of the study and then tested 95 of the most promising SNPs in another 3,994 individuals with Graves' disease and 3,510 controls. In the process, they not only verified associations with four known loci but also identified new Graves' disease-associated loci on chromosomes 4 and 6 that seem to influence the expression of genes on those chromosomes. The team reports their findings in Nature Genetics.

"Our findings offer new insights into the genetic architecture of Graves' disease and could ultimately impact on the clinical management of this disease," the study authors wrote.


A study in Cancer Epidemiology, Biomarkers and Prevention suggests variants in five genes — LEPR, RNASEL, IL4, CRY1, and ARVCF — may help differentiate between the most aggressive prostate cancer cases and cases with lower mortality risk. An international team genotyped 937 SNPs in 156 suspicious genes in blood samples from 1,309 individuals enrolled in the Seattle area who had been diagnosed with prostate cancer between the ages of 35 and 74 years old. Five of the top 22 SNPs detected in this discovery set were significantly associated with prostate cancer death risk in a validation group of nearly 2,900 Swedish prostate cancer patients.

"The ability to distinguish patients at elevated risk for having aggressive, life-threatening prostate cancer at the time of diagnosis could improve care for the subset of cases most likely to benefit from aggressive therapy and help avoid over-treatment of patients whose tumors are likely to remain indolent," senior author Janet Stanford of the University of Washington and the Fred Hutchinson Cancer Research Center, and co-authors wrote.


Researchers from the US, Canada, and Mexico found genetic evidence that the sunflower plant was domesticated just once in eastern North America and did not undergo a secondary domestication event in Mexico as once suspected. As they report in the early, online edition of the Proceedings of the National Academy of Science, the team's haplotype analyses and targeted sequencing of three early domestication genes in wild and domesticated Mexican sunflower, along with genotyping at a dozen microsatellite loci, point to a single domestication event rooted in eastern North America.

"Our results affirm that the eastern United States was an independent center of plant domestication and that all known living cultivated sunflowers shared a common origin there," first author Benjamin Blackman, who is affiliated with Indiana and Duke Universities, said in a statement.


In the American Journal of Human Genetics, researchers from the US and Luxembourg describe how they did genetic variant phasing with an algorithm called Haploscribe to decipher genetic variation combinations along the chromosomes of individuals from two families, generating chromosomal haplotype maps. Using genome resequencing data for seven members of the two families who were sequenced by Complete Genomics, the investigators were able to determine haplotype patterns for four children from each of the families as well as their parents. Those involved in the study say the approach is complementary to population-based inference methods for determining haplotype and molecular haplotyping methods based on short read sequence data.

"The implementation of our algorithm, Haploscribe, brings a powerful approach to chromosomal haplotype specification that will open up new possibilities for exploring the functional implication of phasing of various types of chromosomal variants across short to large chromosomal spans," Institute for System Biology researcher Arian Smit, senior author on the study, and co-authors wrote.

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