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Genomics In The Journals: Jul 7, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In PLoS Genetics, an international group describes a relatively rare allele that ups the risk of sudden cardiac arrest. The researchers first did a genome-wide association study meta-analysis using samples from 1,283 individuals with sudden cardiac death and more than 20,000 unaffected controls, all of European descent, who'd been sampled through five studies in the US and Europe. In a series of follow-up experiments, the team genotyped suspicious SNPs from the discovery phase and narrowed in on a new risk locus on chromosome 2 that appears to increase the risk of sudden cardiac death by 1.92 times per allele.

Genetic changes in a handful of genes can provide prognostic information that could help target treatment of a bone marrow and blood cancer known as myelodysplastic syndrome, according to a study in the New England Journal of Medicine. Through a combination of mass spectrometry-based genotyping and targeted gene sequencing experiments, a Brigham and Women's Hospital-led team found 18 genes that were mutated in MDS samples compared to matched controls. Five of the genes appear to provide prognostic information, showing independent associations with better or worse overall survival outcomes, leading researchers to suggest that testing for such genetic glitches may eventually help determine which MDS patients get the most aggressive treatment.

"Information about gene mutations is not used clinically at the moment for patients with MDS," senior author Levine Ebert, an oncology researcher at BWH, said in a statement. "[U]sing these mutations to determine the prognosis of patients can help dictate appropriate treatment for patients based on the current state of the disease."

Japanese researchers report on a chromosome 22 locus linked to progression from chronic hepatitis C virus infection to liver cancer in Japanese individuals in Nature Genetics. The team did a GWAS involving 977 individuals over 55 years old from Japan who had chronic HCV infection, including 212 who had developed hepatocellular carcinoma and 765 who had not. The search turned up a potential risk locus within the intron of a gene called DEPDC5 — an association that the team subsequently verified in 710 more individuals with HCV and liver cancer and 1,625 individuals with HCV alone.

In the Proceedings of the National Academy of Science, members of the 1000 Genomes Project and others describe how they used data from the project's pilot phase to discern genetic diversity and rare allele sharing in human populations. Using site frequency spectra from low coverage, whole-genome sequence data for 179 European, Asian, and African individuals and high-coverage, targeted exon sequence data for nearly 700 individuals from seven populations, the team estimated the number of yet-undetected variants in human populations. From their analysis, they suggest roughly 1,000 chromosomes and about 2,500 chromosomes will have to be sequenced to detect 100,000 non-synonymous and synonymous variants, respectively, in each population.

"Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations," corresponding author Carlos Bustamante, a genetics researcher at Stanford University, and co-authors wrote. "Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

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