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This Week in PLoS: Feb 1, 2010

In PLoS Biology this week, Duke University researcher David Goldstein and his co-workers report that "synthetic associations" between rare and common variants may be behind the results of some genome-wide association studies. The conclusion is based on the team's simulation experiments as well as GWAS of sickle cell anemia and hearing loss. "[E]ven those signals that have been detected for common variants could, in principle, come from the effect of rare ones," they write. As Nicholas Wade reports in the New York Times, the findings have some calling for more genome sequencing studies. For more on the study and reaction from geneticists, check out a related Nature News story.

UCLA researchers report in PLoS Genetics that they have used the ABI SOLiD platform to sequence the genome of a glioblastoma multiforme brain cancer cell line called U87MG. The cell line, derived a grade IV glioma, contained almost 2.4 million SNPs, more than 191,700 small insertions and deletions, 1,315 structural variations, and 35 inter-chromosomal translocations. For more information, check out a related news story in our sister publication GenomeWeb Daily News.

In PLoS ONE, researchers from Howard University and the National Institutes of Health report on copy number alterations in colorectal tumors. The team used genome-wide array comparative genome hybridization to find copy number changes in tumors from 15 African Americans, comparing these patterns with aCGH patterns in Caucasian tumors and information on known colon cancer genes. Their results suggest tumors in African-American patients often involve X chromosome amplifications and chromosome 4, 8, and 18 deletions.

And a New Zealand research team sequenced the genome of the methane-producing archaeal species Methanobrevibacter ruminantium M1, found in ruminant livestock. The team used pyrosequencing and PCR-based approaches to sequence the 2.93 million base genome and started identifying genes involved in methane production — insights that they say may eventually help curb methane emissions from livestock.

The Scan

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.

Study Points to Synonymous Mutation Effects on E. Coli Enzyme Activity

Researchers in Nature Chemistry saw signs of enzyme activity shifts in the presence of synonymous mutations in a multiscale modeling analysis of three Escherichia coli genes.

Team Outlines Paternal Sample-Free Single-Gene Approach for Non-Invasive Prenatal Screening

With data for nearly 9,200 pregnant individuals, researchers in Genetics in Medicine demonstrate the feasibility of their carrier screening and reflex single-gene non-invasive prenatal screening approach.

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.