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This Week in PLoS: Mar 8, 2010

This week in PLoS One, researchers report that missense mutations in FMR1 are not a cause of the Fragile X syndrome phenotype in patients who have normal-length CGG-repeat expansions. To decipher this, the team used an array-based method to sequence FMR1 in 51 individuals exhibiting features of FXS with normal CGG-repeat tracts of the gene. The team suggests that "screening for small deletions of FMR1 may be of clinically utility."

A team at the University of Connecticut contends that circular plasmid DNA is unsuitable as a standard for qPCR because it leads to "serious overestimation." Yubo Hou et al. report their quantitative comparison between qPCR accuracies based on circular plasmid and linear DNA standards; they observed that PCR performed using "circular plasmids as template gave 2.65-4.38 more of the threshold cycle number than did equimolar linear standards." Further, the team writes that while the reported genome sequence of Thalassiosira pseudonana shows only one copy of PCNA, qPCR using a circular plasmid standard showed more than seven copies per genome. Using the linear standard, the team wrote, gave 1.02 copies of PCNA per genome.

In PLoS Computational Biology this week, a trio of researchers provides a review of the challenges that metagenomics might ― and already do ― pose for bioinformaticians. The authors refer to metagenomic sequencing data as "noisy and partial." Their review specifically addresses the computational requirements presented by metagenomics, rather than a comprehensive review of the current technologies. The review concludes with a "representative studies illustrating different facets of recent scientific discoveries made using metagenomics."

International researchers report their analysis of genetic ancestry using GWAS of pooled DNA from African American, Native Hawaiian, Latina, and Jamaican samples that were genotyped using an Affymetrix array in PLoS Genetics this week. Using a regression-based method to estimate the amount of admixture in each cohort based on the allele frequencies they calculated from pooling and HapMap reference populations, the team identified ancestry informative markers for each population. "Through validation by individual genotyping, we demonstrated that pooling is quite effective for identifying SNPs with large allele frequency differences, and that these [ancestry informative markers] AIMs are able to differentiate two closely related populations," the team writes.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.