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This Week in PLOS: May 14, 2013

In PLOS Biology, University of California, Davis, researchers Peter Ralph and Graham Coop present results from a population genomics study of almost 2,300 individuals from Europe. With data collected from individuals in 40 populations for the Population Reference Sample effort, the pair looked for long shared stretches of sequence suspected of being inherited from shared ancestors in different individuals — known as identity-by-descent, or IBD, blocks — in an effort to start untangling relationships between populations in Europe during the past 3,000 years or so. Findings from the analysis reinforced the notion that European populations tend to share ancestry over the past couple thousand years, though the researchers also refined some relationships between these groups.

Our sister publication GenomeWeb Daily News has more on the study, here.

Variants on chromosome 27 can contribute to a canine version of the skin condition atopic dermatitis, according to a study in PLOS Genetics by researchers at Uppsala University, the Broad Institute, the Swedish University of Agricultural Sciences, and elsewhere. Along with ELISA analyses revealing lower-than-usual IgA levels in pooches with canine atopic dermatitis, the team performed a genome-wide association study involving 179 German shepherds — a breed known to be especially prone to the allergic skin condition. When they compared genotyping patterns in German shepherds from Sweden with or without canine atopic dermatitis, the investigators found a particularly suspicious set of SNPs in and around eight genes on chromosome 27. Through targeted sequencing and genotyping analyses in additional dogs, they narrowed the locus down to a stretch of sequence containing the plakophilin 2 gene PKP2.

A proteomics-based analysis in PLOS One indicates that the proteins produced by mitochondria in placental tissue shift during the development of the pregnancy complication pre-eclampsia. Researchers from Nanjing Medical University profiled mitochondrial proteins in placental tissue from four women with pre-eclampsia and four women without using a peptide-labling approach called iTRAQ, coupled with liquid chromatography-tandem mass spectrometry. The search unearthed four proteins with higher-than-usual expression in the pre-eclampsia samples, along with almost two-dozen more proteins whose expression was dialed down during pre-eclampsia.

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.