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This Week in Nature: Mar 11, 2010

In an advance, online publication of Nature this week, an international research collaboration reports their resequencing of the chicken genome. Using a massively parallel sequencing approach, the team sequenced and analyzed the Gallus gallus domesticus genome to 44.5-fold coverage and identified selective sweeps of favorable alleles, as well as candidate mutations which may have played a role in the animal's domestication. The authors also suggest that their results imply "the importance of the domestic chicken as a model organism for biomedical research."

In a paper also published online, University of Chicago researchers highlight the "power of high-throughput sequencing for the joint analysis of variation in transcription, splicing, and allele-specific expression across individuals," demonstrated in their RNA sequencing analyses of 69 lymphoblastoid cell lines derived from Nigerian individuals. By pooling all data generated with the genotypes for these cell lines archived in the HapMap database, Joseph Pickrell et al. generated a map the the cells' transcriptional landscapes. "We demonstrate that eQTLs near genes generally act by a mechanism involving allele-specific expression, and that variation that influences the inclusion of an exon is enriched within and near the consensus splice sites," the authors write.

In Nature this week, researchers at the Max Planck Institute for Infection Biology and their colleagues report their analysis of the primary transcriptome of Helicobacter pylori, a pathogen which infects approximately 50 percent of all humans. Using a novel differential approach, dRNA-seq, which is selective for the 5' end of primary transcripts, the team mapped the transcriptional start sites and operons across the H. pylori genome. The authors write that they discovered an unexpected number of small RNAs and potential regulators of cis- and trans-encoded target mRNAs.

Researchers in Austria and Germany present their systematic analysis of muscle morphogenesis and function in Drosophila melanogaster using genome-wide transgenic RNAi libraries. In applying their method, the team identified a role in muscle for 2,785 genes — many of which they've assigned to functions in the organization of muscles, myofibrils, or sarcomeres. "Many of these genes are phylogenetically conserved, including genes implicated in mammalian sarcomere organization and human muscle diseases," the team writes.

In Nature Genetics, researchers report on a genome-wide association study to identify variants associated with the severe and often painful food allergy in children called eosinophilic esophagitis. The researchers found that EoE was linked to a region of chromosome 5 that includes two genes. The most likely candidate in that region is TSLP, which has higher activity levels in children with EoE, as compared to healthy subjects. TSLP is involved in cytokine production, which regulates the inflammation that occurs in allergic diseases.

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.