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This Week in Genome Research: Apr 6, 2011

In a paper published online in advance in Genome Research this week, a trio of investigators at the University of Chicago describes the genetic architecture of regulatory variation in Arabidopsis thaliana, which it deduced by mapping genome-wide association of gene expression in an F1 hybrid diversity panel. "By association mapping of allele-specific expression, we detect a significant enrichment for cis-acting variation in local regulatory variation," the authors write, adding that their association mapping of splicing variation also revealed "both local and distant genetic regulation for intron and exon level traits."

Investigators at the Genome Institute of Singapore and elsewhere this week show that "single segmental tandem duplication spanning several genes is a major source of the fusion gene transcripts in both [breast cancer] cell lines and primary tumors involving adjacent genes placed in the reverse-order position by the duplication event." Using paired-end sequencing, the team discovered other structural mutations in eight breast cancer genomes that they say "tend to attenuate gene expression."

Researchers in Tokyo this week report on their genome-wide analysis of transcriptional start sites in human genes, which they performed using 800 million sequences derived from a variety of transcriptome analysis methods. Overall, the team characterized 140 million transcriptional start site tags in 12 human cell types. "Nucleosome-seq analysis revealed highly ordered nucleosome structures, ChIP-seq analysis detected clear RNA polymerase II binding signals in their surrounding regions, evaluations of previously sequenced and newly shotgun-sequenced complete cDNA sequences showed that they encode preferable transcripts for protein translation, and RNA-seq analysis of polysome-incorporated RNAs yielded direct evidence that those transcripts are actually translated into proteins," the authors write in a Genome Research paper published online in advance.

Another Genome Institute of Singapore-led team reports its use of a long-span paired-end-tag approach on 15 cancer and two non-cancer genomes, with which it identified "characteristic patterns of structural variations in epithelial cancer genomes." Among other things, the researchers write, "our analyses revealed that most inversions, deletions, and insertions are germ-line [structural variations], whereas tandem duplications, unpaired inversions, inter-chromosomal translocations, and complex rearrangements are over-represented among somatic rearrangements in cancer genomes."

The Scan

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.