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Around the Literature


Soybean Genome

Schmutz J, Cannon S, Schlueter J, Ma
J, et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature. (463): 178-183.

A large team comprised of researchers from Purdue University, the US Department of Energy's Joint Genome Institute, and the US Department of Agriculture's Agricultural Research Service used whole-genome shotgun sequencing to sequence roughly 85 percent of the 1.1-gigabase soybean, Glycine max, genome. The paper describes how the team integrated the shotgun approach with physical and high-density genetic maps to assemble a chromosome-scale draft sequence. The team predicted 46,430 protein-coding genes, 70 percent more than another polyploid, Arabidposis thaliana.

Reproducible Research System

Mesirov JP. (2010). Accessible reproducible research. Science. 327(5964): 415-416.

Mesirov proposes a novel model for embedding bioinformatics workflows directly into published research papers. The model outlined in the paper is called the Reproducible Research System (RRS) and is comprised of a Reproducible Research Environment — a framework that provides computational tools and the ability to track and package data, analyses, and results — and a document-preparation system called the Reproducible Research Publisher. She used the Broad Institute's GenePattern along with Microsoft Word and embedded the informatics analysis pipelines into Word, allowing the author to link text, tables, and figures to executed pipelines.

Synthetic Genome-Wide Associations

Dickson SP, Wang K, Krantz I, Hakonarson H, and Goldstein DB (2010). Rare variants create synthetic genome-wide associations. PLoS Biology. 8(1): e1000294.

In this paper, Dickson and his colleagues use computer simulations to show the conditions under which "synthetic associations" arise and how they may be recognized. The authors show that these associations are not only possible, but inevitable, and that under simple but reasonable genetic models, they are likely to account for or contribute to many of the recently identified signals reported in genome-wide association studies. The paper concludes that careful consideration in the interpretation and follow-up of GWAS signals is required because uncommon genetic variants can easily create synthetic associations that are connected to common variants.

Integrated Genomic Analysis of GBM

Verhaak RGW, Hoadley KA, Purdom E, Wang V, et al. (2010). Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 17(1): 98-110.

This paper describes a robust gene expression-based molecular classification of giloblastoma multiforme into proneural, neural, classical, and mesenchymal subtypes and integrates multidimensional genomic data to establish patterns of somatic mutations and DNA copy number. All subtypes have different responses to aggressive therapy response, with the greatest benefit seen in the classical subtype and no benefit in the proneural subtype. Through this approach, the authors provide a framework that unifies transcriptomic and genomic dimensions for GBM molecular stratification.

The Scan

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.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.