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This Week in Genome Research: Dec 14, 2011

Writing in Genome Research, the Wellcome Trust Sanger Institute's Jared Simpson and Richard Durbin present memory-efficient data structures and algorithms for genome assembly "using the FM-index derived from the compressed Burrows-Wheeler transform, and a new assembler based on these called SGA," or string graph assembler. Simpson and Durbin also present "algorithms to error correct, assemble, and scaffold large sets of sequence data." The Wellcome Trust researchers say that using their approach, it's possible to assemble a human genome using 54 GB of memory.

In another paper published online in advance, a team led by investigators at the University of Tokyo reports whole-exome sequencing data for 15 pancreatic tumor cell lines and their matched normal samples, through which it found that "the diversity of the mutation rates was significantly correlated with the distinct MLH1 copy-number status." The team goes on to suggest that "MLH1 hemizygous deletion, through increasing the rate of indel mutations, could drive the development and progression of sporadic cancers."

The Scan

Wolf Howl Responses Offer Look at Vocal Behavior-Related Selection in Dogs

In dozens of domestic dogs listening to wolf vocalizations, researchers in Communication Biology see responses varying with age, sex, reproductive status, and a breed's evolutionary distance from wolves.

Facial Imaging-Based Genetic Diagnoses Appears to Get Boost With Three-Dimensional Approach

With data for more than 1,900 individuals affected by a range of genetic conditions, researchers compared facial phenotype-based diagnoses informed by 2D or 3D images in the European Journal of Human Genetics.

Survey Suggests Multigene Cancer Panel VUS Reporting May Vary Across Genetic Counselors

Investigators surveyed dozens of genetic counselors working in clinical or laboratory settings, uncovering attitudes around VUS reporting after multigene cancer panel testing in the Journal of Genetic Counseling.

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.