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This Week in Genome Research: Feb 4, 2015

Researchers from Brown University, the Broad Institute, and elsewhere looked at the level of genetic phenotypic diversity present in Candida albicans, an opportunistic fungal pathogen that usually lives relatively innocuously in the human gut. Using multi-locus sequence typing, genome sequencing, RNA sequencing, and other strategies, the team profiled 21 clinical isolates of C. albicans collected from bloodstream, oral, or vaginal infection cases. The analysis revealed widespread variation amongst the isolates — from single nucleotide changes to copy number variants and chromosome-level alterations, including genetic differences that appear to affect virulence, drug resistance, and other clinically-relevant features.

A University of Washington-led team describes the potentially actionable incidental findings it found in the protein-coding sequences of more than 6,500 individuals of European and African descent who enrolled in the National Heart, Lung, and Blood Institute Exome Sequencing Project, using a set of 112 genes that may contain medically actionable mutations. Using their classification criteria, the researchers identified pathogenic single nucleotide variants in 0.7 percent and 0.3 percent of individuals with European or African ancestry, respectively. Another 1.2 percent of European-ancestry individuals carried variants deemed likely pathogenic, as did 0.3 percent of the African-ancestry participants.

Finally, investigators from Lawrence Berkeley National Laboratory and other international centers introduce the latest update to the Drosophila melanogaster reference genome, which reflects sequence and scaffold improvements to portions of the genome that close hundreds of gaps and stretch out chromosome assemblies by millions of bases. The release 6 reference includes nearly 144 million bases of sequence and "effectively exhausts clone-based technologies for mapping and sequencing," the study authors explain, noting that "[f]urther significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads."

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.