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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

Pfizer-BioNTech Seek Full Vaccine Approval

According to the New York Times, Pfizer and BioNTech are seeking full US Food and Drug Administration approval for their SARS-CoV-2 vaccine.

Viral Integration Study Critiqued

Science writes that a paper reporting that SARS-CoV-2 can occasionally integrate into the host genome is drawing criticism.

Giraffe Species Debate

The Scientist reports that a new analysis aiming to end the discussion of how many giraffe species there are has only continued it.

Science Papers Examine Factors Shaping SARS-CoV-2 Spread, Give Insight Into Bacterial Evolution

In Science this week: genomic analysis points to role of human behavior in SARS-CoV-2 spread, and more.