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Nobody's Perfect

A non-genomics researcher mentioned to Mike the Mad Biologist that there was a lot of criticism of the E. coli 104:H4 outbreak sequences, and Mike writes on his blog that he wasn't sure what his colleague was referring to. Then he realized that assessments of the quality of the sequence data could look like criticism of the science to an outsider, even when it's not. With a high-quality sequence, Mike writes that the error rate could be between 1 in 100,000 and 1 in 1,000,000 per base. "That sounds good until you realize that a typical E. coli genome is around five million bases long," Mike says, later adding that "no genome sequence, even a finished one, is perfect. But we can still do good science, even as we recognize the flaws in the data."

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.