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This Week in Nucleic Acids Research: May 10, 2017

McGill University researchers report on a web-based resource called MicrobiomeAnalyst that's intended to help out investigators doing meta-analyses, statistical investigations, and visualization on large microbiome sequence datasets. The tool includes modules focused on microbial markers such as 16S ribosomal RNA gene sequences, shotgun sequence data, taxon set enrichment, and visualization alongside publicly available reference sequence data, the team notes, and is intended for addressing everything from microbial diversity to comparative analyses.

A team from Spain presents a tool for profiling potential driver genes in personal cancer genomes. The tool, known as Cancer PanorOmics, is designed to put somatic mutations, copy number changes, or expression shifts in personal cancer genomes in context by analyzing them in combination with available sequence, clinical, and other data for almost 20,700 samples from more than two dozen tumor types, the authors explain. They propose that the "'PanorOmic' molecular view of individual tumors, together with the appropriate genetic counseling and medical advice, should contribute to the identification of actionable alterations, ultimately guiding the clinical decision-making process." 

Researchers from the UK, US, and Denmark describe a model for DNA degradation and preservation, based on available sequence data for 185 ancient samples  — spanning more than 150 humans, along with Neanderthals, mammoths, horses, polar bears, and ancient herbarium plant samples. To develop the model, the team considered cytosine deamination, DNA fragmentation, and other degradation features, in concert with sample age preservation-related environmental features such as temperature. Based on their results, the authors suggest that "fragmentation rapidly reaches a threshold, then subsequently slows" in ancient DNA, while "observed loss of DNA over time may be due to a bulk diffusion process in many cases."

The Scan

Genetic Ancestry of South America's Indigenous Mapuche Traced

Researchers in Current Biology analyzed genome-wide data from more than five dozen Mapuche individuals to better understand their genetic history.

Study Finds Variants Linked to Diverticular Disease, Presents Polygenic Score

A new study in Cell Genomics reports on more than 150 genetic variants associated with risk of diverticular disease.

Mild, Severe Psoriasis Marked by Different Molecular Features, Spatial Transcriptomic Analysis Finds

A spatial transcriptomics paper in Science Immunology finds differences in cell and signaling pathway activity between mild and severe psoriasis.

ChatGPT Does As Well As Humans Answering Genetics Questions, Study Finds

Researchers in the European Journal of Human Genetics had ChatGPT answer genetics-related questions, finding it was about 68 percent accurate, but sometimes gave different answers to the same question.