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This Week in PLOS: Jul 21, 2014

As they report in PLOS One, the National Cancer Institute's Yves Pommier and colleagues from the US and Brazil brought together whole-exome sequence data with pharmacological response profiles for the NCI-60 collection, a set of publicly available cancer cell lines from nine tissues of origin. Along with almost 1,200 homozygous variants predicted to upend the function of resulting proteins, the exome sequencing experiments uncovered more than 2,500 genes with altered expression profiles in cancer lines compared to controls from the same tissue type. Moreover, the researchers identified more than 103,000 variants that seem to impact response to one or more of the nearly 20,000 compounds tested on the NCI-60 lines.

In PLOS Genetics, an international team led by investigators at the University of California, Los Angeles, and Stanford University highlights the coronary artery disease-related pathways and gene networks it identified using an integrative genomics approach. Using data for tens of thousands of cases and controls enrolled through GWAS performed by the CARDIoGRAM consortium or the Ottawa Heart Institute — together with available gene expression, pathway, and tissue-specific gene network data — the researchers saw signs of coronary artery disease contributions from lipid metabolism, immunity, and coagulation-related pathways, as well as networks of genes with poorly understood functions. "Our results suggest genetic influences on a diverse set of both known and novel biological processes that contribute to [coronary artery disease] risk," the study's authors say. "The key driver genes for these networks highlight potential novel targets for further mechanistic studies and therapeutic interventions."

Researchers from Brazil and the US did transcriptome sequencing on tissues taken during different stages of development in Anopheles aquasalis, a mosquito species known for carrying malaria in South and Central America. The team described results from its analysis of 419,000 complementary DNA reads in PLOS Neglected Tropical Diseases, noting that the mosquito appears to produce transcripts coding for proteins similar to those found in the related malaria-transmitting mosquito An. darlingi. The work also revealed transcripts that are specifically expressed during different stages of An. aquasalis development, as well as genes showing enhanced or diminished expression in female mosquitoes during blood feeding and digestion.

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.