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This Week in Genome Biology: Oct 3, 2018

Chinese Academy of Sciences researchers map DNA methylation in dozens of soybean accessions, searching for epigenetic variants contributing to crop domestication and improvement. The team did whole-genome bisulfite sequencing and whole-genome resequencing on representatives from nine wild soybean, 12 landrace, and 24 cultivar groups, identifying more than 5,400 differentially methylated regions that appeared to correspond to soybean domestication and improvement. "Intriguingly," the authors write, "genes in the [differentially methylated regions] that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways."

A University of Tartu-led team explores genetic ancestry in more than a dozen populations speaking Uralic language family languages. Using array-based genotyping profiles for 135 individuals from 15 Uralic-speaking populations in Europe and Siberia, the researchers examined Eastern and Western Eurasian ancestry contributions in these groups. Comparing the individuals to one another and to other European populations, they saw genetic ties between the Uralic speakers and their geographic neighbors. Nevertheless, the authors note that "most of the Uralic speakers and some of their neighbors share a genetic component of possibly Siberian origin," consistent with some language spread by human migration. 

Researchers from the City University of New York and elsewhere report on results from a meta-analysis of transcriptomes in tumors from several colorectal cancer subtypes. The team brought together gene expression data for more than 3,700 colorectal cancer patients, but did not see strong evidence for well defined transcriptional subtypes in this large tumor set. Rather, the results point to "robust, continuously varying subtype scores" that seem to coincide with tumor stage, grade, location, survival patterns, and other features, the investigators report, suggesting that the transcriptional scores "better represent overall transcriptional activity than do discrete subtypes."

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.