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This Week in Genome Research: Jul 24, 2014

An international team led by investigators in the UK and Saudi Arabia used genome sequencing to characterize apicomplexan protozoan pests in the Eimeria genus that cause a deleterious intestinal disease known as coccidiosis in domestic chickens. The researchers sequenced and annotated the genomes of seven coccidiosis-causing Eimeria species, uncovering genomic features behind the parasites' features and interactions with their hosts. The analysis pointed to notable genomic features, too. For instance, the genomes contained sequences coding for a protein set that's exceptionally homopolymer repeat-rich and revealed retrotransposons in the Eimeria genomes (a first amongst apicomplexan protozoans).

Japanese researchers describe mutations they detected in a form of malignant bone tumor called chondrosarcoma and a related, non-cancerous condition called enchondroma. Through whole-genome sequencing on matched tumor and normal samples from 10 individuals with chondrosarcoma, the team saw several recurrent somatic mutations and structural changes in the chondrosarcomas, including frequent alterations affecting the skeletal development-related gene COL2A1 and genes coding for epigenetic regulators and activin signaling pathway members. The study's authors saw similar mutations when they did targeted sequencing on chondrosarcoma and enchondroma samples, suggesting similar epigenetic and genetic changes may be behind both conditions.

Using Caenorhabditis elegans as a model organism, a UK-led team tracked the mutational processes that occurred over time in 17 populations of worms with defective DNA repair. The team did whole-genome sequencing on 183 worms from the populations that were either grown over many generations or treated with carcinogenic compounds. Results from the study revealed the baseline mutation rate in the worms, which remained unaltered over time, and highlighted the mutational signatures associated with various DNA damaging agents or events. From the patterns detected so far, the study's authors argue that "experimental model systems combined with genome sequencing can recapture and mechanistically explain mutational signatures associated with human disease."

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.