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This Week in Genome Biology: May 17, 2017

Researchers from Switzerland, China, the US, and South Africa describe population dynamics for the tuberculosis-causing pathogen Mycobacterium tuberculosis over time within the same individuals. Using deep whole-genome sequencing, the team tracked within-host genetic patterns from M. tuberculosis isolates in sputum samples taken biweekly from a dozen individuals with tuberculosis over two months. Based on the patterns they saw, the study's authors note that "purifying selection constrains the evolutionary trajectory to resistance in effectively treated individuals," though "a continuous turnover of minor variants" in the isolates "could give rise to the emergence of drug resistance in cases of drug pressure weakening."

A Broad Institute-led team takes a look at longitudinal population dynamics related to artemisinin drug resistance in malaria-causing Plasmodium falciparum parasites in northwest Thailand. The researchers focused on 194 P. falciparum isolates from five sites in the region between 2001 and 2014, using retrospective whole-genome sequencing to get a look at alterations affecting the artemisinin resistance-related gene kelch13 and other sequences. From these data, they followed P. falciparum SNP frequency changes in kelch13 and beyond during this period, when there was a documented rise in artemisinin resistance.

Finally, investigators from Australia and China explore mapping precision in genome-wide association studies with whole-genome sequence data-centered simulations. Based on genome sequence data for more than 3,600 unrelated individuals, the team estimated that common variants picked out of past GWASs typically turned up within roughly 33,500 bases of variants considered causal for the condition in question, on average. "Our findings provide a benchmark to inform future design and development of fine-mapping experiments and technologies to pinpoint the causal variants at GWAS loci," the authors write.

The Scan

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.

Sequencing Analysis Examines Gene Regulatory Networks of Honeybee Soldier, Forager Brains

Researchers in Nature Ecology & Evolution find gene regulatory network differences between soldiers and foragers, suggesting bees can take on either role.

Analysis of Ashkenazi Jewish Cohort Uncovers New Genetic Loci Linked to Alzheimer's Disease

The study in Alzheimer's & Dementia highlighted known genes, but also novel ones with biological ties to Alzheimer's disease.

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.