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PLOS Papers on Pediatric Cancer Variants, Colombian TB Surveillance, Fasciola Reference Genome

In PLOS One, investigators at Brigham Young University and the University of Utah describe a strategy for flagging candidate common or rare variant risk contributors to pediatric cancer. The nuclear family-focused approach relies on germline whole-genome sequencing, genome phasing, variant filtering, and inheritance analyses, the team says, and they applied it to find affected children with benign low-grade astrocytoma, Wilms tumor, or Burkitt's lymphoma from three different nuclear families in proof-of-principle analyses. "For initial variant filtering, we used global minor allele frequencies, deleteriousness scores, and functional-impact annotations," the authors note, explaining that "we used genetic variation in the unaffected siblings as a guide to filter the remaining variants."

A team from Colombia looks at the feasibility of evaluating Mycobacterium tuberculosis features such as tuberculosis (TB) drug resistance with whole-genome sequencing (WGS). As they report in PLOS One, the researchers brought together genetic, phylogenetic, epidemiological, cell culture, drug response profiles, and other clues for clinical M. tuberculosis isolates collected in a Colombian town with particularly high levels TB levels, focusing on whole-genome-sequenced samples from half a dozen patients treated in 2020. "The present study is the first to provide information on the phylogenetic characteristics and the identification of predominant strains in Chinchiná, a municipality with a high incidence of TB" they say, noting that "our team showed that it is possible to add WGS results to the surveillance data without significant changes in the laboratory setup or considerable investments in computing power."

For a paper in PLOS Neglected Tropical Diseases, researchers from the Chinese Academy of Agricultural Sciences and elsewhere present a reference genome sequence for Fasciola gigantica, which can cause the liver condition fascioliasis. Using PacBio single-molecule long-reads, Illumina paired-end short reads, chromosome conformation capture sequencing, and other approaches, the team put together a 1.35 gigabase genome assembly spanning 10 pseudo-chromosomes, bringing in RNA sequencing data to identify more than 12,500 predicted protein-coding genes. With these and other data, the authors looked at the characteristics marking F. gigantica evolution, host interactions, and more. "[W]e found the evidence of transposon-mediated evolution … contributing to the speciation and adaptation of the Fasciola ancestors," they report, adding that "we identified F. gigantica specific gene duplications including 98 gene families and 3,300 protein-protein interactions between F. gigantica and the host in the small intestine and liver environment."

The Scan

Looking for Omicron

NPR reports that SARS-CoV-2 testing in the US has gotten better but also that some experts say more needs to be done to better track the Omicron variant.

Holmes Alleges Abuse

The Associated Press reports that Theranos' Elizabeth Holmes has testified at her wire fraud trial that her business and romantic partner abused her.

Bit More Diverse, But More to Do

While Black and Hispanic patients are more likely to participate in cancer clinical trials than previously, they are still underrepresented, according to US News & World Report.

PNAS Papers on Yeast Gene Silencing, Zika Virus Inhibition, Immunoglobulin Hypermutation

In PNAS this week: gene silencing in Saccharomyces cerevisiae, possible neuroprotective role for SHFL in a mouse model of Zika virus infection, and more.