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PLOS Papers on Y-Chromosome Sequencing, Blood Methylation Markers, CLL Mutations

In PLOS Genetics, a Belgian team led by investigators at KU Leuven presents a Y-chromosome-specific sequencing strategy for targeting informative Y-chromosome SNPs (Y-SNPs) and short tandem repeats (Y-STRs). The investigators' CSYseq method "simultaneously identifies slow mutating Y-SNPs as evolution markers and rapidly mutating Y-STRs as patrilineage markers," they say, noting that the CSYseq panel includes 202 "slow," "moderate," fast," and "rapid" mutating Y-STRs and more than 15,600 informative SNPs, including variants linked to more than 1,400 haplogroup subtypes. The authors applied the massively parallel sequencing approach to 130 male participants spanning nearly 1,300 generations across dozens of human pedigrees for their validation analyses. "The CSYseq is interesting for research on different time scales: to identify evolutionary ancestry, to find distant family, and to discriminate closely related males," they write, adding that the CSYseq panel "serves as a unique tool valuable for a wide range of genetic-genealogical applications in interdisciplinary research within evolutionary, population, molecular, medical, and forensic genetics."

A team from the University of Edinburgh, Sun Yat-Sen University, and Edinburgh BioQuarter examine ties between DNA methylation, smoking behavior, and body mass index (BMI) for another paper in PLOS Genetics. Using array-based genotyping and blood DNA methylation profiles for some 18,000 participants in the Generation Scotland study, together with self-reported smoking behavior data, the researchers analyzed genetic, environmental, and gene-by-environment patterns that were subsequently validated using UK Biobank data. Their results suggest that the inclusion of blood methylation profiles could bump up the BMI variation linked to smoking from around 2 percent to more than 20 percent, for example, while roughly half of BMI variation appeared to be related to genetic contributors. "This work highlights the potential of using biomarkers to proxy lifestyle measures and expand our knowledge on disease," they write, "and suggests that the environment may have long-term effects on our health through its impact on the methylation of disease-associated loci."

Investigators in Spain search for somatic gene mutations that may offer clues to patient outcomes in those with chronic lymphocytic leukemia (CLL) for a paper in PLOS One. The team did targeted deep sequencing on blood samples from 71 treatment-naïve individuals with progressive CLL who were participating in a clinical trial exploring the effects of fludarabine, cyclophosphamide, and rituximab (FCR)-based chemoimmunotherapy followed by three years of rituximab maintenance therapy, searching for outcome-related alterations in more than two dozen genes with recurrent alterations in past studies of the blood cancer. Among other results, the authors note that "[m]utations of most recurrent driver genes in CLL, except for the TP53 gene, do not seem to affect the sustained clinical response obtained with front-line FCR treatment followed by rituximab maintenance for three years in our cohort of patients."

The Scan

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