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This Week in Genome Biology: Mar 22, 2017

An international team led by investigators in China and the Netherlands uncovers genes with apparent ties to Hirschsprung disease, a congenital condition characterized by altered enteric nervous system progenitor cell activity that leads to bowel obstruction. Through exome sequencing on two dozen individuals with Hirschsprung disease and their parents, the researchers detected 28 de novo mutations affecting 21 genes. While eight of the de novo mutations turned up in RET, a gene already implicated in Hirschsprung disease, their analysis and follow-up experiments also highlighted potential roles for genes such as NUP98 or DENND3 in enteric nervous system function.

Researchers from the US, Italy, Portugal, and the Netherlands explore structural variant patterns in the genomes of almost 700 individuals with autism spectrum disorder. The team used long-insert whole-genome sequencing to profile structural variants in 686 individuals with idiopathic ASD and three unrelated participants with other neurodevelopmental conditions. The search uncovered new and known structural variants from seven classes, affecting nearly 12,000 sites in the genome, along with instances of widespread chromosomal rearrangements associated with chromothripsis. The authors note that their results "provided an initial atlas of [structural variations] in the morbid germline that can be used as a benchmarking resource for future investigations."

A University of British Columbia-led team describes a computational strategy for defining cancer clones with complementary sequence data from bulk tumor samples and individual tumor cells subjected to single-cell analyses. The probabilistic statistical model, dubbed ddClone, is designed to "leverage the strengths of both sequencing methods for optimal computational inference of clonal genotypes and prevalences," the team notes. For its proof-of-principle study, the group applied ddClone to simulate real datasets, including a sample set comprised of genome sequence and single-cell genotyping data for 30 tumor xenograft lines developed from triple-negative breast cancer tumors.