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This Week in Genome Research: Jul 20, 2016

To uncover the cause of sudden death in a cohort of 350 infants and young children, investigators from Baylor College of Medicine and the Harris County Institute of Forensic Sciences turned to a custom exon capture array targeting some five dozen genes coupled with next-generation sequencing. The genes targeted were selected because of their involvement in diseases — both cardiac and non-cardiac diseases — linked to sudden death. As they report in Genome Research, the investigators found likely pathogenic variants in 13 individuals. Since testing cost about $600, the researchers say such a molecular autopsy approach could be cost-effective to aid in sudden death investigations in Harris County, though they note that the low yield may limit its cost-effectiveness.

A team of Spanish researchers reports that methylation at sub-telomeric regions controls telomere length homeostasis. The group analyzed genome-wide methylation levels in Arabidopsis thaliana from a number of bisulfite sequencing studies and gauged the methylation status of plant telomeres. They found that studies that were less efficient at producing C-rich telomeric strands had higher levels of telomeric DNA methylation, a pattern that they say held in mitochondrial DNA as well, but that was likely due to technical limitations. Instead, based on studies of high telomeric C-rich strand production efficiencies, the team found that Arabidopsis telomeres aren't actually methylated, which they confirmed through an enzyme analysis. This, in combination with other data, suggests to the researchers that sub-telomeric region methylation controls telomere length homeostasis.

A trio from the Universidade Federal do Rio de Janeiro developed a software tool to automatically construct anonymous loci and anchor loci datasets from genomic sequence data for phylogenetic analysis. As they report in Genome Research, they tested their approach by applying it to the hominoid lineage of humans, chimpanzees, gorillas, and orangutans for which complete genomes and phylogenetic analyses are available. Their software tool yielded a dataset of 292 ALs in about three hours and presented a picture of hominoid evolution that was in agreement with previous studies.