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This Week in Genome Research: Jan 8, 2014

Researchers from Saudi Arabia and Egypt describe a form of primordial dwarfism stemming from truncating mutations affecting a gene called CRIPT. The mutations were detected through the team's exome sequencing-based analysis of 16 individuals with primary dwarfism. Two of those individuals carried homozygous mutations that abbreviated CRIPT, while other affected individuals in the study had mutations affecting genes implicated in primary dwarfism in the past. The work also revealed more tenuous ties between primary dwarfism and mutations in the XRCC4 gene, as well a locus with apparent links to a dwarfism-related condition known as Seckel syndrome.

A team from the University of California, San Diego, and the Moores Cancer Center in La Jolla present an approach called "Amplification of Breakpoints" (AmBre) for finding the breakpoints of somatic structural variants in tumor samples. The AmBre method involves PCR-based breakpoint amplification followed by single-molecule real time sequencing on the Pacific Biosciences RS instrument and a computational analysis, the study authors note, and can be applied to heterogeneous samples containing tumor and germline DNA. In its proof-of-principle experiments, the group used it to detect the breakpoint for a RUNX1-RUNX1T1 translocation in acute myeloid leukemia cell line and breakpoints coinciding with CDKN2 deletions in several other cancer cell lines.

Researchers from Aarhus University, the University of Copenhagen, and elsewhere tapped into the natural characteristics of aged DNA to detect cytosine methylation and identify nucleosome occupancy sites in ancient human DNA samples. Taking advantage of read depth fluctuation and substitution events in sequence data generated for ancient samples, the team picked up nucleosome and methylation patterns in a 4,000-year-old samples from a Paleo-Eskimo belonging to the Saqqaq culture. Those profiles corresponded with nucleosome and methylation characteristics tested using other approaches, study authors note, suggesting the methods can detect authentic epigenetic information. Our sister publication In Sequence has more on the study, here.