In this week's Nature, an international team of researchers presents the sequence of the barley genome. Though barley is one of the first grains to be cultivated, its genome has been difficult to sequence due to features such as repetitive elements and large pericentromeric regions almost entirely devoid of meiotic recombination. By combining shotgun sequencing and a new technique called chromosome-scale scaffolding, the researchers were able to produce a high-quality reference barley genome. They also demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion. GenomeWeb has more on this here.
And in Nature Methods, investigators from the New York Genome Center describe a new method for genotyping and phasing short tandem repeats (STRs) from Illumina sequencing data. Called haplotype inference and phasing for STRs — or HipSTR — the freely available technique was used to perform a genome-wide analysis and validation of de novo STR mutations.
Finally, in Nature Genetics, a multi-institute research group presents a study demonstrating that the genomic effects of aberrant DNA repair processes can be used to stratify ovarian cancer histotypes. In their analysis of 133 ovarian tumors, the scientists found that "properties of the somatic genome on both the structural and point mutation scales are powerful, discriminant biomarkers between and within histotypes" for the disease. In particular, a pattern of foldback inversions associated with high-level amplifications could be used to stratify patients into prognostically significant groups, superseding BRCA mutation status and gene expression biomarkers. They findings, the investigators state, represent a new way to stratify ovarian cancer and may help clinicians tailor treatment regimens for patients. GenomeWeb also covers this here.