Skip to main content
Premium Trial:

Request an Annual Quote

This Week in Genome Research: Dec 7, 2016

Researchers from Illumina, the Wellcome Trust Centre for Human Genetics, and the University of Oxford present a Platinum variant catalog, comprised of 5.4 million phased human variants, that was produced using genome sequence data for 17 individuals from a three-generation pedigree. The team analyzed deep whole-genome sequences for the individuals with a variety of algorithms, producing a phased variant set that includes 4.7 million SNPs and 0.7 million small insertions and deletions. It also delved into hundreds of thousands of single nucleotide variants that were picked up by multiple analytical methods, but did not fit with the broader haplotype transmission patterns, uncovering de novo variants and cell line mutations.

A team from the US and China profile histone modification patterns associated with poised gene enhancers in developing Drosophila fruit fly embryos. When they used RNA sequencing and chromatin immunoprecipitation sequencing experiments to map histone markers implicated in poised enhancer contexts as Drosophila embryos being forming a dorsal-ventral axis, the researchers found that these marks tended to turn up when enhancers are repressed during tissue patterning. The authors say their findings "suggest that, rather than serving exclusively as an intermediate step before future activation, the poised enhancer state may be a mark for spatial regulation during tissue patterning."

Finally, UK researchers discuss a combined algorithm strategy for upgrading fragmented short read animal genome assemblies. The team brought together algorithms for ordering and amalgamating sequence scaffolds into chromosomal fragments, verifying scaffolds by PCR, physically mapping sequences to chromosomes with help from bacterial artificial chromosome probes, and comparing sequences from related animals — an approach applied to improving the fragmented pigeon and peregrine falcon genomes. "The resulting chromosome level assemblies contain [more than 80 percent] of the genomes … and, in continuity are comparable to those obtained by combining the traditional sequencing and mapping techniques but require much less cost and resources."