Shendure Team Finds Subassembly Technique Improves Accuracy of Short-Read Sequencing

January 19, 2010

The method uses tag sequences to recognize groups of short reads that are derived from the same larger fragment during library construction, and could be particularly useful for de novo genome assembly and metagenome sequencing, the authors reported.

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Chromosome-Scale Selective Sweeps and Genomic Diversity in C. elegans
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Researchers at Princeton University and elsewhere discuss the effects of chromosome-scale selective sweeps on genomic diversity in Caenorhabditis elegans. Taking a high-throughput selective sequencing approach on a collection of 200 wild C. elegans strains, the team found that the nematode's "genome variation is dominated by a set of commonly shared haplotypes on four of its six chromosomes, each spanning many megabases." Further, the team reports on its population genetic modeling experiments, which showed that "this pattern was generated by chromosome-scale selective sweeps that have reduced variation worldwide; at least one of these sweeps probably occurred in the last few hundred years," it writes.

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A team led by investigators at the University of Chicago this week report their use of a "Bayesian hierarchical model to estimate the enrichment of eQTLs [expression quantitative trait loci] in a wide variety of regulatory annotations" derived from 1,000 Genomes Project data. "We find that [approximately] 40 percent of eQTLs occur in open chromatin, and that they are particularly enriched in transcription factor binding sites, suggesting that many directly impact protein-DNA interactions," the authors write.
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