Baylor College of Medicine's Richard Gibbs and his colleagues report in Genome Biology that regions of the genome located outside of the consensus coding DNA sequence don't perform as efficiently in sequence capture experiments as those within that consensus region. The group designed new capture reagents to expand the targeted sequences, and those reagents allow it to ascertain the "relative 'capture-ability' of subregions of the genome." The team found that regions outside the consensus coding DNA sequence "almost uniformly demonstrated decreased capture-ability, as measured by average target coverage, when compared to the CCDS regions."
Daehwan Kim and Steven Salzberg describe using TopHat-Fusion, an updated version of the RNA-seq aligner TopHat, to uncover fusion gene products in RNA-seq data from breast and prostate cancer cell lines. "In experiments using multiple cell lines from previous studies, TopHatFusion identified 34 of 38 previously known fusions," Kim and Salzberg write. "It also found 61 fusion genes not previously reported in those data, each of which had solid support from multiple reads or pairs of reads." The open-source software is available at SourceForge.
The Broad Institute's Daniel Neafsey and his colleagues discuss a protocol to enrich pathogen DNA from clinical samples. The researchers adapted a solution hybrid selection approach and tested it using mixtures of human and Plasmodium falciparum DNA, in addition to clinical samples. After hybrid selection, they had approximately 40-fold enrichment of P. falciparum DNA. "We achieved significant enrichment of P. falciparum DNA, to a level that allowed us to conduct whole genome sequencing on samples which otherwise would have been prohibitively expensive to sequence," they write.
Finally, researchers in Germany report in Genome Biology the transcriptomes of planarian flatworms at different stages of head regeneration. Using more than 300 million paired-end reads, the researchers found 6,018 putative transcripts, and when focusing on the first three days of regeneration, they identified temporal synexpression classes and genes that were induced shortly after injury. "We highlighted differentially regulated genes, as well as clusters of genes with similar gene expression dynamics as a starting point for further investigations," they say. "Finally, we demonstrated that smed-runtlike1 is required for eye regeneration as a proof of principle that our approach allows for the identification of genes that are functionally relevant during planarian head regeneration."