In a method paper published online in Genome Biology this week, the University of Washington's Jay Shendure and his colleagues describe an approach for shotgun fragment library construction based on high-density in vitro transposition. When applied to the sequencing of a human genome, Shedure et al. say their method produced coverage biases "comparable with conventional protocols," though it is more efficient than other methods. In addition, the Washington team "[extends] its capabilities by developing protocols for sub-nanogram library construction, exome capture from 50 nanograms of input DNA, PCR-free and colony PCR library construction, and 96-plex sample indexing."
Amy Williams and her colleagues at MIT describe Hapi, "a new dynamic programming algorithm that ignores uninformative states and state transitions in order to efficiently compute minimum-recombinant and maximum likelihood haplotypes." Williams et al. applied Hapi to a data set containing information from 103 families and found that it performed "3.8-320 times faster than state-of-the-art algorithms," the team says.
The University of Maryland's David Kelley and Steven Salzberg, along with Cold Spring Harbor Laboratory's Michael Schatz, introduce an open-source software that works to "detect and correct errors in DNA sequencing reads." The package, dubbed Quake, uses a "maximum likelihood approach incorporating quality values and nucleotide specific miscall rates," the authors write. Quake is freely available online, here.
And in a recent paper published online in Genome Biology, an international research team describes its "systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing." Using a breast cancer and lymphoblast cell lines from the same individual, the researchers obtained exome and transcriptome sequence data and found "86 and 50 genes with allele specific expression events" in the respective cell lines. "Many of these genes identified by loss of heterozygosity and allele specific expression are known or putative tumor suppressor genes such as BRCA1, MSH3, and SETX, which participate in DNA repair pathways," the authors write.