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This Week in Genome Research: Nov 12, 2014

University of Washington researchers present findings from an effort to characterize pathogenic forms of Escherichia coli found outside the intestine, such as in blood or urine samples. The team detected extensive genomic heterogeneity when it did whole-genome sequencing and de novo genome assembly on more than 300 isolates of extraintestinal, pathogenic E. coli, known as ExPEC, For instance, the bugs appeared to have distinct antibiotic resistance profiles and virulence features depending on what part of the body they infected, though investigators' subsequent epidemiological analyses pointed to a small number of lineages contributing to the ExPEC bloodstream infections considered.

A Washington University-led team introduces a single haplotype human genome assembly that was developed using DNA from a hydatidiform mole, a rare haploid mass that can form during pregnancy when sperm fertilizes a nucleus-free egg. Using Illumina and BAC-based sequence generated for the mole sample and information from the human reference genome, the researchers put together and started analyzing a draft genome assembly for the hydatidiform mole sample, which has also been sequenced with Pacific Biosciences single-molecule, real-time reads. Though some misassembled regions were identified in the new assembly, the study's authors note that the overall quality and contiguity of the assembly is high and is expected to help in the ongoing improvement of the reference genome.

The use of shallow whole-genome sequencing can accurately resolve copy number profiles in both fresh and formalin-fixed tissue samples provided particularly problematic parts of the genome are excluded from the analysis, according to a study by researchers in the Netherlands, Finland, and the US. The team described its QDNAseq analytical pipeline for copy number analysis on low-coverage genome sequences, which is designed to correct errors in the genome and exclude "blacklisted" regions.