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Genomics in the Journals: May 9, 2013

NEW YORK (GenomeWeb News) – In Nature Methods, researchers from Pacific Biosciences, the US Department of Energy's Joint Genome Institute, and the University of Washington outlined an automated, non-hybrid method for assembling microbial genomes de novo using single molecule, real-time sequence data generated using the PacBio RS platform.

For the study, the group provided data for three microbial genomes — Escherichia coli, Meiothermus ruber, and Pedobacter heparinus — assembled using the hierarchical genome-assembly process, or HGAP, demonstrating that the resulting high quality assemblies were nearly identical to finished reference genomes for the bugs.

"Our approach is currently capable of producing near-finished, high quality genomes in terms of contiguity and error rate," PacBio CSO Jonas Korlach, the study's senior author, and colleagues wrote, "and it should thereby facilitate closing of the large gap that currently exists between drafted and finished genomes."

The method also proved useful for doing de novo assembly of PacBio sequence data for a bacterial artificial chromosome corresponding to some 175,000 bases of sequence from the human chromosome 15. In Sequence described the HGAP approach in more detail late last year.


Researchers from Germany and the Netherlands did two genome-wide association studies and a meta-analysis in their effort to find genetic variants affecting individuals' susceptibility to infection by the stomach ulcer-causing bacterial species Helicobacter pylori — work that they described in the Journal of the American Medical Association.

Results from the analyses — which involved nearly 11,000 individuals whose blood samples were positive or negative for antibodies targeting H. pylori — revealed two main loci with ties to infection susceptibility.

One of the loci turned up at the FCGR2A locus on chromosome 1, researchers reported. The other fell near a toll-like receptor region on chromosome 4 that contained several genes. Among them: TLR1, a gene whose expression coincided with the version of H. pylori-associated SNP present on chromosome 4 and with H. pylori infection status.


A mosaic somatic mutation is associated with both port-wine stains and Sturge-Weber syndrome, researchers from Johns Hopkins University reported in the New England Journal of Medicine.

Sturge-Weber syndrome is marked by such facial birthmarks as well as by glaucoma, seizures, and intellectual disability. Researchers had theorized that port-wine stains, which occur in about one in 20,000 to 50,000 newborns — most of whom are otherwise healthy — and Sturge-Weber syndrome share a common cause, with the difference in manifestation due to when and where the somatic mutation arose during development.

In this study, researchers performed whole-genome sequencing of affected and normal tissue of people with Sturge-Weber syndrome. By functionally annotating and ranking the thousand-odd somatic SNPs they found, they homed in on one somatic non-synonymous SNV in GNAQ that was present only in affected samples.

Further, using amplicon sequencing and SNaPshot assays, the researchers found this SNV in 88 percent of a further 26 participants with Sturge-Weber syndrome and in 92 percent of participants with non-syndromic port-wine stains, though not in participants with an unrelated cerebrovascular malformation or in any other controls.

"Now that we know the underlying genetic mutation responsible for both conditions, we're hopeful that we can move quickly towards targeted therapies, offering families the promise of new treatments for the first time," Hopkins' Anne Comi, a co-senior author on the study, said in a statement.


Uropathogenic bacteria causing recurrent urinary tract infections in women thrive equally well in the gut and the urinary tract, according to a Science Translational Medicine study.

Researchers from Washington University in St. Louis examined 45 uropathogenic Escherichia coli strains isolated from the feces and urine of four women with recurrent UTIs, as bacteria are thought to migrate from the gut to the bladder to cause infection. Through multi-locus sequence typing and whole genome sequencing, the researchers found two patterns: Half the women had stable and clonal E. coli populations at both body sites during different bouts of the disease, while the other half exhibited shifts in the dominant E. coli strains at the two body sites during different UTI episodes.

Through in vivo competition studies in mice of E. coli obtained from one of the women with different gut and urinary tract bacteria, the researchers found that that the strain had increased fitness in both the gut and urinary tract, as compared to previous E. coli strains that had infected that patient. Improved fitness, the researchers further noted, was associated with changes in gene repertoire and metabolism.

"Thus, UPEC appear capable of persisting in both the gut and urinary tract without a fitness trade-off, emphasizing the need to widen our consideration of potential reservoirs for strains causing recurrent UTI," the researchers added.


Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

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