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Last Week's Clinical Sequencing Papers of Note: Sep 7, 2011


Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion.
Bass AJ, Lawrence MS, Brace LE, et al.
Nat Genet. 2011 Sep 4. [Epub ahead of print]

Deep third variable sequencing for HIV type 1 tropism in treatment-naive patients: A reanalysis of the MERIT trial of maraviroc.
Swenson LC, Mo T, Dong WW, et al.
Clin Infect Dis. 2011 Oct;53(7):732-42.

'Sentinel' mutations in standard population sequencing can predict the presence of HIV-1 reverse transcriptase major mutations detectable only by ultra-deep pyrosequencing.
Alteri C, Santoro MM, Abbate I, et al.
J Antimicrob Chemother. 2011 Sep 2. [Epub ahead of print]

Rapid detection and subtyping of human influenza a viruses and reassortants by pyrosequencing.
Deng YM, Caldwell N, Barr IG.
PLoS One. 2011;6(8):e23400.

Homozygosity mapping and targeted genomic sequencing reveal the gene responsible for cerebellar hypoplasia and quadrupedal locomotion in a consanguineous kindred.
Gulsuner S, Tekinay AB, Doerschner K, et al.
Genome Res. 2011 Sep 1. [Epub ahead of print]

A general framework for detecting disease associations with rare variants in sequencing studies.
Lin DY, Tang ZZ.
Am J Hum Genet. 2011 Aug 30. [Epub ahead of print]

Identification of improved IL28B SNPs and haplotypes for prediction of drug response in treatment of hepatitis C using massively parallel sequencing in a cross-sectional European cohort.
Smith KR, Suppiah V, O'Connor K, et al.
Genome Med. 2011 Aug 31;3(8):57. [Epub ahead of print]

Direct sequencing and characterization of a clinical isolate of Epstein-Barr virus from nasopharyngeal carcinoma tissue using next-generation sequencing technology.
Liu P, Fang X, Feng Z, et al.
J Virol. 2011 Aug 31. [Epub ahead of print]

Challenges translating breast cancer gene signatures into the clinic.
Weigelt B, Pusztai L, Ashworth A, Reis-Filho JS.
Nat Rev Clin Oncol. 2011 Aug 30. [Epub ahead of print]

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.