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Clinical Sequencing Papers of Note: May 17, 2011


Genetic diversity of near genome-wide hepatitis C virus sequences during chronic infection: evidence for protein structural conservation over time.
Li H, Hughes AL, Bano N, et al.
PLoS One. 2011 May 5;6(5):e19562.

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations
O'Roak BJ, Deriziotis P, Lee C, et al.
Nat Genet. 2011 May 15. [Epub ahead of print]

Recessive LAMC3 mutations cause malformations of occipital cortical development.
Barak T, Kwan KY, Louvi A, et al.
Nat Genet. 2011 May 15. [Epub ahead of print]

Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing.
Kannan K, Wang L, Wang J, Ittmann MM, Li W, Yen L.
Proc Natl Acad Sci U S A. 2011 May 12. [Epub ahead of print]

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.
Daumer M, Kaiser R, Klein R, Lengauer T, Thiele B, Thielen A.
BMC Med Inform Decis Mak. 2011 May 13;11(1):30.

Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies.
Parisi F, Ariyan S, Narayan D, et al.
BMC Genomics. 2011 May 11;12(1):230.

Complete exon sequencing of all known Usher syndrome genes greatly improves molecular diagnosis.
Bonnet C, Grati M, Marlin S, et al.
Orphanet J Rare Dis. 2011 May 11;6(1):21.

A complete deficiency of hyaluronoglucosaminidase 1 (HYAL1) presenting as familial juvenile idiopathic arthritis.
Imundo L, Leduc CA, Guha S, et al.
J Inherit Metab Dis. 2011 May 11. [Epub ahead of print]

Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder.
Frank RA, McRae AF, Pocklington AJ, et al.
PLoS One. 2011 Apr 29;6(4):e19011.

A comprehensive deep sequencing strategy for full-length genomes of influenza A.
Höper D, Hoffmann B, Beer M.
PLoS One. 2011 Apr 29;6(4):e19075.

Exome sequencing reveals germline NPAT mutation as a candidate risk factor for Hodgkin lymphoma.
Saarinen S, Aavikko M, Aittomäki K, et al.
Blood. 2011 May 11. [Epub ahead of print]

Development of a next-generation sequencing platform for retinal dystrophies, with LCA and RP as proof of concept.
Coppieters F, De Baere E, Leroy B.
Bull Soc Belge Ophtalmol. 2011;(317):59-60.

Identification of novel disease gene for primary congenital glaucoma (PCG) through homozygosity mapping and next-generation sequencing.
Verdin H, De Baere E, Kestelyn P.
Bull Soc Belge Ophtalmol. 2011;(317):49-50.

Transplantation monitoring by plasma DNA sequencing.
Lo YM.
Clin Chem. 2011 May 12. [Epub ahead of print]

Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy.
Hornsey M, Loman N, Wareham DW, et al.
J Antimicrob Chemother. 2011 May 12. [Epub ahead of print]

Gain-of-function mutations of ARHGAP31, a Cdc42/Rac1 GTPase regulator, cause syndromic cutis aplasia and limb anomalies.
Southgate L, Machado RD, Snape KM, et al.
Am J Hum Genet. 2011 May 13;88(5):574-85.

Characterization of fecal microbial communities in patients with liver cirrhosis.
Chen Y, Yang F, Lu H, Wang B, Chen Y, Lei D, Wang Y, Zhu B, Li L.
Hepatology. 2011 May 13. doi: 10.1002/hep.24423. [Epub ahead of print]

A clinical perspective on ethical issues in genetic testing.
Sijmons RH, Van Langen IM, Sijmons JG.
Account Res. 2011 May;18(3):148-62.

A variable region within the genome of Streptococcus pneumoniae contributes to strain-strain variation in virulence.
Harvey RM, Stroeher UH, Ogunniyi AD, Smith-Vaughan HC, Leach AJ, Paton JC.
PLoS One. 2011 May 5;6(5):e19650.

Benchmarking of mutation diagnostics in clinical lung cancer specimens.
Querings S, Altmüller J, Ansén S, et al.
PLoS One. 2011 May 5;6(5):e19601.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.