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Recent Clinical Sequencing Papers of Note: Aug 27, 2014


Single-molecule long read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia.
Toma I, Siegel MO, Keiser J, Yakovleva A, et al.
J Clin Microbiol. 2014 Aug 20. [Epub ahead of print]

ENAM mutations with incomplete penetrance.
Seymen F, Lee KE, Koruyucu M, Gencay K, et al.
J Dent Res. 2014 Aug 20. [Epub ahead of print]

OptiType: precision HLA typing from next-generation sequencing data.
Szolek A, Schubert B, Mohr C, Sturm M, et al.
Bioinformatics. 2014 Aug 20. [Epub ahead of print]

Novel microdeletion in LOR causing autosomal dominant Loricrin keratoderma.
Kinsler VA, Drury S, Khan A, Waelchli R, et al.
Br J Dermatol. 2014 Aug 21. [Epub ahead of print]

A Japanese SCA5 family with a novel three-nucleotide in-frame deletion mutation in the SPTBN2 gene: a clinical and genetic study.
Wang Y, Koh K, Miwa M, Yamashiro N, et al.
J Hum Genet. 2014 Aug 21. [Epub ahead of print]

DYT16 revisited: Exome sequencing identifies PRKRA mutations in a European dystonia family.
Zech M, Castrop F, Schormair B, Jochim A, et al.
Mov Disord. 2014 Aug 20. [Epub ahead of print]

Personalized pharmacogenomics profiling using whole-genome sequencing.
Mizzi C, Peters B, Mitropoulou C, Mitropoulos K, et al.
Pharmacogenomics. 2014 Jun;15(9):1223-34.

Somatic mutations in cerebral cortical malformations.
Jamuar SS, Lam AT, Kircher M, D'Gama AM, et al.
N Engl J Med. 2014 Aug 21;371(8):733-743.
(See our coverage of this paper here.)

Similar prevalence of low-abundance drug-resistant variants in treatment-naive patients with genotype 1a and 1b hepatitis C virus infections as determined by ultradeep pyrosequencing.
Margeridon-Thermet S, Le Pogam S, Li L, Liu TF, et al.
PLOS One. 2014 Aug 20;9(8):e105569.

A missense variant of the ATP1A2 gene is associated with a novel phenotype of progressive sensorineural hearing loss associated with migraine.
Oh SK, Baek JI, Weigand KM, Venselaar H, et al.
Eur J Hum Genet. 2014 Aug 20. [Epub ahead of print]

Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome.
Kuechler A, Zink AM, Wieland T, Lüdecke HJ, et al.
Eur J Hum Genet. 2014 Aug 20. [Epub ahead of print]

Whole exome sequencing in early-onset cerebral SLE identifies a pathogenic variant in TREX1.
Ellyard JI, Jerjen R, Martin JL, Lee A, et al.
Arthritis Rheumatol. 2014 Aug 19. [Epub ahead of print]

Comprehensive next-generation sequencing analyses of hypoparathyroidism: identification of novel GCM2 mutations.
Mitsui T, Narumi S, Inokuchi M, Nagasaki K, et al.
J Clin Endocrinol Metab. 2014 Aug 19 [Epub ahead of print]

Assessment of EGFR mutations in circulating tumor cell preparations from NSCLC patients by next generation sequencing: toward a real-time liquid biopsy for treatment.
Marchetti A, Del Grammastro M, Felicioni L, Malatesta S, et al.
PLOS One. 2014 Aug 19;9(8):e103883.

Genetic testing in hereditary breast and ovarian cancer using massive parallel sequencing.
Ruiz A, Llort G, Yagüe C, Baena N, et al.
Biomed Res Int. 2014;2014:542541.

RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas.
Bao ZS, Chen HM, Yang MY, Zhang CB, et al.
Genome Res. 2014 Aug 18. [Epub ahead of print]

The genomic landscape of hepatoblastoma and their progenies with HCC-like features.
Eichenmüller M, Trippel F, Kreuder M, Beck A, et al.
J Hepatol. 2014 Aug 15. [Epub ahead of print]

Next-generation sequencing is a credible strategy for blood group genotyping.
Fichou Y, Audrézet MP, Guéguen P, Le Maréchal C, Férec C.
Br J Haematol. 2014 Aug 19. [Epub ahead of print]

Exome sequencing in the clinical diagnosis of sporadic or familial cerebellar ataxia.
Fogel BL, Lee H, Deignan JL, Strom SP, et al.
JAMA Neurol. 2014 Aug 18. [Epub ahead of print]

Evaluation of exome sequencing to estimate tumor burden in plasma.
Klevebring D, Neiman M, Sundling S, Eriksson L, et al.
PLOS One. 2014 Aug 18;9(8):e104417.

Mutation screening of retinal dystrophy patients by targeted capture from tagged pooled DNAs and next generation sequencing.
Watson CM, El-Asrag M, Parry DA, Morgan JE, et al.
PLOS One. 2014 Aug 18;9(8):e104281.

Elevated levels of circulating DNA in cardiovascular disease patients: metagenomic profiling of microbiome in the circulation.
Dinakaran V, Rathinavel A, Pushpanathan M, Sivakumar R, et al.
PLOS One. 2014 Aug 18;9(8):e105221.

Targeted next-generation sequencing reveals novel USH2A mutations associated with diverse disease phenotypes: implications for clinical and molecular diagnosis.
Chen X, Sheng X, Liu X, Li H, et al.
PLOS One. 2014 Aug 18;9(8):e105439.

Next-generation sequencing of colorectal cancers in Chinese: identification of a recurrent frame-shift and gain-of-function indel mutation in the TFDP1 gene.
Chen C, Liu J, Zhou F, Sun J, et al.
OMICS. 2014 Aug 18. [Epub ahead of print]

A human immunodeficiency caused by mutations in the PIK3R1 gene.
Deau MC, Heurtier L, Frange P, Suarez F, et al.
J Clin Invest. 2014 Aug 18. [Epub ahead of print]

Haplotype counting by next-generation sequencing for ultrasensitive human DNA detection.
Debeljak M, Freed DN, Welch JA, Haley L, et al.
J Mol Diagn. 2014 Sep;16(5):495-503.

Mutations in NOTCH1 cause Adams-Oliver syndrome.
Stittrich AB, Lehman A, Bodian DL, Ashworth J, et al.
Am J Hum Genet. 2014 Aug 12. [Epub ahead of print]

Characterizing genetic variation of adrenergic signalling pathways in Takotsubo (stress) cardiomyopathy exomes.
Goodloe AH, Evans JM, Middha S, Prasad A, Olson TM.
Eur J Heart Fail. 2014 Aug 8. [Epub ahead of print]

Malignant effects of multiple rare variants in sarcomere genes on the prognosis of patients with hypertrophic cardiomyopathy.
Wang J, Wang Y, Zou Y, Sun K, et al.
Eur J Heart Fail. 2014 Jul 31. [Epub ahead of print]

Clinical whole exome sequencing in child neurology practice.
Srivastava S, Cohen JS, Vernon H, Barañano K, et al.
Ann Neurol. 2014 Aug 18. [Epub ahead of print]
(See our coverage of this paper here.)

Hypoxic signature of microRNAs in glioblastoma: insights from small RNA deep sequencing.
Agrawal R, Pandey P, Jha P, Dwivedi V, et al.
BMC Genomics. 2014 Aug 17;15(1):686.

The Scan

Billions for Antivirals

The US is putting $3.2 billion toward a program to develop antivirals to treat COVID-19 in its early stages, the Wall Street Journal reports.

NFT of the Web

Tim Berners-Lee, who developed the World Wide Web, is auctioning its original source code as a non-fungible token, Reuters reports.

23andMe on the Nasdaq

23andMe's shares rose more than 20 percent following its merger with a special purpose acquisition company, as GenomeWeb has reported.

Science Papers Present GWAS of Brain Structure, System for Controlled Gene Transfer

In Science this week: genome-wide association study ties variants to white matter stricture in the brain, and more.