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Last Week's Clinical Sequencing Papers of Note: Feb 5, 2014


Adenylate cyclase 1 (ADCY1) mutations cause recessive hearing impairment in humans and defects in hair cell function and hearing in zebrafish.
Santos-Cortez RL, Lee K, Giese AP, Ansar M, et al.
Hum Mol Genet. 2014 Jan 29. [Epub ahead of print]

Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders.
Novarino G, Fenstermaker AG, Zaki MS, Hofree M, et al.
Science. 2014 Jan 31;343(6170):506-11.

A generalized genetic random field method for the genetic association analysis of sequencing data.
Li M, He Z, Zhang M, Zhan X, et al.
Genet Epidemiol. 2014 Jan 30. [Epub ahead of print]

Single-cell genetic analysis reveals the composition of initiating clones and phylogenetic patterns of branching and parallel evolution in myeloma.
Melchor L, Brioli A, Wardell CP, Murison A, et al.
Leukemia. 2014 Jan 13. [Epub ahead of print]

The utility of exome sequencing for genetic diagnosis in a familial microcephaly epilepsy syndrome.
McDonell LM, Warman Chardon J, Schwartzentruber J, Foster D, et al.
BMC Neurol. 2014 Jan 31;14(1):22.

Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis.
Lim YW, Evangelista JS 3rd, Schmieder R, Bailey B, et al.
J Clin Microbiol. 2014 Feb;52(2):425-37.

Patient-specific induced-pluripotent stem cells derived cardiomyocytes recapitulate the pathogenic phenotypes of dilated cardiomyopathy due to a novel DES mutation identified by whole exome sequencing.
Tse HF, Ho JC, Choi SW, Butler AW, et al.
Hum Mol Genet. 2014 Jan 29. [Epub ahead of print]

Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound.
Carss KJ, Hillman SC, Parthiban V, McMullan DJ, et al.
Hum Mol Genet. 2014 Jan 29. [Epub ahead of print]

Comprehensive molecular characterization of urothelial bladder carcinoma.
The Cancer Genome Atlas Research Network, Weinstein JN, Akbani R, et al.
Nature. 2014 Jan 29. [Epub ahead of print]

Evaluation of a target region capture sequencing platform using monogenic diabetes as a study-model.
Gao R, Liu Y, Gjesing AP, Hollensted M, et al.
BMC Genet. 2014 Jan 29;15(1):13.

Prevalence and evolution of low frequency HIV drug resistance mutations detected by ultra deep sequencing in patients experiencing first line antiretroviral therapy failure.
Vandenhende MA, Bellecave P, Recordon-Pinson P, Reigadas S, et al.
PLOS One. 2014 Jan 27;9(1):e86771.

Evidence for autosomal recessive inheritance in SPG3A caused by homozygosity for a novel ATL1 missense mutation.
Khan TN, Klar J, Tariq M, Anjum Baig S, et al.
Eur J Hum Genet. 2014 Jan 29. [Epub ahead of print]

Exome analysis resolves differential diagnosis of familial kidney disease and uncovers a potential confounding variant.
Gibson J, Gilbert RD, Bunyan DJ, Angus EM, et al.
Genet Res (Camb). 2014 Jan 28:1-9.

High prevalence of GPRC5A germline mutations in BRCA1-mutant breast cancer patients.
Sokolenko AP, Bulanova DR, Iyevleva AG, Aleksakhina SN, et al.
Int J Cancer. 2013 Oct 31. [Epub ahead of print]

Whole-genome sequencing identifies genomic heterogeneity at a nucleotide and chromosomal level in bladder cancer.
Morrison CD, Liu P, Woloszynska-Read A, Zhang J, et al.
Proc Natl Acad Sci U S A. 2014 Jan 27. [Epub ahead of print]

CD74-NRG1 fusions in lung adenocarcinoma.
Thomas RK, Fernandez-Cuesta L, Plenker D, Osada H, et al.
Cancer Discov. 2014 Jan 27. [Epub ahead of print]

Sensitive deep sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism.
Gibson RM, Meyer AM, Winner D, Archer J, et al.
Antimicrob Agents Chemother. 2014 Jan 27. [Epub ahead of print]

A novel recurrent mutation in ATP1A3 causes CAPOS syndrome.
Demos MK, van Karnebeek CD, Ross CJ, Adam S, et al.
Orphanet J Rare Dis. 2014 Jan 28;9(1):15.

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants.
Brooks B, Firek BA, Miller CS, Sharon I, et al.
Microbiome. 2014 Jan 28;2(1):1.

Identification of rare DNA sequence variants in high-risk autism families and their prevalence in a large case/control population.
Matsunami N, Hensel CH, Baird L, Stevens J, et al.
Mol Autism. 2014 Jan 27;5(1):5.

Human liver cell trafficking mutants: characterization and whole exome sequencing.
Yuan F, Snapp EL, Novikoff PM, Suadicani SO, et al.
PLOS One. 2014 Jan 23;9(1):e87043.

Somatic mutaome profile in human cancer tissues.
Kim N, Hong Y, Kwon D, Yoon S.
Genomics Inform. 2013 Dec;11(4):239-44.

Identification of low-frequency and rare sequence variants associated with elevated or reduced risk of type 2 diabetes.
Steinthorsdottir V, Thorleifsson G, Sulem P, Helgason H, et al.
Nat Genet. 2014 Jan 26. [Epub ahead of print]

Clinical whole-genome sequencing in severe early-onset epilepsy reveals new genes and improves molecular diagnosis.
Martin HC, Kim GE, Pagnamenta AT, Murakami Y, et al.
Hum Mol Genet. 2014 Jan 25. [Epub ahead of print]

A polygenic burden of rare disruptive mutations in schizophrenia.
Purcell SM, Moran JL, Fromer M, Ruderfer D, et al.
Nature. 2014 Jan 22. [Epub ahead of print]

Diagnosis and molecular basis of mitochondrial respiratory chain disorders: Exome sequencing for disease gene identification.
Ohtake A, Murayama K, Mori M, Harashima H, et al.
Biochim Biophys Acta. 2014 Jan 23. [Epub ahead of print]

Decoding complex patterns of genomic rearrangement in hepatocellular carcinoma.
Fernandez-Banet J, Lee NP, Chan KT, Gao H, et al.
Genomics. 2014 Jan 21. [Epub ahead of print]

A founder mutation in PET100 causes isolated complex IV deficiency in Lebanese individuals with Leigh syndrome.
Lim SC, Smith KR, Stroud DA, Compton AG, et al.
Am J Hum Genet. 2014 Jan 21. [Epub ahead of print]

Exome sequencing identifies a novel variant in ACTC1 associated with familial atrial septal defect.
Greenway SC, McLeod R, Hume S, Roslin NM, et al.
Can J Cardiol. 2014 Feb;30(2):181-7.

Phenotypic spectrum of eleven patients and five novel MTFMT mutations identified by exome sequencing and candidate gene screening.
Haack TB, Gorza M, Danhauser K, Mayr JA, et al.
Mol Genet Metab. 2013 Dec 25. [Epub ahead of print]

Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study.
Bryant JM, Harris SR, Parkhill J, Dawson R, et al.
Lancet Respir Med. 2013 Dec;1(10):786-92.

Clinical and pathological heterogeneity of a congenital disorder of glycosylation manifesting as a myasthenic/myopathic syndrome.
Monies DM, Al-Hindi HN, Al-Muhaizea MA, Jaroudi DJ, et al.
Neuromuscul Disord. 2014 Jan 4. [Epub ahead of print]

HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies in Saudis using next generation sequencing technique.
Hajeer AH, Al Balwi MA, Aytül Uyar F, Alhaidan Y, et al.
Tissue Antigens. 2013 Oct;82(4):252-8.

Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing.
Lange V, Böhme I, Hofmann J, Lang K, et al.
BMC Genomics. 2014 Jan 24;15(1):63.

Using single cell sequencing data to model the evolutionary history of a tumor.
Kim KI, Simon R.
BMC Bioinformatics. 2014 Jan 24;15(1):27.