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Recent Clinical Sequencing Papers of Note: Oct 29, 2014

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Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing.
Bittinger K, Charlson ES, Loy E, Shirley DJ, et al.
Genome Biol. 2014 Oct 25;15(10):487.


Recurrent ETNK1 mutations in atypical chronic myeloid leukemia.
Gambacorti-Passerini CB, Donadoni C, Parmiani A, Pirola A, et al.
Blood. 2014 Oct 24. [Epub ahead of print]


High-throughput profiling identifies clinically actionable mutations in salivary duct carcinoma.
Ku B, Jung H, Sun JM, Ko Y, et al.
J Transl Med. 2014 Oct 25;12(1):299.


Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.
Moncunill V, Gonzalez S, Beà S, Andrieux LO, et al.
Nat Biotechnol. 2014 Oct 26. [Epub ahead of print]


Summarizing polygenic risks for complex diseases in a clinical whole-genome report.
Kong SW, Lee IH, Leshchiner I, Krier J, et al.
Genet Med. 2014 Oct 23. [Epub ahead of print]


Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality.
Weng SL, Chiu CM, Lin FM, Huang WC, et al.
PLOS One. 2014 Oct 23;9(10):e110152.


Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing.
Lee MC, Lopez-Diaz FJ, Khan SY, Tariq MA, et al.
Proc Natl Acad Sci U S A. 2014 Oct 22. [Epub ahead of print]


Metagenomic analysis of viruses in feces from unsolved outbreaks of gastroenteritis in humans.
Moore NE, Wang J, Hewitt J, Croucher D, et al.
J Clin Microbiol. 2014 Oct 22. [Epub ahead of print]


Whole-genome sequencing of Burkholderia pseudomallei isolates from an unusual melioidosis case identifies a polyclonal infection with the same multilocus sequence type.
Price EP, Sarovich DS, Viberg L, Mayo M, et al.
J Clin Microbiol. 2014 Oct 22. [Epub ahead of print]


Disease-targeted sequencing of ion channel genes identifies de novo mutations in patients with non-familial Brugada syndrome.
Juang JM, Lu TP, Lai LC, Ho CC, et al.
Sci Rep. 2014 Oct 23;4:6733.


Feasibility of low-throughput next generation sequencing for germline DNA screening.
Sapari NS, Elahi E, Wu M, Loh M, et al.
Clin Chem. 2014 Oct 22. [Epub ahead of print]


Combined examination of sequence and copy number variations in human deafness genes improves diagnosis for cases of genetic deafness.
Ji H, Lu J, Wang J, Li H, Lin X.
BMC Ear Nose Throat Disord. 2014 Sep 10;14:9.


Mixed adenoneuroendocrine carcinomas (MANECs) of the gastrointestinal tract: targeted next generation sequencing suggests a monoclonal origin of the two components.
Scardoni M, Vittoria E, Volante M, Rusev B, et al.
Neuroendocrinology. 2014 Oct 20. [Epub ahead of print]


The role of genome sequencing in personalized breast cancer prevention.
Sieh W, Rothstein JH, McGuire V, Whittemore AS.
Cancer Epidemiol Biomarkers Prev. 2014 Oct 23. [Epub ahead of print]


Mutation analysis of the main hypertrophic cardiomyopathy genes using multiplex amplification and semiconductor next-generation sequencing.
Gómez J, Reguero JR, Morís C, Martín M, et al.
Circ J. 2014 Oct 22. [Epub ahead of print]


Smoking status impacts microRNA mediated prognosis and lung adenocarcinoma biology.
Vucic EA, Thu KL, Pikor LA, Enfield KS, et al.
BMC Cancer. 2014 Oct 24;14(1):778.


Whole exome sequencing in family trios reveals de novo mutations in PURA as a cause of severe neurodevelopmental delay and learning disability.
Hunt D, Leventer RJ, Simons C, Taft R, et al.
J Med Genet. 2014 Oct 23. [Epub ahead of print]


Exome sequencing identifies a dominant TNNT3 mutation in a large family with distal arthrogryposis.
Daly SB, Shah H, O'Sullivan J, Anderson B, et al.
Mol Syndromol. 2014 Aug;5(5):218-28.


Relapse or reinfection with tuberculosis: a whole genome sequencing approach in a large population-based cohort with high HIV prevalence and active follow-up.
Guerra-Assunção JA, Houben RM, Crampin AC, Mzembe T, et al.
J Infect Dis. 2014 Oct 21. [Epub ahead of print]


Application of next-generation sequencing technology for comprehensive aneuploidy screening of blastocysts in clinical preimplantation genetic screening cycles.
Fiorentino F, Bono S, Biricik A, Nuccitelli A, et al.
Hum Reprod. 2014 Oct 21. [Epub ahead of print]


Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing.
Cozzi-Lepri A, Noguera-Julian M, Di Giallonardo F, Schuurman R, et al.
J Antimicrob Chemother. 2014 Oct 21. [Epub ahead of print]


Exome sequencing as a differential diagnosis tool: resolving mild trichohepatoenteric syndrome.
Oz-Levi D, Weiss B, Lahad A, Greenberger S, et al.
Clin Genet. 2014 Oct 21. [Epub ahead of print]


Expanding the mutational spectrum of LZTR1 in schwannomatosis.
Paganini I, Chang VY, Capone GL, Vitte J, et al.
Eur J Hum Genet. 2014 Oct 22. [Epub ahead of print]


Exome sequencing is an efficient tool for variant late-infantile neuronal ceroid lipofuscinosis molecular diagnosis.
Patiño LC, Battu R, Ortega-Recalde O, Nallathambi J, et al.
PLOS One. 2014 Oct 15;9(10):e109576.


Disease variants in genomes of 44 centenarians.
Freudenberg-Hua Y, Freudenberg J, Vacic V, Abhyankar A, et al.
Mol Genet Genomic Med. 2014 Sep;2(5):438-50.


Disease-related mutations among Caribbean Hispanics with familial dementia.
Lee JH, Kahn A, Cheng R, Reitz C, et al.
Mol Genet Genomic Med. 2014 Sep;2(5):430-7.


Diagnosis of autosomal dominant polycystic kidney disease using efficient PKD1 and PKD2 targeted next-generation sequencing.
Trujillano D, Bullich G, Ossowski S, Ballarín J, et al.
Mol Genet Genomic Med. 2014 Sep;2(5):412-21.


Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease.
Laurell T, Nilsson D, Hofmeister W, Lindstrand A, et al.
Mol Genet Genomic Med. 2014 Sep;2(5):402-11.


Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome.
Krawitz PM, Schiska D, Krüger U, Appelt S, et al.
Mol Genet Genomic Med. 2014 Sep;2(5):393-401.


AP5Z1/SPG48 frequency in autosomal recessive and sporadic spastic paraplegia.
Schlipf NA, Schüle R, Klimpe S, Karle KN, et al.
Mol Genet Genomic Med. 2014 Sep;2(5):379-82.


Next generation sequencing in the identification of a rare genetic disease from preconceptional couple screening to preimplantation genetic diagnosis.
Dello Russo C, Di Giacomo G, Mesoraca A, D'Emidio L, et al.
J Prenat Med. 2014 Jan;8(1-2):17-24.


Whole-exome Sequencing Identifies a Variant in TMEM132E Causing Autosomal-Recessive Nonsyndromic Hearing Loss DFNB99.
Li J, Zhao X, Xin Q, Shan S, et al.
Hum Mutat. 2014 Oct 21. [Epub ahead of print]


A Weighted U-Statistic for Genetic Association Analyses of Sequencing Data.
Wei C, Li M, He Z, Vsevolozhskaya O, et al.
Genet Epidemiol. 2014 Oct 20. [Epub ahead of print]


Next Generation Sequencing Identifies a Novel Rearrangement in the HBB Cluster Permitting to-the-Base Characterization.
Shooter C, Rooks H, Thein SL, Clark B.
Hum Mutat. 2014 Oct 21. [Epub ahead of print]


Multidrug-resistant Escherichia coli soft tissue infection investigated with bacterial whole genome sequencing.
Buchanan R, Stoesser N, Crook D, Bowler IC.
BMJ Case Rep. 2014 Oct 19;2014.


EVI1-rearranged acute myeloid leukemias are characterized by distinct molecular alterations.
Lavallée VP, Gendron P, Lemieux S, D'Angelo G, et al.
Blood. 2014 Oct 20. [Epub ahead of print]


Global transcriptome analysis and enhancer landscape of human primary T follicular helper and T effector lymphocytes.
Weinstein JS, Lezon-Geyda K, Maksimova Y, Craft S, et al.
Blood. 2014 Oct 20. [Epub ahead of print]


Mutations Predisposing to Breast Cancer in 12 Candidate Genes in Breast Cancer Patients from Poland.
Cybulski C, Lubiński J, Wokołorczyk D, Kuźniak W, et al.
Clin Genet. 2014 Oct 20. [Epub ahead of print]


Microbial Communities in the Upper Respiratory Tract of Patients with Asthma and Chronic Obstructive Pulmonary Disease.
Park H, Shin JW, Park SG, Kim W.
PLOS One. 2014 Oct 16;9(10):e109710.


Integrated microRNA and mRNA Transcriptome Sequencing Reveals the Potential Roles of miRNAs in Stage I Endometrioid Endometrial Carcinoma.
Xiong H, Li Q, Liu S, Wang F, et al.
PLOS One. 2014 Oct 17;9(10):e110163.


The Feasibility Study of Non-Invasive Fetal Trisomy 18 and 21 Detection with Semiconductor Sequencing Platform.
Jeon YJ, Zhou Y, Li Y, Guo Q, et al.
PLOS One. 2014 Oct 20;9(10):e110240.

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.