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Recent Clinical Sequencing Papers of Note: Nov 12, 2014

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Mutant SNAP25B causes myasthenia, cortical hyperexcitability, ataxia, and intellectual disability.
Shen XM, Selcen D, Brengman J, Engel AG.
Neurology. 2014 Nov 7. [Epub ahead of print]


Characterization of gene mutations and copy number changes in acute myeloid leukemia using a rapid target enrichment protocol.
Bolli N, Manes N, McKerrel T, Chi J, et al.
Haematologica. 2014 Nov 7. [Epub ahead of print]


Whole exome sequencing reveals novel COL4A3 and COL4A4 mutations and resolves diagnosis in Chinese families with kidney disease.
Lin F, Bian F, Zou J, Wu X, et al.
BMC Nephrol. 2014 Nov 7;15(1):175.


Identification of a novel MSH6 germline variant in a family with multiple gastro-intestinal malignancies by next generation sequencing.
Connor AA, Katzov-Eckert H, Whelan T, Aronson M, et al.
Fam Cancer. 2014 Nov 8. [Epub ahead of print]


A comprehensive genomic approach for neuromuscular diseases gives a high diagnostic yield.
Ankala A, Da Silva C, Gualandi F, Ferlini A, et al.
Ann Neurol. 2014 Nov 7. [Epub ahead of print]


Severe vascular calcification and tumoral calcinosis in a family with hyperphosphatemia: a fibroblast growth factor 23 mutation identified by exome sequencing.
Shah A, Miller CJ, Nast CC, Adams MD, et al.
Nephrol Dial Transplant. 2014 Nov 5. [Epub ahead of print]


Comparative analysis of subtyping methods against a whole genome sequencing standard in Salmonella enteric serotype Enteritidis.
Deng X, Shariat N, Driebe EM, Roe CC, et al.
J Clin Microbiol. 2014 Nov 5. [Epub ahead of print]


High-resolution hepatitis C virus (HCV) subtyping, using NS5B deep sequencing and phylogeny, an alternative to current methods.
Quer J, Gregori J, Rodríguez-Frias F, Buti M, et al.
J Clin Microbiol. 2014 Nov 5. [Epub ahead of print]


Whole genome sequencing to understand the genetic architecture of common gene expression and biomarker phenotypes.
Wood AR, Tuke MA, Nalls M, Hernandez D, et al.
Hum Mol Genet. 2014 Nov 6. [Epub ahead of print]


Ion Torrent next-generation sequencing for routine identification of clinically relevant mutations in colorectal cancer patients.
Malapelle U, Vigliar E, Sgariglia R, Bellevicine C, et al.
J Clin Pathol. 2014 Nov 5. [Epub ahead of print]


Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma.
Vogt N, Gibaud A, Lemoine F, de la Grange P, et al..
Nucleic Acids Res. 2014 Nov 6. [Epub ahead of print]


Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines.
Suzuki A, Makinoshima H, Wakaguri H, Esumi H, et al.
Nucleic Acids Res. 2014 Nov 6. [Epub ahead of print]


Deep sequencing identifies genetic heterogeneity and recurrent convergent evolution in chronic lymphocytic leukemia.
Ojha J, Ayres J, Secreto C, Tschumper R, et al.
Blood. 2014 Nov 6. [Epub ahead of print]


Non-invasive prenatal testing for Wilson disease by use of circulating single-molecule amplification and resequencing technology (cSMART).
Lv W, Wei X, Guo R, Liu Q, et al.
Clin Chem. 2014 Nov 6. [Epub ahead of print]


A novel ERCC6 splicing variant associated with a mild Cockayne syndrome phenotype.
Swartz JM, Akinci A, Andrew SF, Siğirci A, et al.
Horm Res Paediatr. 2014 Nov 1:344-352. [Epub ahead of print]


Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains.
Salipante SJ, Roach DJ, Kitzman JO, Snyder MW, et al.
Genome Res. 2014 Nov 4. [Epub ahead of print]


The α1-A680T variant in GUCY1A3 as a candidate conferring protection from pulmonary hypertension among Kyrgyz highlanders.
Wilkins MR, Aldashev AA, Wharton J, Rhodes CJ, et al.
Circ Cardiovasc Genet. 2014 Nov 4. [Epub ahead of print]


Identification of novel single nucleotide polymorphisms associated with acute respiratory distress syndrome by exome-seq.
Shortt K, Chaudhary S, Grigoryev D, Heruth DP, et al.
PLOS One. 2014 Nov 5;9(11):e111953.


High-throughput sequencing and copy number variation detection using formalin fixed embedded tissue in metastatic gastric cancer.
Kim S, Lee J, Hong ME, Do IG, et al.
PLOS One. 2014 Nov 5;9(11):e111693.


Case-only exome sequencing and complex disease susceptibility gene discovery: study design considerations.
Wu L, Schaid DJ, Sicotte H, Wieben ED, et al.
J Med Genet. 2014 Nov 4. [Epub ahead of print]


Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing.
Quick J, Cumley N, Wearn CM, Niebel M, et al.
BMJ Open. 2014 Nov 4;4(11):e006278.


A novel pathogenic mutation of the CYP27B1 gene in a patient with vitamin D-dependent rickets type 1: a case report.
Babiker AM, Al Gadi I, Al-Jurayyan NA, Al Nemri AM, et al.
BMC Res Notes. 2014 Nov 5;7(1):783.


Deep sequencing identifies noncanonical editing of Ebola and Marburg virus RNAs in infected cells.
Shabman RS, Jabado OJ, Mire CE, Stockwell TB, et al.
MBio. 2014 Nov 4;5(6).


No evidence for rare recessive and compound heterozygous disruptive variants in schizophrenia.
Ruderfer DM, Lim ET, Genovese G, Moran JL, et al.
Eur J Hum Genet. 2014 Nov 5. [Epub ahead of print]


Diagnostic approach for FSHD revisited: SMCHD1 mutations cause FSHD2 and act as modifiers of disease severity in FSHD1.
Larsen M, Rost S, El Hajj N, Ferbert A, et al.
Eur J Hum Genet. 2014 Nov 5. [Epub ahead of print]


RNA-seq profiling of a radiation resistant and radiation sensitive prostate cancer cell line highlights opposing regulation of DNA repair and targets for radiosensitization.
Young A, Berry R, Holloway AF, Blackburn NB, et al.
BMC Cancer. 2014 Nov 4;14(1):808.


Classification models for clear cell renal carcinoma stage progression, based on tumor RNAseq expression trained supervised machine learning algorithms.
Jagga Z, Gupta D.
BMC Proc. 2014 Oct 13;8:S2.


Exome-wide rare variant analysis identifies TUBA4A mutations associated with familial ALS.
Smith BN, Ticozzi N, Fallini C, Gkazi AS, et al.
Neuron. 2014 Oct 22;84(2):324-31.


A recurrent deletion mutation in OPA1 causes autosomal dominant optic atrophy in a Chinese family.
Zhang L, Shi W, Song L, Zhang X, et al.
Sci Rep. 2014 Nov 6;4:6936.


Profiling status epilepticus-induced changes in hippocampal RNA expression using high-throughput RNA sequencing.
Hansen KF, Sakamoto K, Pelz C, Impey S, Obrietan K.
Sci Rep. 2014 Nov 6;4:6930.


Early-onset Crohn's disease and autoimmunity associated with a variant in CTLA-4.
Zeissig S, Petersen BS, Tomczak M, Melum E, et al.
Gut. 2014 Nov 3. [Epub ahead of print]


Maturity-onset diabetes of the young type 5 in a family with diabetes and mild kidney disease diagnosed by whole exome sequencing.
Wentworth JM, Lukic V, Bahlo M, Finlay M, et al.
Intern Med J. 2014 Nov;44(11):1137-40.


Next-generation deep sequencing improves detection of BCR-ABL1 kinase domain mutations emerging under tyrosine kinase inhibitor treatment of chronic myeloid leukemia patients in chronic phase.
Machova Polakova K, Kulvait V, Benesova A, Linhartova J, et al.
J Cancer Res Clin Oncol. 2014 Nov 4. [Epub ahead of print]


Mutational analysis of BRCA1/2 in a group of 134 consecutive ovarian cancer patients. Novel and recurrent BRCA1/2 alterations detected by next generation sequencing.
Ratajska M, Krygier M, Stukan M, Kuźniacka A, et al.
J Appl Genet. 2014 Nov 1. [Epub ahead of print]


MetaGeniE: characterizing human clinical samples using deep metagenomic sequencing.
Rawat A, Engelthaler DM, Driebe EM, Keim P, Foster JT.
PLOS One. 2014 Nov 3;9(11):e110915


Defining the alloreactive T cell repertoire using high-throughput sequencing of mixed lymphocyte reaction culture.
Emerson RO, Mathew JM, Konieczna IM, Robins HS, Leventhal JR.
PLOS One. 2014 Nov 3;9(11):e111943.


Quantifying the expression of tumor marker genes in lung squamous cell cancer with RNA sequencing.
Wang L, Zhan C, Zhang Y, Ma J, et al.
J Thorac Dis. 2014 Oct;6(10):1380-7.


The contribution of de novo coding mutations to autism spectrum disorder.
Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, et al.
Nature. 2014 Oct 29. [Epub ahead of print]


The mutational landscapes of genetic and chemical models of Kras-driven lung cancer.
Westcott PM, Halliwill KD, To MD, Rashid M, et al.
Nature. 2014 Nov 2. [Epub ahead of print]


Synaptic, transcriptional and chromatin genes disrupted in autism.
De Rubeis S, He X, Goldberg AP, Poultney CS, et al.
Nature. 2014 Oct 29. [Epub ahead of print]


Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes.
Schubert J, Siekierska A, Langlois M, May P, et al.
Nat Genet. 2014 Nov 2. [Epub ahead of print]


Trans-ancestry mutational landscape of hepatocellular carcinoma genomes.
Totoki Y, Tatsuno K, Covington KR, Ueda H, et al.
Nat Genet. 2014 Nov 2. [Epub ahead of print]

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.