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Recent Clinical Sequencing Papers of Note: Jun 11, 2014

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Molecular profiling of soft tissue sarcomas using next-generation sequencing: a pilot study toward precision therapeutics.
Jour G, Scarborough JD, Jones RL, Loggers E, et al.
Hum Pathol. 2014 Apr 24. [Epub ahead of print]


Mutations in zinc finger 407 [ZNF407] cause a unique autosomal recessive cognitive impairment syndrome.
Kambouris M, Maroun RC, Ben-Omran T, Al-Sarraj Y, et al.
Orphanet J Rare Dis. 2014 Jun 7;9(1):80.


Rare complement factor H variant associated with age-related macular degeneration in the Amish.
Hoffman JD, Cooke Bailey JN, D'Aoust LN, Cade W, et al.
Invest Ophthalmol Vis Sci. 2014 Jun 6. [Epub ahead of print]


HITS-CLIP reveals key regulators of nuclear receptor signaling in breast cancer.
Pillai MM, Gillen AE, Yamamoto TM, Kline E, Brown J, Flory K, et al.
Breast Cancer Res Treat. 2014 Jun 7. [Epub ahead of print]


Monoallelic and biallelic mutations in MAB21L2 cause a spectrum of major eye malformations.
Rainger J, Pehlivan D, Johansson S, Bengani H, et al.
Am J Hum Genet. 2014 Jun 5;94(6):915-923.


Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families.
Blumenthal I, Ragavendran A, Erdin S, Klei L, et al.
Am J Hum Genet. 2014 Jun 5;94(6):870-883.


FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project.
Beaulieu CL, Majewski J, Schwartzentruber J, Samuels ME et al.
Am J Hum Genet. 2014 Jun 5;94(6):809-817.


ARMC5 mutations are common in familial bilateral macronodulcar adrenal hyperplasia.
Gagliardi L, Schreiber AW, Hahn CN, Feng J, et al.
J Clin Endocrinol Metab. 2014 Jun 6 [Epub ahead of print]


Whole-exome sequencing in an individual with severe global developmental delay and intractable epilepsy identifies a novel, de novo GRIN2A mutation.
Venkateswaran S, Myers KA, Smith AC, Beaulieu CL, Schwartzentruber JA; et al.
Epilepsia. 2014 Jun 5. [Epub ahead of print]


Accurate mitochondrial DNA sequencing using off-target reads provides a single test to identify pathogenic point mutations.
Griffin HR, Pyle A, Blakely EL, Alston CL, Duff J, et al.
Genet Med. 2014 Jun 5. [Epub ahead of print]


The usefulness of whole-exome sequencing in routine clinical practice.
Iglesias A, Anyane-Yeboa K, Wynn J, Wilson A, et al.
Genet Med. 2014 Jun 5. [Epub ahead of print]


Next generation sequencing of translocation renal cell carcinomas reveals novel RNA splicing partners and frequent mutations of chromatin remodeling genes.
Malouf GG, Su X, Yao H, Gao J, et al.
Clin Cancer Res. 2014 Jun 4. [Epub ahead of print]


A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.
Naccache SN, Federman S, Veeeraraghavan N, Zaharia M, et al.
Genome Res. 2014 Jun 4. [Epub ahead of print]


Autosomal dominant inheritance of rapidly progressive amyotrophic lateral sclerosis due to a truncation mutation in the fused in sarcoma (FUS) gene.
Kent L, Vizard TN, Smith BN, Topp SD, et al.
Amyotroph Lateral Scler Frontotemporal Degener. 2014 Jun 5:1-6.


Rare mutations in SQSTM1 modify susceptibility to frontotemporal lobar degeneration.
van der Zee J, Van Langenhove T, Kovacs GG, Dillen L, Deschamps W, et al.
Acta Neuropathol. 2014 Jun 5. [Epub ahead of print]


Rare and common variants in extracellular matrix gene Fibrillin 2 (FBN2) are associated with macular degeneration.
Ratnapriya R, Zhan X, Fariss RN, Branham KE, et al.
Hum Mol Genet. 2014 Jun 4. [Epub ahead of print]


Characterization of a novel HLA-A*33 allele, A*33:47, using next-generation sequencing.
Stückler C, Danzer M, Raml E, Steitzer H, Gabriel C.
Tissue Antigens. 2014 Jun 5. [Epub ahead of print]


Structural variation and missense mutation in SBDS associated with Shwachman-Diamond syndrome.
Carvalho CM, Zuccherato LW, Williams CL, Neill NJ, et al.
BMC Med Genet. 2014 Jun 4;15(1):64.


Donor splice-site mutation in CUL4B is likely cause of X-linked intellectual disability.
Londin ER, Adijanto J, Philp N, Novelli A, et al.
Am J Med Genet A. 2014 Jun 4. [Epub ahead of print]


Deep Sequencing reveals new aspects of progesterone receptor signaling in breast cancer cells.
Kougioumtzi A, Tsaparas P, Magklara A.
PLOS One. 2014 Jun 4;9(6):e98404.


Deep sequencing of cancer-related genes revealed GNAS mutations to be associated with intraductal papillary mucinous neoplasms and its main pancreatic duct dilation.
Takano S, Fukasawa M, Maekawa S, Kadokura M, et al.
PLOS One. 2014 Jun 4;9(6):e98718.


Pregnancy's stronghold on the vaginal microbiome.
Walther-António MR, Jeraldo P, Berg Miller ME, Yeoman CJ, et al.
PLOS One. 2014 Jun 4;9(6):e98514.


Actionable diagnosis of neuroleptospirosis by next-generation sequencing.
Wilson MR, Naccache SN, Samayoa E, Biagtan M, et al.
N Engl J Med. 2014 Jun 4. [Epub ahead of print]


Genome sequencing identifies major causes of severe intellectual disability.
Gilissen C, Hehir-Kwa JY, Thung DT, van de Vorst M, et al.
Nature. 2014 Jun 4. [Epub ahead of print]


Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers.
Sun Z, Wang L, Eckloff BW, Deng B, et al.
BMC Med Genomics. 2014 Jun 4;7(1):32.


EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing.
Francis JM, Zhang CZ, Maire CL, Jung J, et al.
Cancer Discov. 2014 Jun 3. [Epub ahead of print]


Towards a molecular characterization of autism spectrum disorders: an exome sequencing and systems approach.
An JY, Cristino AS, Zhao Q, Edson J, et al.
Transl Psychiatry. 2014 Jun 3;4:e394.


Validation of ambiguous MLPA results by targeted next-generation sequencing discloses a nonsense mutation in the DMD gene.
Niba ET, Tran VK, Tuan-Pham LA, Vu DC, et al.
Clin Chim Acta. 2014 May 31. [Epub ahead of print]


Dubowitz syndrome is a complex comprised of multiple, genetically distinct and phenotypically overlapping disorders.
Stewart DR, Pemov A, Johnston JJ, Sapp JC, et al.
PLOS One. 2014 Jun 3;9(6):e98686.


SLC39A5 mutations interfering with the BMP/TGF-β pathway in non-syndromic high myopia.
Guo H, Jin X, Zhu T, Wang T, et al.
J Med Genet. 2014 Jun 2. [Epub ahead of print]


Identification of four novel genes contributing to familial elevated plasma HDL cholesterol in humans.
Singaraja RR, Tietjen I, Hovingh GK, Franchini PL, et al.
J Lipid Res. 2014 Jun 2. [Epub ahead of print]


Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia.
Rajasagi M, Shukla SA, Fritsch EF, Keskin DB, et al.
Blood. 2014 Jun 2. [Epub ahead of print]


Improved detection of emerging drug-resistant mutant cytomegalovirus subpopulations by deep sequencing.
Chou S, Ercolani RJ, Sahoo MK, Lefterova MI, et al.
Antimicrob Agents Chemother. 2014 Jun 2. [Epub ahead of print]


Early onset epileptic encephalopathy caused by de novo SCN8A mutations.
Ohba C, Kato M, Takahashi S, Lerman-Sagie T, et al.
Epilepsia. 2014 Jun 2. [Epub ahead of print]


Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis.
Luo T, Yang C, Peng Y, Lu L, et al.
Tuberculosis. 2014 May 5. [Epub ahead of print]


Novel NFKB2 mutation in early-onset CVID.
Liu Y, Hanson S, Gurugama P, Jones A, et al.
J Clin Immunol. 2014 Jun 3. [Epub ahead of print]


Novel de novo heterozygous FGFR1 mutation in two siblings with Hartsfield syndrome: A case of gonadal mosaicism.
Dhamija R, Kirmani S, Wang X, Ferber MJ, et al.
Am J Med Genet A. 2014 May 28. [Epub ahead of print]


A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions.
Brunner AL, Li J, Guo X, Sweeney RT, et al.
Genome Biol. 2014 May 23;15(5):R71.


Copy number variants in clinical next-generation sequencing data can define the relationship between simultaneous tumors in an individual patient.
Sehn JK, Abel HJ, Duncavage EJ.
Exp Mol Pathol. 2014 May 30. [Epub ahead of print]


De novo SOX11 mutations cause Coffin-Siris syndrome.
Tsurusaki Y, Koshimizu E, Ohashi H, Phadke S, et al.
Nat Commun. 2014 Jun 2;5:4011.


Exome sequencing identifies a novel mutation in PIK3R1 as the cause of SHORT syndrome.
Bárcena C, Quesada V, De Sandre-Giovannoli A, Puente DA, et al.
BMC Med Genet. 2014 May 2;15(1):51.


De novo variants in the KMT2A (MLL) gene causing atypical Wiedemann-Steiner syndrome in two unrelated individuals identified by clinical exome sequencing.
Strom SP, Lozano R, Lee H, Dorrani N, et al.
BMC Med Genet. 2014 May 1;15(1):49.


Implementation of cloud based next generation sequencing data analysis in a clinical laboratory.
Onsongo G, Erdmann J, Spears MD, Chilton J, et al.
BMC Res Notes. 2014 May 23;7(1):314.


Identification of candidate risk gene variations by whole-genome sequence analysis of four rat strains commonly used in inflammation research.
Bäckdahl L, Ekman D, Jagodic M, Olsson T, Holmdahl R.
BMC Genomics. 2014 May 21;15(1):391.


Detection of a divergent parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing.
Bialasiewicz S, McVernon J, Nolan T, Lambert SB, et al.
BMC Infect Dis. 2014 May 19;14(1):275.


Whole exome sequencing reveals concomitant mutations of multiple FA genes in individual Fanconi anemia patients.
Chang L, Yuan W, Zeng H, Zhou Q, et al.
BMC Med Genomics. 2014 May 15;7(1):24.


Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.
Giraud M, Salson M, Duez M, Villenet C, et al.
BMC Genomics. 2014 May 28;15(1):409.


PhenoVar: a phenotype-driven approach in clinical genomics for the diagnosis of polymalformative syndromes.
Trakadis YJ, Buote C, Therriault JF, Jacques PÉ, et al.
BMC Med Genomics. 2014 May 12;7(1):22.


Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads.
Bai Y, Ni M, Cooper B, Wei Y, Fury W.
BMC Genomics. 2014 May 1;15(1):325.


Mutations of CEP83 cause infantile nephronophthisis and intellectual disability.
Failler M, Gee HY, Krug P, Joo K, et al.
Am J Hum Genet. 2014 Jun 5;94(6):905-914.

The Scan

Review of Approval Process

Stat News reports the Department for Health and Human Services' Office of the Inspector General is to investigate FDA's approval of Biogen's Alzheimer's disease drug.

Not Quite Right

A new analysis has found hundreds of studies with incorrect nucleotide sequences reported in their methods, according to Nature News.

CRISPR and mRNA Together

Time magazine reports on the use of mRNA to deliver CRISPR machinery.

Nature Papers Present Smartphone Platform for DNA Diagnosis of Malaria, Mouse Lines for Epigenomic Editing

In Nature this week: a low-cost tool to detect infectious diseases like malaria, and more.