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In Print: Clinical Sequencing Papers of Note of the Last Two Weeks: Aug 14, 2013


Exome sequencing and linkage analysis identified tenascin-C (TNC) as a novel causative gene in nonsyndromic hearing loss.
Zhao Y, Zhao F, Zong L, Zhang P, et al.
PLoS One. 2013 Jul 30;8(7):e69549.

Using complete genome comparisons to identify sequences whose presence accurately predicts clinically important phenotypes.
Hall BG, Cardenas H, Barlow M.
PLoS One. 2013 Jul 23;8(7):e68901.

Clinical spectrum of SCN2A mutations expanding to Ohtahara syndrome.
Nakamura K, Kato M, Osaka H, Yamashita S, et al.
Neurology. 2013 Aug 9. [Epub ahead of print]

De novo mutations in epileptic encephalopathies.
Epi4K Consortium, Allen AS, Berkovic SF, Cossette P, Delanty N, et al.
Nature. 2013 Aug 11. [Epub ahead of print]

Congenital myopathy is caused by mutation of HACD1.
Muhammad E, Reish O, Ohno Y, Scheetz T, et al.
Hum Mol Genet. 2013 Aug 9. [Epub ahead of print]

Reliable noninvasive prenatal testing by massively parallel sequencing of circulating cell-free DNA from maternal plasma processed up to 24 hours after venipuncture.
Buysse K, Beulen L, Gomes I, Gilissen C, et al.
Clin Biochem. 2013 Aug 8. [Epub ahead of print]

Next generation sequencing for human papillomavirus genotyping.
Arroyo LS, Smelov V, Bzhalava D, Eklund C, et al.
J Clin Virol. 2013 Aug 8. [Epub ahead of print]

Biallelic SZT2 mutations cause infantile encephalopathy with epilepsy and dysmorphic corpus callosum.
Basel-Vanagaite L, Hershkovitz T, Heyman E, Raspall-Chaure M, et al.
Am J Hum Genet. 2013 Aug 6. [Epub ahead of print]

The utility of the traditional medical genetics diagnostic evaluation in the context of next-generation sequencing for undiagnosed genetic disorders.
Shashi V, McConkie-Rosell A, Rosell B, Schoch K, et al.
Genet Med. 2013 Aug 8. [Epub ahead of print]

A founder mutation in COL4A3 causes autosomal recessive Alport syndrome in the Ashkenazi Jewish population.
Webb BD, Brandt T, Liu L, Jalas C, et al.
Clin Genet. 2013 Aug 8. [Epub ahead of print]

GFI1B mutation causes a bleeding disorder with abnormal platelet function.
Stevenson WS, Morel-Kopp MC, Chen Q, Liang HP, et al.
J Thromb Haemost. 2013 Aug 8. [Epub ahead of print]

Whole-exome sequencing identifies a polymorphism in the BMP5 gene associated with SSRI treatment response in major depression.
Tammiste A, Jiang T, Fischer K, Mägi R, et al.
J Psychopharmacol. 2013 Aug 7. [Epub ahead of print]

OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes.
Yau C.
Bioinformatics. 2013 Aug 7. [Epub ahead of print]

Mutational signature of aristolochic Acid exposure as revealed by whole-exome sequencing.
Hoang ML, Chen CH, Sidorenko VS, He J, et al.
Sci Transl Med. 2013 Aug 7;5(197):197ra102.

Genome-wide mutational signatures of aristolochic Acid and its application as a screening tool.
Poon SL, Pang ST, McPherson JR, Yu W, et al.
Sci Transl Med. 2013 Aug 7;5(197):197ra101.

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line.
Adey A, Burton JN, Kitzman JO, Hiatt JB, et al.
Nature. 2013 Aug 8;500(7461):207-11.

Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome.
Bhatt AS, Freeman SS, Herrera AF, Pedamallu CS, et al.
N Engl J Med. 2013 Aug 8;369(6):517-28.

Genetic aberrations in imatinib-resistant dermatofibrosarcoma protuberans revealed by whole genome sequencing.
Hong JY, Liu X, Mao M, Li M, et al.
PLoS One. 2013 Jul 29;8(7):e69752.

Deep sequencing analysis of HCV NS3 resistance-associated variants and mutation linkage in liver transplant recipients.
Kirst ME, Li EC, Wang CX, Dong HJ, et al.
PLoS One. 2013 Jul 29;8(7):e69698.

Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis.
McCourt CM, McArt DG, Mills K, Catherwood MA, et al.
PLoS One. 2013 Jul 26;8(7):e69604.

Return of whole-genome sequencing results in paediatric research: a statement of the P3G international paediatrics platform.
Knoppers BM, Avard D, Sénécal K, Zawati MH, et al.
Eur J Hum Genet. 2013 Aug 7. [Epub ahead of print]

Infantile mitochondrial hepatopathy is a cardinal feature of MEGDEL syndrome (3-Methylglutaconic aciduria type IV with sensorineural deafness, encephalopathy and leigh-Like Syndrome) caused by novel mutations in SERAC1.
Sarig O, Goldsher D, Nousbeck J, Fuchs-Telem D, et al.
Am J Med Genet A. 2013 Aug 5. [Epub ahead of print]

Non-exomic and synonymous variants in ABCA4 are an important cause of Stargardt disease.
Braun TA, Mullins RF, Wagner AH, Andorf JL, et al.
Hum Mol Genet. 2013 Aug 4. [Epub ahead of print]

Neonatal diabetes, gallbladder agenesis, duodenal atresia, and intestinal malrotation caused by a novel homozygous mutation in RFX6.
Concepcion JP, Reh CS, Daniels M, Liu X, et al.
Pediatr Diabetes. 2013 Aug 5. [Epub ahead of print]

Exomic landscape of MED12 mutation negative and positive uterine leiomyomas.
Mäkinen N, Vahteristo P, Bützow R, Sjöberg J, Aaltonen LA.
Int J Cancer. 2013 Aug 3. [Epub ahead of print]

Somatic mutations in ATP1A1 and CACNA1D underlie a common subtype of adrenal hypertension.
Azizan EA, Poulsen H, Tuluc P, Zhou J, et al.
Nat Genet. 2013 Aug 4. [Epub ahead of print]

Exome capture sequencing reveals new insights into hepatitis B virus-induced hepatocellular carcinoma at the early stage of tumorigenesis.
Chen Y, Wang L, Xu H, Liu X, Zhao Y.
Oncol Rep. 2013 Aug 2. [Epub ahead of print]

Genetic alterations associated with progression from pancreatic intraepithelial neoplasia to invasive pancreatic tumor.
Murphy SJ, Hart SN, Lima JF, Kipp BR, et al.
Gastroenterology. 2013 Aug 1. [Epub ahead of print]

NKX2-1 mutation in a family diagnosed with ataxic dyskinetic cerebral palsy.
McMichael G, Haan E, Gardner A, Yap TY, et al.
Eur J Med Genet. 2013 Jul 30. [Epub ahead of print]

Short-rib polydactyly and Jeune syndromes are caused by mutations in WDR60.
McInerney-Leo AM, Schmidts M, Cortés CR, Leo PJ, et al.
Am J Hum Genet. 2013 Jul 31. [Epub ahead of print]

Recurrent gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic dissections.
Guo DC, Regalado E, Casteel DE, Santos-Cortez RL, et al.
Am J Hum Genet. 2013 Jul 30. [Epub ahead of print]

Exome sequencing reveals a novel partial deletion in the progranulin gene causing primary progressive aphasia.
Rohrer JD, Beck J, Plagnol V, Gordon E, et al.
J Neurol Neurosurg Psychiatry. 2013 Aug 2. [Epub ahead of print]

Autosomal dominant diabetes arising from a Wolfram syndrome 1 mutation.
Bonnycastle LL, Chines PS, Hara T, Huyghe JR, et al.
Diabetes. 2013 Jul 31. [Epub ahead of print]

Mutations in eIF4ENIF1 are associated with primary ovarian insufficiency.
Kasippillai T, Macarthur DG, Kirby A, Thomas B, et al.
J Clin Endocrinol Metab. 2013 Jul 31. [Epub ahead of print]

Recommendations for returning genomic incidental findings? We need to talk!
Burke W, Matheny Antommaria AH, Bennett R, Botkin J, et al.
Press Genet Med. 2013 Aug 1. [Epub ahead of print]

Next-generation sequencing-based multi-gene mutation profiling of solid tumors using fine needle aspiration samples: promises and challenges for routine clinical diagnostics.
Kanagal-Shamanna R, Portier BP, Singh RR, Routbort MJ, et al.
Mod Pathol. 2013 Aug 2. [Epub ahead of print]

A comprehensive molecular study on Coffin-Siris and Nicolaides-Baraitser syndromes identifies a broad molecular and clinical spectrum converging on altered chromatin remodeling.
Wieczorek D, Bögershausen N, Beleggia F, Steiner-Haldenstätt S, et al.
Hum Mol Genet. 2013 Aug 1. [Epub ahead of print]

Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma.
Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, et al.
Proc Natl Acad Sci U S A. 2013 Jul 30. [Epub ahead of print]

A 3-base pair deletion, c.9711_9713del, in DMD results in intellectual disability without muscular dystrophy.
de Brouwer AP, Nabuurs SB, Verhaart IE, Oudakker AR, et al.
Eur J Hum Genet. 2013 Jul 31. [Epub ahead of print]

Computational approaches to identify functional genetic variants in cancer genomes.
International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group, Gonzalez-Perez A, Mustonen V, et al.
Nat Methods. 2013 Jul 30;10(8):723-9.

Exome sequencing identifies RDH12 compound heterozygous mutations in a family with severe retinitis pigmentosa.
Chacon-Camacho OF, Jitskii S, Buentello-Volante B, Quevedo-Martinez J, Zenteno JC.
Gene. 2013 Jul 27. [Epub ahead of print]

Utility of DNA sequencing for direct identification of invasive fungi from fresh and formalin-fixed specimens.
Moncada PA, Budvytiene I, Ho DY, Deresinski SC, et al.
Am J Clin Pathol. 2013 Aug;140(2):203-8.

Validation of a yeast functional assay for p53 mutations using clonal sequencing.
Iggo R, Rudewicz J, Monceau E, Sevenet N, et al.
J Pathol. 2013 Jul 29. [Epub ahead of print]

A translational study of resistance emergence using sequential direct-acting antiviral agents for hepatitis C using ultra-deep sequencing.
Abe H, Hayes CN, Hiraga N, Imamura M, et al.
Am J Gastroenterol. 2013 Jul 30. [Epub ahead of print]

THetA: Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data.
Oesper L, Mahmoody A, Raphael BJ.
Genome Biol. 2013 Jul 29;14(7):R80.

Detection of low-frequency HIV-1 RT drug ResAIDSistance mutations by ultra-deep sequencing in naïve HIV-1 infected individuals.
Fleury HJ, Bellecave P, Recordon-Pinson P, Papuchon J, et al.
Res Hum Retroviruses. 2013 Jul 29. [Epub ahead of print]

A blood based 12-miRNA signature of Alzheimer disease patients.
Leidinger P, Backes C, Deutscher S, Schmitt K, et al.
Genome Biol. 2013 Jul 29;14(7):R78.

An integrated tool to study MHC region: accurate SNV detection and HLA genes typing in human MHC region using targeted high-throughput sequencing.
Cao H, Wu J, Wang Y, Jiang H, et al.
PLoS One. 2013 Jul 24;8(7):e69388.

Clinical next-generation sequencing successfully applied to fine-needle aspirations of pulmonary and pancreatic neoplasms.
Young G, Wang K, He J, Otto G, et al.
Cancer Cytopathol. 2013 Jul 24. [Epub ahead of print]

Detection of clinically relevant copy number variants with whole exome sequencing.
de Ligt J, Boone PM, Pfundt R, Vissers LE, et al.
Hum Mutat. 2013 Jul 24. [Epub ahead of print]

CPAP: Cancer Panel Analysis Pipeline.
Huang PJ, Yeh YM, Gan RC, Lee CC, et al.
Hum Mutat. 2013 Jul 24. [Epub ahead of print]

The silent mutational landscape of infant MLL-AF4 pro-B acute lymphoblastic leukemia.
Dobbins SE, Sherborne AL, Ma YP, Bardini M, et al.
Genes Chromosomes Cancer. 2013 Jul 26. [Epub ahead of print]

TrAp: a tree approach for fingerprinting subclonal tumor composition.
Strino F, Parisi F, Micsinai M, Kluger Y.
Nucleic Acids Res. 2013 Jul 27. [Epub ahead of print]

Mutations in ZMYND10, a gene essential for proper axonemal assembly of inner and outer dynein arms in humans and flies, cause primary ciliary dyskinesia.
Moore DJ, Onoufriadis A, Shoemark A, Simpson MA, et al.
Am J Hum Genet. 2013 Jul 24. [Epub ahead of print]

ZMYND10 is mutated in primary ciliary dyskinesia and interacts with LRRC6.
Zariwala MA, Gee HY, Kurkowiak M, Al-Mutairi DA, et al.
Am J Hum Genet. 2013 Jul 24. [Epub ahead of print]

Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat.
Atanur SS, Diaz AG, Maratou K, Sarkis A, et al.
Cell. 2013 Jul 23. [Epub ahead of print]

Melanomas of unknown primary have a mutation profile consistent with cutaneous sun exposed melanoma.
Dutton-Regester K, Kakavand H, Aoude LG, Stark MS, et al.
Pigment Cell Melanoma Res. 2013 Jul 25. [Epub ahead of print]

Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement.
Wang K, Kim C, Bradfield J, Guo Y, et al.
Genome Med. 2013 Jul 26;5(7):67.

Mutations in SETBP1 are recurrent in myelodysplastic syndromes and often coexist with cytogenetic markers associated with disease progression.
Fernandez-Mercado M, Pellagatti A, Di Genua C, Larrayoz MJ, et al.
Br J Haematol. 2013 Jul 24. [Epub ahead of print]