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In Print: Last Week's Clinical Sequencing Papers of Note: Nov 20, 2013


Genetic variation of human papillomavirus type 16 in individual clinical specimens revealed by deep sequencing.
Kukimoto I, Maehama T, Sekizuka T, Ogasawara Y, et al.
PLOS One. 2013 Nov 13;8(11):e80583.

Molecular typing of lung adenocarcinoma on cytological samples using a multigene next generation sequencing panel.
Scarpa A, Sikora K, Fassan M, Rachiglio AM, et al.
PLOS One. 2013 Nov 13;8(11):e80478.

LRP4 third β-propeller domain mutations cause novel congenital myasthenia by compromising agrin-mediated musk signaling in a position-specific manner.
Ohkawara B, Cabrera-Serrano M, Nakata T, Milone M, et al.
Hum Mol Genet. 2013 Nov 13. [Epub ahead of print]

Abnormal centrosome and spindle morphology in a patient with autosomal recessive primary microcephaly type 2 due to compound heterozygous WDR62 gene mutations.
Farag HG, Froehler S, Oexle K, Ravindran E, et al.
Orphanet J Rare Dis. 2013 Nov 14;8(1):178.

Whole-exome sequencing identifies novel compound heterozygous mutations in USH2A in Spanish patients with autosomal recessive retinitis pigmentosa.
Méndez-Vidal C, González-Del Pozo M, Vela-Boza A, Santoyo-López J, et al.
Mol Vis. 2013 Nov 7;19:2187-95.

Targeted next-generation sequencing using fine-needle aspirates from adenocarcinomas of the lung.
Karnes HE, Duncavage EJ, Bernadt CT.
Cancer Cytopathol. 2013 Nov 12. [Epub ahead of print]

ICO amplicon NGS data analysis: a web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next generation sequencing.
Lopez-Doriga A, Feliubadaló L, Menéndez M, Lopez-Doriga S, et al.
Hum Mutat. 2013 Nov 14. [Epub ahead of print]

Whole genome sequencing as a diagnostic test: challenges and opportunities.
Chrystoja CC, Diamandis EP.
Clin Chem. 2013 Nov 13. [Epub ahead of print]

A new mutation in the C-SH2 domain of PTPN11 causes Noonan syndrome with multiple giant cell lesions.
Carapito R, Paul N, Untrau M, Ott L, et al.
J Hum Genet. 2013 Nov 14. [Epub ahead of print]

Novel mutations of ABCB6 associated with autosomal dominant dyschromatosis universalis hereditaria.
Cui YX, Xia XY, Zhou Y, Gao L, et al.
PLOS One. 2013 Nov 5;8(11):e79808.

An integrated model of the transcriptome of HER2-positive breast cancer.
Kalari KR, Necela BM, Tang X, Thompson KJ, et al.
PLOS One. 2013 Nov 1;8(11):e79298.

Reflections on the cost of "low-cost" whole genome sequencing: framing the health policy debate.
Caulfield T, Evans J, McGuire A, McCabe C, et al.
PLOS Biol. 2013 Nov;11(11):e1001699.

HLA typing from 1000 genomes whole genome and whole exome Illumina data.
Major E, Rigó K, Hague T, Bérces A, Juhos S.
PLOS One. 2013 Nov 6;8(11):e78410.

Diagnostic accuracy of random massively parallel sequencing for non-invasive prenatal detection of common autosomal aneuploidies: a collaborative study in Europe.
Stumm M, Entezami M, Haug K, Blank C, et al.
Prenat Diagn. 2013 Nov 12. [Epub ahead of print]

Establishing the origin of metastatic deposits in the setting of multiple primary malignancies: The role of massively parallel sequencing.
De Mattos-Arruda L, Bidard FC, Won HH, Cortes J, et al.
Mol Oncol. 2013 Oct 31. [Epub ahead of print]

Landscape of genetic lesions in 944 patients with myelodysplastic syndromes.
Haferlach T, Nagata Y, Grossmann V, Okuno Y, et al.
Leukemia. 2013 Nov 13. [Epub ahead of print]

Integrated profiling of microRNA expression in membranous nephropathy using high-throughput sequencing technology.
Chen W, Lin X, Huang J, Tan K, et al.
Int J Mol Med. 2013 Nov 12. [Epub ahead of print]

Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England.
Wong TH, Dearlove BL, Hedge J, Giess AP, et al.
Virol J. 2013 Nov 13;10(1):335.

SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory.
Roy S, Durso MB, Wald A, Nikiforov YE, Nikiforova MN.
J Mol Diagn. 2013 Nov 9. pii: S1525-1578(13)00220-1. [Epub ahead of print]

Autosomal-recessive cerebellar ataxia caused by a novel ADCK3 mutation that elongates the protein: clinical, genetic and biochemical characterisation.
Liu YT, Hersheson J, Plagnol V, Fawcett K, et al.
J Neurol Neurosurg Psychiatry. 2013 Nov 11. [Epub ahead of print]

Whole genome sequencing demonstrates fidaxomicin is superior to vancomycin for prevention of Clostridium difficile relapse and reinfection.
Eyre DW, Babakhani F, Griffiths D, Seddon J, et al.
J Infect Dis. 2013 Nov 11. [Epub ahead of print]

DNAJC13 mutations in Parkinson disease.
Vilariño-Güell C, Rajput A, Milnerwood AJ, Shah B, et al.
Hum Mol Genet. 2013 Nov 11. [Epub ahead of print]

Targeted exome sequencing for mitochondrial disorders reveals high genetic heterogeneity.
Dare JT, Vasta V, Penn J, Tran NT, Hahn SH.
BMC Med Genet. 2013 Nov 11;14(1):118.

Discovery of recurrent structural variants in nasopharyngeal carcinoma.
Valouev A, Weng Z, Sweeney R, Varma S, et al.
Genome Res. 2013 Nov 8. [Epub ahead of print]

Dysfunctional nitric oxide signalling increases risk of myocardial infarction.
Erdmann J, Stark K, Esslinger UB, Rumpf PM, et al.
Nature. 2013 Nov 10. [Epub ahead of print]

A large-scale screen for coding variants predisposing to psoriasis.
Tang H, Jin X, Li Y, Jiang H, et al.
Nat Genet. 2013 Nov 10. [Epub ahead of print]

Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis.
Weedon MN, Cebola I, Patch AM, Flanagan SE, et al.
Nat Genet. 2013 Nov 10. [Epub ahead of print]

Colorectal carcinomas with CpG island methylator phenotype 1 frequently contain mutations in chromatin regulators.
Tahara T, Yamamoto E, Madireddi P, Suzuki H, et al.
Gastroenterology. 2013 Nov 6. pii: S0016-5085(13)01578-3. [Epub ahead of print]

Validation of a next-generation sequencing assay for clinical molecular oncology.
Cottrell CE, Al-Kateb H, Bredemeyer AJ, Duncavage EJ, et al.
J Mol Diagn. 2013 Nov 5. pii: S1525-1578(13)00219-5. [Epub ahead of print]

A dominant mutation in FBXO38 causes distal spinal muscular atrophy with calf predominance.
Sumner CJ, d'Ydewalle C, Wooley J, Fawcett KA, et al.
Am J Hum Genet. 2013 Nov 7;93(5):976-83.

De novo loss-of-function mutations in CHD2 cause a fever-sensitive myoclonic epileptic encephalopathy sharing features with Dravet syndrome.
Suls A, Jaehn JA, Kecskés A, Weber Y, et al.
Am J Hum Genet. 2013 Nov 7;93(5):967-75.

Gain-of-function mutations in SCN11A cause familial episodic pain.
Zhang XY, Wen J, Yang W, Wang C, et al.
Am J Hum Genet. 2013 Nov 7;93(5):957-66.

Mutations in SERPINB7, encoding a member of the serine protease inhibitor superfamily, cause Nagashima-type palmoplantar keratosis.
Kubo A, Shiohama A, Sasaki T, Nakabayashi K, et al.
Am J Hum Genet. 2013 Nov 7;93(5):945-56.

ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer.
Bysani M, Wallerman O, Bornelöv S, Zatloukal K, et al.
BMC Med Genomics. 2013 Nov 8;6(1):50.

Novel compound heterozygous mutations in the MYO15A gene in autosomal recessive hearing loss identified by whole-exome sequencing.
Gao X, Zhu QY, Song YS, Wang GJ, et al.
J Transl Med. 2013 Nov 9;11(1):284.