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Recent Clinical Sequencing Papers of Note: Oct 8, 2014


First steps in exploring prospective exome sequencing of consanguineous couples.
Teeuw M, Waisfisz Q, Zwijnenburg PJ, Sistermans EA, et al.
Eur J Med Genet. 2014 Oct 1. [Epub ahead of print]

Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer.
Doughty EL, Sergeant MJ, Adetifa I, Antonio M , Pallen MJ.
PeerJ. 2014 Sep 23;2:e585.

The antibody genetics of multiple sclerosis: comparing next-generation sequencing to Sanger sequencing.
Rounds WH, Ligocki AJ, Levin MK, Greenberg BM, et al.
Front Neurol. 2014 Sep 16;5:166.

Somatic mutations are not observed by exome sequencing of lymphocyte DNA from monozygotic twins discordant for congenital hypothyroidism due to thyroid dysgenesis.
Magne F, Serpa R, Van Vliet G, Samuels ME, Deladoëy J.
Horm Res Paediatr. 2014 Sep 23. [Epub ahead of print]

High-frequency aberrantly methylated targets in pancreatic adenocarcinoma identified via global DNA methylation analysis using methylCap-seq.
Zhao Y, Sun J, Zhang H, Guo S, et al.
Clin Epigenetics. 2014 Sep 22;6(1):18.

Sequence analysis of six blood pressure candidate regions in 4,178 individuals: the cohorts for heart and aging research in genomic epidemiology (CHARGE) targeted sequencing study.
Morrison AC, Bis JC, Hwang SJ, Ehret GB, et al.
PLOS One. 2014 Oct 2;9(10):e109155.

The head and neck cancer cell oncogenome: A platform for the development of precision molecular therapies.
Martin D, Abba MC, Molinolo AA, Vitale-Cross L, et al.
Oncotarget. 2014 Sep 20. [Epub ahead of print]

Direct detection and prediction of all pneumococcal serogroups by target enrichment based next generation sequencing.
Ip M, Liyanapathirana V, Ang I, Fung K, et al.
J Clin Microbiol. 2014 Oct 1. [Epub ahead of print]

HSJ1-related hereditary neuropathies: Novel mutations and extended clinical spectrum.
Gess B, Auer-Grumbach M, Schirmacher A, Strom T, et al.
Neurology. 2014 Oct 1. [Epub ahead of print]

Translating Sanger-based routine DNA diagnostics into generic massive parallel ion semiconductor sequencing.
Diekstra A, Bosgoed E, Rikken A, van Lier B, et al.
Clin Chem. 2014 Oct 1. [Epub ahead of print]

Genomic profile of pseudomyxoma peritonei analyzed using next-generation sequencing and immunohistochemistry.
Nummela P, Saarinen L, Thiel A, Järvinen P, et al.
Int J Cancer. 2014 Oct 1. [Epub ahead of print]

A novel familial mutation in the PCSK1 gene that alters the oxyanion hole residue of proprotein convertase 1/3 and impairs its enzymatic activity.
Wilschanski M, Abbasi M, Blanco E, Lindberg I, et al.
PLOS One. 2014 Oct 1;9(10):e108878.

Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer.
Ju YS, Alexandrov LB, Gerstung M, Martincorena I, et al.
Elife. 2014 Oct 1;3. [Epub ahead of print]

Efficient application of next-generation sequencing for the diagnosis of rare genetic syndromes.
Madrigal I, Alvarez-Mora MI, Karlberg O, Rodríguez-Revenga L, et al.
J Clin Pathol. 2014 Sep 30. [Epub ahead of print]

The genomic landscape of childhood and adolescent melanoma.
Lu C, Zhang J, Nagahawatte P, Easton J, et al.
J Invest Dermatol. 2014 Sep 30. [Epub ahead of print]

Whole exome analysis identifies frequent CNGA1 mutations in Japanese population with autosomal recessive retinitis pigmentosa.
Katagiri S, Akahori M, Sergeev Y, Yoshitake K, et al.
PLOS One. 2014 Sep 30;9(9):e108721.

The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data.
Wilks C, Cline MS, Weiler E, Diehkans M, et al.
Database. 2014 Sep 29;2014.

ASCL1 is a lineage oncogene providing therapeutic targets for high-grade neuroendocrine lung cancers.
Augustyn A, Borromeo M, Wang T, Fujimoto J, et al.
Proc Natl Acad Sci U S A. 2014 Sep 29. [Epub ahead of print]

Targeted exon sequencing fails to identify rare coding variants with large effect in rheumatoid arthritis.
Bang SY, Na YJ, Kim K, Joo Y, et al.
Arthritis Res Ther. 2014 Sep 30;16(5):447.

Identification of a novel NHS mutation in a Chinese family with Nance-Horan syndrome.
Li A, Li B, Wu L, Yang L, et al.
Curr Eye Res. 2014 Sep 30:1-5. [Epub ahead of print]

Open-access synthetic spike-in mRNA-seq data for cancer gene fusions.
Tembe WD, Pond SJ, Legendre C, Chuang HY, et al.
BMC Genomics. 2014 Sep 30;15(1):824.

Expanding the phenotype associated with the NEFL mutation: neuromuscular disease in a family with overlapping myopathic and neurogenic findings.
Agrawal PB, Joshi M, Marinakis NS, Schmitz-Abe K, et al.
JAMA Neurol. 2014 Sep 29. [Epub ahead of print]

Efficiency of exome sequencing for the molecular diagnosis of pseudoxanthoma elasticum.
Hosen MJ, Van Nieuwerburgh F, Steyaert W, Deforce D, et al.
J Invest Dermatol. 2014 Sep 29. [Epub ahead of print]

The challenge of informed consent and return of results in translational genomics: empirical analysis and recommendations.
Henderson GE, Wolf SM, Kuczynski KJ, Joffe S, et al.
J Law Med Ethics. 2014 Sep;42(3):344-55.

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next generation sequencing data.
Woo S, Cha SW, Na S, Guest C, et al.
Proteomics. 2014 Sep 29. [Epub ahead of print]

Early manifestations of BPAN in a pediatric patient.
Okamoto N, Ikeda T, Hasegawa T, Yamamoto Y, et al.
Am J Med Genet A. 2014 Sep 26. [Epub ahead of print]

De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies.
EuroEPINOMICS-RES Consortium, et al.
Am J Hum Genet. 2014 Sep 24. [Epub ahead of print]

Utilizing ethnic-specific differences in minor allele frequency to recategorize reported pathogenic deafness variants.
Shearer AE, Eppsteiner RW, Booth KT, Ephraim SS, et al.
Am J Hum Genet. 2014 Oct 2;95(4):445-53.

Genome-wide analysis of noncoding regulatory mutations in cancer.
Weinhold N, Jacobsen A, Schultz N, Sander C, Lee W.
Nat Genet. 2014 Sep 28. [Epub ahead of print]

Molecular characterization of long-term survivors of glioblastoma using genome- and transcriptome-wide profiling.
Reifenberger G, Weber RG, Riehmer V, Kaulich K, et al.
Int J Cancer. 2014 Oct 15;135(8):1822-31.