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In Print: Last Week's Clinical Sequencing Papers of Note: Sep 11, 2013

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Exome sequencing and functional analysis identifies a novel mutation in EXT1 gene that causes multiple osteochondromas.
Zhang F, Liang J, Guo X, Zhang Y, et al.
PLOS One. 2013 Aug 29;8(8):e72316.


Systematic pharmacogenomics analysis of a malay whole genome: proof of concept for personalized medicine.
Salleh MZ, Teh LK, Lee LS, Ismet RI, et al.
PLOS One. 2013 Aug 23;8(8):e71554.


Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery.
Zhang G, Hoersch S, Amsterdam A, Whittaker CA, et al.
PLOS Genet. 2013 Aug;9(8):e1003734.


Somatic mutations in MAP3K5 attenuate its pro-apoptotic function in melanoma through increased binding to thioredoxin.
Prickett TD, Zerlanko B, Gartner JJ, Parker SC, et al.
J Invest Dermatol. 2013 Sep 5. [Epub ahead of print]


Whole transcriptome sequencing identifies tumor-specific mutations in human oral squamous cell carcinoma.
Zhang Q, Zhang J, Jin H, Sheng S.
BMC Med Genomics. 2013 Sep 4;6(1):28.


Detecting the somatic mutations spectrum of Chinese lung cancer by analyzing the whole mitochondrial DNA genomes.
Fang Y, Huang J, Zhang J, Wang J, et al.
Mitochondrial DNA. 2013 Sep 6. [Epub ahead of print]


MetaRanker 2.0: a web server for prioritization of genetic variation data.
Pers TH, Dworzyński P, Thomas CE, Lage K, Brunak S.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W104-8.


Multi-lineage somatic activating mutations in HRAS and NRAS cause mosaic cutaneous and skeletal lesions, elevated FGF23, and hypophosphatemia.
Lim YH, Ovejero D, Sugarman JS, Deklotz CM, et al.
Hum Mol Genet. 2013 Sep 4. [Epub ahead of print]


Archival bone marrow trephines are suitable for high-throughput mutation analysis using next generation sequencing technology.
Hasemeier B, Geffers R, Bartels S, Schlegelberger B, et al.
Haematologica. 2013 Sep;98(9):e115-6.


Deep sequencing reveals increased DNA methylation in chronic rat epilepsy.
Kobow K, Kaspi A, Harikrishnan KN, Kiese K, et al.
Acta Neuropathol. 2013 Sep 5. [Epub ahead of print]


Direct RNA sequencing mediated identification of mRNA localized in protrusions of human MDA-MB-231 metastatic breast cancer cells.
Jakobsen KR, Sørensen E, Brøndum KK, Daugaard TF, et al.
J Mol Signal. 2013 Sep 1;8(1):9. [Epub ahead of print]


Nager syndrome: report on 14 families and confirmation of SF3B4 haploinsufficiency as the major cause.
Petit F, Escande F, Jourdain AS, Porchet N, et al.
Clin Genet. 2013 Sep 4. [Epub ahead of print]


A rare WNT1 missense variant overrepresented in ASD leads to increased Wnt signal pathway activation.
Martin PM, Yang X, Robin N, Lam E, et al.
Transl Psychiatry. 2013 Sep 3;3:e301.


Molecular diagnosis of infantile onset inflammatory bowel disease by exome sequencing.
Dinwiddie DL, Bracken JM, Bass JA, Christenson K, et al.
Genomics. 2013 Aug 31. pii: S0888-7543(13)00180-8. [Epub ahead of print]


Identification of novel OTOF compound heterozygous mutations by targeted next-generation sequencing in a Chinese patient with auditory neuropathy spectrum disorder.
Zhang LP, Chai YC, Yang T, Wu H.
Int J Pediatr Otorhinolaryngol. 2013 Aug 16. pii: S0165-5876(13)00392-3. [Epub ahead of print]


Lens subluxation and retinal dysfunction in a girl with homozygous VSX2 mutation.
Khan AO, Aldahmesh MA, Noor J, Salem A, Alkuraya FS.
Ophthalmic Genet. 2013 Sep 3. [Epub ahead of print]


Novel TRAF1-ALK fusion identified by deep RNA sequencing of anaplastic large cell lymphoma.
Feldman AL, Vasmatzis G, Asmann YW, Davila J, et al.
Genes Chromosomes Cancer. 2013 Sep 2. [Epub ahead of print]


Novel MIR143-NOTCH fusions in benign and malignant glomus tumors.
Mosquera JM, Sboner A, Zhang L, Chen CL, et al.
Genes Chromosomes Cancer. 2013 Sep 2. [Epub ahead of print]


Exome sequencing in multiplex autism families suggests a major role for heterozygous truncating mutations.
Toma C, Torrico B, Hervás A, Valdés-Mas R, et al.
Mol Psychiatry. 2013 Sep 3. [Epub ahead of print]


Validation of next-generation sequencing technologies in genetic diagnosis of dementia.
Beck J, Pittman A, Adamson G, Campbell T, et al.
Neurobiol Aging. 2013 Aug 31. pii: S0197-4580(13)00322-9. [Epub ahead of print]

The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.