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In Print: Last Week's Clinical Sequencing Papers of Note: May 16, 2012


Disruption of RAB40AL function leads to Martin-Probst syndrome, a rare X-linked multisystem neurodevelopmental human disorder.
Bedoyan JK, Schaibley VM, Peng W, Bai Y, et al.
J Med Genet. 2012 May;49(5):332-40.

A paradigm shift in the delivery of services for diagnosis of inherited retinal disease.
O'Sullivan J, Mullaney BG, Bhaskar SS, Dickerson JE, et al.
J Med Genet. 2012 May;49(5):322-6.

Clinical application of exome sequencing in undiagnosed genetic conditions.
Need AC, Shashi V, Hitomi Y, Schoch K, et al.
J Med Genet. 2012 May 11. [Epub ahead of print]
(see our coverage in CSN 5/9/2012)

Ultrasensitive measurement of hotspot mutations in tumor DNA in blood using error-suppressed multiplexed deep sequencing.
Narayan A, Carriero NJ, Gettinger SN, Kluytenaar J, et al.
Cancer Res. 2012 May 10. [Epub ahead of print]

BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration.
Flockhart RJ, Webster DE, Qu K, Mascarenhas N, et al.
Genome Res. 2012 May 11. [Epub ahead of print]

Towards a mtDNA locus-specific mutation database using the LOVD platform.
Elson JL, Sweeney MG, Procaccio V, Yarham JW, et al.
Hum Mutat. 2012 May 11. [Epub ahead of print]

Paralogous annotation of disease-causing variants in Long QT syndrome genes.
Ware JS, Walsh R, Cunningham F, Birney E, Cook SA.
Hum Mutat. 2012 May 11. [Epub ahead of print]

Strelka: Accurate somatic small-variant calling from sequenced tumor-normal sample pairs.
Saunders CT, Wong W, Swamy S, Becq J, et al.
Bioinformatics. 2012 May 10. [Epub ahead of print]

Combined deep microRNA and mRNA sequencing identifies protective transcriptomal signature of enhanced PI3Kα signaling in cardiac hypertrophy.
Yang KC, Ku YC, Lovett M, Nerbonne JM.
J Mol Cell Cardiol. 2012 May 10. [Epub ahead of print]

GPSM2 mutations cause the brain malformations and hearing loss in Chudley-McCullough syndrome.
Doherty D, Chudley AE, Coghlan G, Ishak GE, et al.
Am J Hum Genet. 2012 May 9. [Epub ahead of print]

Genomic characterisation of acral melanoma cell lines.
Furney SJ, Turajlic S, Fenwick K, Lambros MB, et al.
Pigment Cell Melanoma Res. 2012 May 12. [Epub ahead of print]

Whole exome sequencing identifies a splicing mutation in NSUN2 as a cause of a Dubowitz-like syndrome.
Martinez FJ, Lee JH, Lee JE, Blanco S, et al.
J Med Genet. 2012 May 10. [Epub ahead of print]

Hereditary myopathy with early respiratory failure associated with a mutation in A-band titin.
Ohlsson M, Hedberg C, Brådvik B, Lindberg C, et al.
Brain. 2012 May 9. [Epub ahead of print]

Titin mutation segregates with hereditary myopathy with early respiratory failure.
Pfeffer G, Elliott HR, Griffin H, Barresi R, et al.
Brain. 2012 May 9. [Epub ahead of print]

Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance.
Dudley DM, Chin EN, Bimber BN, Sanabani SS, et al.
PLoS One. 2012;7(5):e36494.

Intraclonal heterogeneity and distinct molecular mechanisms characterize the development of t(4;14) and t(11;14) myeloma.
Walker BA, Wardell CP, Melchor L, Hulkki S, et al.
Blood. 2012 May 9. [Epub ahead of print]

Noninvasive prenatal detection of chromosomal aneuploidies using different next generation sequencing strategies and algorithms.
Stumm M, Entezami M, Trunk N, Beck M, et al.
Prenat Diagn. 2012 May 9:1-9.

Whole exome sequencing identifies multiple, complex etiologies in an idiopathic hereditary pancreatitis kindred.
Larusch J, Barmada MM, Solomon S, Whitcomb DC.
JOP. 2012 May 10;13(3):258-62.

HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing next generation sequencing data set.
Yin L, Yao J, Gardner BP, Chang K, et al.
Bioinformation. 2012;8(8):388-90.

The characteristics of genome-wide DNA methylation in naïve CD4+ T cells of patients with psoriasis or atopic dermatitis.
Han J, Park SG, Bae JB, Choi J, et al.
Biochem Biophys Res Commun. 2012 Apr 30. [Epub ahead of print]

A deleterious mutation in DNAJC6 encoding the neuronal-specific clathrin-uncoating co-chaperone auxilin is associated with juvenile Parkinsonism.
Edvardson S, Cinnamon Y, Ta-Shma A, Shaag A, et al.
PLoS One. 2012;7(5):e36458.

Concordant signaling pathways produced by pesticide exposure in mice correspond to pathways identified in human Parkinson's disease.
Gollamudi S, Johri A, Calingasan NY, Yang L, et al.
PLoS One. 2012;7(5):e36191.

Detection of microdeletion 22q11.2 in a fetus by next-generation sequencing of maternal plasma.
Jensen TJ, Dzakula Z, Deciu C, van den Boom D, Ehrich M.
Clin Chem. 2012 May 4. [Epub ahead of print]

Gut microbial colonisation in premature neonates predicts neonatal sepsis.
Madan JC, Salari RC, Saxena D, Davidson L, et al.
Arch Dis Child Fetal Neonatal. Ed. 2012 May 6. [Epub ahead of print]

Homozygous missense mutation in BOLA3 causes multiple mitochondrial dysfunctions syndrome in two siblings.
Haack TB, Rolinski B, Haberberger B, Zimmermann F, et al.
J Inherit Metab Dis. 2012 May 5. [Epub ahead of print]

Exome sequencing of liver fluke-associated cholangiocarcinoma.
Ong CK, Subimerb C, Pairojkul C, Wongkham S, et al.
Nat Genet. 2012 May 6. [Epub ahead of print]

Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma.
Guichard C, Amaddeo G, Imbeaud S, Ladeiro Y, et al.
Nat Genet. 2012 May 6. [Epub ahead of print]

Hereditary mixed polyposis syndrome is caused by a 40-kb upstream duplication that leads to increased and ectopic expression of the BMP antagonist GREM1.
Jaeger E, Leedham S, Lewis A, Segditsas S, et al.
Nat Genet. 2012 May 6. [Epub ahead of print]

A human homeotic transformation resulting from mutations in PLCB4 and GNAI3 causes auriculocondylar syndrome.
Rieder MJ, Green GE, Park SS, Stamper BD, et al.
Am J Hum Genet. 2012 May 4;90(5):907-14.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.