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Recent Clinical Sequencing Papers of Note: Jun 4, 2014

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Exome sequencing identifies 2 novel presenilin 1 mutations (p.L166V and p.S230R) in British early-onset Alzheimer's disease.
Sassi C, Guerreiro R, Gibbs R, Ding J , et al.
Neurobiol Aging. 2014 May 2. [Epub ahead of print]


Molecular diagnostics of the HBB gene in an Omani cohort using bench-top DNA Ion Torrent PGM technology.
Hassan SM, Vossen RH, Chessa R, den Dunnen JT, et al.
Blood Cells Mol Dis. 2014 May 28. [Epub ahead of print]


Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas.
Zhang L, Chen LH, Wan H, Yang R, et al.
Nat Genet. 2014 Jun 1. [Epub ahead of print]


Whole exome sequencing identifies three recessive FIG4 mutations in an apparently dominant pedigree with Charcot-Marie-Tooth disease.
Menezes MP, Waddell L, Lenk GM, Kaur S, et al.
Neuromuscul Disord. 2014 May 4. [Epub ahead of print]


Inflammatory myofibroblastic tumors harbor multiple potentially actionable kinase fusions.
Lovly CM, Gupta A, Lipson D, Otto G, et al.
Cancer Discov. 2014 May 29. [Epub ahead of print]


Next generation sequencing reveals microRNA isoforms in liver cirrhosis and hepatocellular carcinoma.
Wojcicka A, Swierniak M, Kornasiewicz O, Gierlikowski W, et al.
Int J Biochem Cell Biol. 2014 May 26. [Epub ahead of print]


How do research participants perceive "uncertainty" in genome sequencing?
Biesecker BB, Klein W, Lewis KL, Fisher TC, et al.
Genet Med. 2014 May 29. [Epub ahead of print]


Targeted next-generation sequencing of deafness genes in hearing-impaired individuals uncovers informative mutations.
Vona B, Müller T, Nanda I, Neuner C, et al.
Genet Med. 2014 May 29. [Epub ahead of print]


Severe ipsilateral musculoskeletal involvement in a Cornelia de Lange patient with a novel NIPBL mutation.
Baquero-Montoya C, Gil-Rodríguez MC, Hernández-Marcos M, Teresa-Rodrigo ME, et al.
Eur J Med Genet. 2014 May 26. [Epub ahead of print]


Squamous cell carcinoma of the oral tongue in young non-smokers is genomically similar to tumors in older smokers.
Pickering CR, Zhang J, Neskey DM, Zhao M, et al.
Clin Cancer Res. 2014 May 29. [Epub ahead of print]


A novel de novo mutation of SCN8A (Nav1.6) with enhanced channel activation in a child with epileptic encephalopathy.
Estacion M, O'Brien JE, Conravey A, Hammer MF, et al.
Neurobiol Dis. 2014 May 26. [Epub ahead of print]


Improved survival with T cell clonotype stability after anti-CTLA-4 treatment in cancer patients.
Cha E, Klinger M, Hou Y, Cummings C, et al.
Sci Transl Med. 2014 May 28;6(238):238ra70.


Regional biases in mutation screening due to intratumoral heterogeneity of prostate cancer.
Kim TM, Jung SH, Baek IP, Lee SH, et al.
J Pathol. 2014 May 28. [Epub ahead of print]


Resistance mechanisms for the Bruton's tyrosine kinase inhibitor ibrutinib.
Woyach JA, Furman RR, Liu TM, Ozer HG, et al.
Engl J Med. 2014 May 28. [Epub ahead of print]


RNA-seq profiling reveals aberrant RNA splicing in patient with adult acute myeloid leukemia during treatment.
Li XY, Yao X, Li SN, Suo AL, et al.
Eur Rev Med Pharmacol Sci. 2014 May;18(9):1426-33.


Transcriptome profiling of prostate tumor and matched normal samples by RNA-seq.
Zhai W, Yao XD, Xu YF, Peng B, et al.
Eur Rev Med Pharmacol Sci. 2014 May;18(9):1354-60.


Multigene mutational profiling of cholangiocarcinomas identifies actionable molecular subgroups.
Simbolo M, Fassan M, Ruzzenente A, Mafficini A, et al.
Oncotarget. 2014 May 15;5(9):2839-52.


A novel homozygous mutation in FGFR3 causes tall stature, severe lateral tibial deviation, scoliosis, hearing impairment, camptodactyly and arachnodactyly.
Makrythanasis P, Temtamy S, Aglan MS, Otaify GA, et al.
Hum Mutat. 2014 May 26. [Epub ahead of print]


Three rare diseases in one Sib pair: RAI1, PCK1, GRIN2B mutations associated with Smith-Magenis syndrome, cytosolic PEPCK deficiency and NMDA receptor glutamate insensitivity.
Adams DR, Yuan H, Holyoak T, Arajs KH, et al.
Mol Genet Metab. 2014 Apr 13. [Epub ahead of print]


Patient experiences with gene panels based on exome sequencing in clinical diagnostics: high acceptance and low distress.
Sie AS, Prins JB, van Zelst-Stams WA, Veltman JA, et al.
Clin Genet. 2014 May 23. [Epub ahead of print]


A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications.
Alemán A, Garcia-Garcia F, Medina I, Dopazo J.
Nucleic Acids Res. 2014 May 26. [Epub ahead of print]


Usability study of clinical exome analysis software: Top lessons learned and recommendations.
Shyr C, Kushniruk A, Wasserman WW.
J Biomed Inform. 2014 May 23. [Epub ahead of print]


Rare deleterious mutations of the gene EFR3A in autism spectrum disorders.
Gupta AR, Pirruccello M, Cheng F, Kang HJ, et al.
Mol Autism. 2014 Apr 29;5:31.


Identification of prognostic biomarkers in hepatitis B virus-related hepatocellular carcinoma and stratification by integrative multi-omics analysis.
Miao R, Luo H, Zhou H, Li G, et al.
J Hepatol. 2014 May 22. [Epub ahead of print]


Comparison of targeted next-generation sequencing with conventional sequencing for predicting the responsiveness to epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) therapy in never-smokers with lung adenocarcinoma.
Han JY, Kim SH, Lee YS, Lee SY, et al.
Lung Cancer. 2014 Apr 29. [Epub ahead of print]


Draft genome sequence of multidrug-resistant Mycobacterium tuberculosis strain CWCFVRF MDRTB 670, isolated from the sputum of a patient from Chennai, India, with clinically suspected tuberculosis.
Lakshmipathy D, Vetrivel U, Irudayam LT, Ramasubban G, et al.
Genome Announc. 2014 May 22;2(3).


Improving mutation screening in familial hematuric nephropathies through next generation sequencing.
Morinière V, Dahan K, Hilbert P, Lison M, et al.
J Am Soc Nephrol. 2014 May 22. [Epub ahead of print]


Loss-of-function variants in schizophrenia risk and SETD1A as a candidate susceptibility gene.
Takata A, Xu B, Ionita-Laza I, Roos JL, et al.
Neuron. 2014 May 21;82(4):773-80.


Rapid and cost effective screening of breast and ovarian cancer genes using novel sequence capture method in clinical samples.
Arvai K, Horváth P, Balla B, Tőkés AM, et al.
Fam Cancer. 2014 May 23. [Epub ahead of print]


Genetic testing for sporadic hearing loss using targeted massively parallel sequencing identifies 10 novel mutations.
Gu X, Guo L, Ji H, Sun S, et al.
Clin Genet. 2014 May 22. [Epub ahead of print]


Whole-exome sequencing confirmation of a novel heterozygous mutation in RUNX1 in a pregnant woman with platelet disorder.
Obata M, Tsutsumi S, Makino S, Takahashi K, et al.
Platelets. 2014 May 22:1-6. [Epub ahead of print]


Mutation in TMEM98 in a large white kindred with autosomal dominant nanophthalmos linked to 17p12-q12.
Awadalla MS, Burdon KP, Souzeau E, Landers J, et al.
JAMA Ophthalmol. 2014 May 22. [Epub ahead of print]


Deep sequencing detects very-low-grade somatic mosaicism in the unaffected mother of siblings with nemaline myopathy.
Miyatake S, Koshimizu E, Hayashi YK, Miya K, et al.
Neuromuscul Disord. 2014 Apr 24. [Epub ahead of print]


Exome sequencing identifies a recessive PIGN splice site mutation as a cause of syndromic congenital diaphragmatic hernia.
Brady PD, Moerman P, De Catte L, Deprest J , et al.
Eur J Med Genet. 2014 May 19. [Epub ahead of print]

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Whale Decline Analysis

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.