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Recent Clinical Sequencing Papers of Note: Oct 15, 2014


Identification of two novel mutations in FAM136A and DTNA genes in autosomal dominant familial Meniere's disease.
Requena T, Cabrera S, Martín-Sierra C, Price SD, et al.
Hum Mol Genet. 2014 Oct 9. [Epub ahead of print]

Next generation sequencing as a rapid molecular diagnosis for Marfan syndrome in a Chinese family with mutations in the fibrillin-1 gene.
Xiao Y, Liu Y, Yang K, Yang Y, et al.
Clin Chim Acta. 2014 Oct 7. [Epub ahead of print]

Next generation sequencing of pancreatic cyst fluid microRNAs from low grade- benign and high grade- invasive lesions.
Wang J, Paris PL, Chen J, Ngo V, et al.
Cancer Lett. 2014 Oct 7. [Epub ahead of print]

Mutational landscape of aggressive cutaneous squamous cell carcinoma.
Pickering CR, Zhou JH, Lee JJ, Drummond JA, et al.
Clin Cancer Res. 2014 [Epub ahead of print]

Phenotypic heterogeneity in monogenic diabetes: The clinical and diagnostic utility of a gene panel-based next-generation sequencing approach.
Alkorta-Aranburu G, Carmody D, Cheng YW, Nelakuditi V, et al.
Mol Genet Metab. 2014 Sep 28. [Epub ahead of print]

Somatic mutations of SUZ12 in malignant peripheral nerve sheath tumors.
Zhang M, Wang Y, Jones S, Sausen M, et al.
Nat Genet. 2014 Oct 12. [Epub ahead of print]

Application of next-generation sequencing to study ascitic microbiome in cirrhotic patients with or without spontaneous bacterial peritonitis.
Feng Y, Chen CL, Chen TH, Liang YH, et al.
J Microbiol Immunol Infect. 2014 Oct 8. [Epub ahead of print]

Targeted sequencing using a 47 gene multiple myeloma mutation panel (M3 P) in -17p high risk disease.
Kortüm KM, Langer C, Monge J, Bruins L, et al.
Br J Haematol. 2014 Oct 10. [Epub ahead of print]

'N-of-1-pathways' unveils personal deregulated mechanisms from a single pair of RNA-seq samples: towards precision medicine.
Gardeux V, Achour I, Li J, Maienschein-Cline M, et al.
J Am Med Inform Assoc. 2014 Nov;21(6):1015-25.

Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing.
Zhang J, Fujimoto J, Zhang J, Wedge DC, et al.
Science. 2014 Oct 10;346(6206):256-9.

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution.
de Bruin EC, McGranahan N, Mitter R, Salm M, et al.
Science. 2014 Oct 10;346(6206):251-6.

Rapid and cost-effective molecular diagnosis using exome sequencing of one proband with autosomal dominant congenital cataract.
Chen JH, Qiu J, Chen H, Pang CP, Zhang M.
Eye. 2014 Oct 10. [Epub ahead of print]

Targeted exon capture and sequencing in sporadic amyotrophic lateral sclerosis.
Couthouis J, Raphael AR, Daneshjou R, Gitler AD.
PLOS Genet. 2014 Oct 9;10(10):e1004704.

Massively parallel sequencing identifies recurrent mutations in TP53 in thymic carcinoma associated with poor prognosis.
Moreira AL, Won HH, McMillan R, Huang J, et al.
J Thorac Oncol. 2014 Oct 8. [Epub ahead of print]

Identifying differential expression genes and single nucleotide variations using RNA-seq in metastatic melanoma.
Liu D, Zhao ZG, Jiao ZL, Li HJ.
Genet Mol Res. 2014 Oct 7;13(4):8153-8162.

Economic regulation of next-generation sequencing.
Evans BJ.
J Law Med Ethics. 2014 Sep;42 Suppl 1:51-66.

Clinical integration of next generation sequencing: coverage and reimbursement challenges.
Deverka PA, Dreyfus JC.
J Law Med Ethics. 2014 Sep;42 Suppl 1:22-41.

Regulation of next generation sequencing.
Javitt GH, Carner KS.
J Law Med Ethics. 2014 Sep;42 Suppl 1:9-21.

Clinical integration of next generation sequencing: a policy analysis.
Kaufman D, Curnutte M, McGuire AL.
J Law Med Ethics. 2014 Sep;42 Suppl 1:5-8.

Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data.
Oesper L, Satas G, Raphael BJ.
Bioinformatics. 2014 Oct 8. [Epub ahead of print]

ExomeAI: detection of recurrent allelic imbalance in tumors using whole exome sequencing data.
Nadaf J, Majewski J, Fahiminiya S.
Bioinformatics. 2014 Oct 8. [Epub ahead of print]

Mutational profiles in triple-negative breast cancer defined by ultradeep multigene sequencing show high rates of PI3K pathway alterations and clinically relevant entity subgroup specific differences.
Kriegsmann M, Endris V, Wolf T, Pfarr N, et al.
Oncotarget. 2014 Sep 16. [Epub ahead of print]

CACNA1B mutation is linked to unique Myoclonus-Dystonia syndrome.
Groen JL, Andrade A, Ritz K, Jalalzadeh H, et al.
Hum Mol Genet. 2014 Oct 8. [Epub ahead of print]

Identification of the rare compound heterozygous variants in the NEB gene in a Korean family with intellectual disability, epilepsy and early-childhood-onset generalized muscle weakness.
Jin HS, Lee JB, Kim K, Lee KY, et al.
J Hum Genet. 2014 Oct 9;0. [Epub ahead of print]

Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing.
Suzuki T, Tsurusaki Y, Nakashima M, Miyake N, et al.
J Hum Genet. 2014 Oct 9. [Epub ahead of print]

Response and acquired resistance to everolimus in anaplastic thyroid cancer.
Wagle N, Grabiner BC, Van Allen EM, Amin-Mansour A, et al.
N Engl J Med. 2014 Oct 9;371(15):1426-1433.

CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors.
Sugathan A, Biagioli M, Golzio C, Erdin S, et al.
Proc Natl Acad Sci U S A. 2014 Oct 7. [Epub ahead of print]

Identification of recurrent FGFR3-TACC3 fusion oncogenes from lung adenocarcinoma.
Capelletti M, Dodge ME, Ercan D, Hammerman PS, et al.
Clin Cancer Res. 2014 Oct 7. [Epub ahead of print]

An exome study of Parkinson's disease in Sardinia, a Mediterranean genetic isolate.
Quadri M, Yang X, Cossu G, Olgiati S, et al.
Neurogenetics. 2014 Oct 8. [Epub ahead of print]

OTX2 mutations cause autosomal dominant pattern dystrophy of the retinal pigment epithelium.
Vincent A, Forster N, Maynes JT, Paton TA, et al.
J Med Genet. 2014 Oct 7. [Epub ahead of print]

Absence of patient-to-patient intrahospital transmission of Staphylococcus aureus as determined by whole-genome sequencing.
Long SW, Beres SB, Olsen RJ, Musser JM1.
MBio. 2014 Oct 7;5(5).

A truncating PET100 variant causing fatal infantile lactic acidosis and isolated cytochrome c oxidase deficiency.
Oláhová M, Haack TB, Alston CL, Houghton JA, et al.
Eur J Hum Genet. 2014 Oct 8. [Epub ahead of print]

Somatic neurofibromatosis type 1 (NF1) inactivation events in cutaneous neurofibromas of a single NF1 patient.
Emmerich D, Zemojtel T, Hecht J, Krawitz P, et al.
Eur J Hum Genet. 2014 Oct 8. [Epub ahead of print]

Gut microbial community structure and complications after kidney transplantation: a pilot study.
Lee JR, Muthukumar T, Dadhania D, Toussaint NC, et al.
Transplantation. 2014 Oct 15;98(7):697-705.

Whole-exome sequencing to decipher the genetic heterogeneity of hearing loss in a Chinese family with deaf by deaf mating.
Qing J, Yan D, Zhou Y, Liu Q, et al.
PLOS One. 2014 Oct 7;9(10):e109178.

Non-invasive prenatal chromosomal aneuploidy testing − clinical experience: 100,000 clinical samples.
McCullough RM, Almasri EA, Guan X, Geis JA, et al.
PLOS One. 2014 Oct 7;9(10):e109173.

Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing.
Bao R, Huang L, Andrade J, Tan W, et al.
Cancer Inform. 2014 Sep 21;13(Suppl 2):67-82.

Integrated analysis of whole-genome paired-end and mate-pair sequencing data for identifying genomic structural variations in multiple myeloma.
Yang R, Chen L, Newman S, Gandhi K, et al.
Cancer Inform. 2014 Sep 21;13(Suppl 2):49-53.

Exome sequencing identifies FANCM as a susceptibility gene for triple-negative breast cancer.
Kiiski JI, Pelttari LM, Khan S, Freysteinsdottir ES, et al.
Proc Natl Acad Sci U S A. 2014 Oct 6. [Epub ahead of print]

Detailed analysis of therapy-driven clonal evolution of TP53 mutations in chronic lymphocytic leukemia.
Malcikova J, Stano-Kozubik K, Tichy B, Kantorova B, et al.
Leukemia. 2014 Oct 7. [Epub ahead of print]

Identification and characterization of a novel HLA-B hybrid allele, B*08:132 with next generation sequencing.
Papazoglou A, Gasiewski A, Huynh A, Duke J, et al.
Tissue Antigens. 2014 Oct 7. [Epub ahead of print]

Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers.
Zhang B, Xing X, Li J, Lowdon RF, et al.
BMC Genomics. 2014 Oct 6;15(1):868.

Comprehensive analysis of genetic alterations and their prognostic impacts in adult acute myeloid leukemia patients.
Kihara R, Nagata Y, Kiyoi H, Kato T, et al.
Leukemia. 2014 Aug;28(8):1586-95.

Next generation sequencing and tumor mutation profiling: are we ready for routine use in the oncology clinic?
Tripathy D, Harnden K, Blackwell K, Robson M.
BMC Med. 2014 Aug 12;12(1):140.

Feasibility of noninvasive prenatal testing for common fetal aneuploidies in an early gestational window.
Shi X, Zhang Z, Cram DS, Liu C.
Clin Chim Acta. 2014 Oct 3. [Epub ahead of print]

Next-generation sequencing analysis of miRNA expression in control and FSHD myogenesis.
Colangelo V, François S, Soldà G, Picco R, et al.
PLOS One. 2014 Oct 6;9(10):e108411.

De novo insertions and deletions of predominantly paternal origin are associated with autism spectrum disorder.
Dong S, Walker MF, Carriero NJ, DiCola M, et al.
Cell Rep. 2014 Oct 1. [Epub ahead of print]

High-throughput multiplex HLA genotyping by next-generation sequencing using multi-locus individual tagging.
Ehrenberg PK, Geretz A, Baldwin KM, Apps R, et al.
BMC Genomics. 2014 Oct 6;15(1):864.

The Scan

Billions for Antivirals

The US is putting $3.2 billion toward a program to develop antivirals to treat COVID-19 in its early stages, the Wall Street Journal reports.

NFT of the Web

Tim Berners-Lee, who developed the World Wide Web, is auctioning its original source code as a non-fungible token, Reuters reports.

23andMe on the Nasdaq

23andMe's shares rose more than 20 percent following its merger with a special purpose acquisition company, as GenomeWeb has reported.

Science Papers Present GWAS of Brain Structure, System for Controlled Gene Transfer

In Science this week: genome-wide association study ties variants to white matter stricture in the brain, and more.