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Recent Clinical Sequencing Papers of Note: Sep 3, 2014


Profiling the T-cell receptor repertoire of patient with pleural tuberculosis by high-throughput sequencing.
Li D, Gao G, Li Z, Sun W, et al.
Immunol Lett. 2014 Aug 27. [Epub ahead of print]

Novel alpha-actinin 2 variant associated with familial hypertrophic cardiomyopathy and juvenile atrial arrhythmias: a massively parallel sequencing study.
Girolami F, Iascone M, Tomberli B, Bardi S, et al.
Circ Cardiovasc Genet. 2014 Aug 30. [Epub ahead of print]

Two rare AKAP9 variants are associated with Alzheimer's disease in African Americans.
Logue MW, Schu M, Vardarajan BN, Farrell J, et al.
Alzheimers Dement. 2014 Aug 26. [Epub ahead of print]

Exome sequencing reveals novel mutation targets in diffuse large B cell lymphomas derived from Chinese patients.
de Miranda NF, Georgiou K, Chen L, Wu C, et al.
Blood. 2014 Aug 29. [Epub ahead of print]

Mutations in IFT172 cause isolated retinal degeneration and Bardet-Biedl syndrome.
Bujakowska KM, Zhang Q, Siemiatkowska AM, Liu Q, et al.
Hum Mol Genet. 2014 Aug 28. [Epub ahead of print]

Exome sequencing reveals mutation in GJA1 as a cause of keratoderma-hypotrichosis-leukonychia totalis syndrome.
Wang H, Cao X, Lin Z, Lee M, et al.
Hum Mol Genet. 2014 Aug 28. [Epub ahead of print]

Inferring copy number and genotype in tumour exome data.
Amarasinghe KC, Li J, Hunter SM, Ryland GL, et al.
BMC Genomics. 2014 Aug 28;15(1):732.

Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing.
Redin C, Gérard B, Lauer J, Herenger Y, et al.
J Med Genet. 2014 Aug 28. [Epub ahead of print]

Next generation sequencing to determine HLA class II genotypes in a cohort of hematopoietic cell transplant patients and donors.
Smith AG, Pyo CW, Nelson W, Gow E, et al.
Hum Immunol. 2014 Aug 25. [Epub ahead of print]

Identification of patients with recurrent gbm that benefit from bevacizumab.
French P, Erdem-Eraslan L, Kros JM, Oosterkamp HM, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii8-iii9.

The treatment-resistant mesenchymal signature in glioblastoma derives from tumor cells independent of stroma.
Sulman EP, Wang Q, Ezhilarasan R, Goodman LD, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii8.

Detection of circulating tumor DNA in early and late stage human malignancies.
Bettegowda C, Sausen M, Leary R, Kinde I, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii7.

Clonal evolution of gliomas is encoded in the evolutionary dynamics of DNA methylation.
Costello JF, Mazor T, Pankov A, Johnson BE, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii51-iii52.

Genome-wide analysis uncovers recurrent alterations in primary central nervous system lymphomas (pcnsl).
Patrick O'Neill B, Braggio E, O'Neill BP, Van Wier S, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii43.

Integrative genomic characterization of lower grade gliomas.
Brat DJ1; TCGA Lower Grade Gliomas Analysis Working Group.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii3.

Intracranial germ cell tumors with mtor mutation are common in basal ganglia.
Nishikawa R, Fukuoka K, Ichimura K.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii28.

Detailed molecular characterisation of diffuse intrinsic pontine gliomas identifies three molecular subgroups and a novel cancer driver, acvr1.
Hawkins C, Buczkowicz P, Hoeman C, Rakopoulos P, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii26-iii27.

Informing treatment decisions in relapsed pediatric malignancies using next-generation diagnostics.
Pfister SM, Jones DT, Capper D, Witt R, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii24.

Assessing the utility of clinical tumor sequencing in the pediatric neuro-oncology clinic.
Parsons DW, Roy A, Monzon FA, López-Terrada DH, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii24.

Structural variants shuffle chromatin to activate gfi1 family oncogenes in medulloblastoma.
Northcott PA, Lee C, Zichner T, Lichter P, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii24.

Whole exome sequencing identified that the MAPK and pi3k pathways are the main targets for mutations in intracranial germ cell tumors.
Ichimura K, Fukushima S, Totoki Y, Matsushita Y, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii23.

Epigenome alterations define lethal cimp positive ependymomas of infancy.
Taylor MD, Mack S, Witt H, Dirks P, et al.
Neuro Oncol. 2014 Jul;16(suppl 3):iii16.

C11orf95-rela fusions drive oncogenic NF-kb signaling in ependymoma.
Gilbertson R, Parker M, Mohankumar KM, Punchihewa C, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii16.

Image guided RNA-seq reveals subtype-specific patterns at the infiltrative margins of glioblastoma.
Canoll P, Sims P, Gil B, Pisapia D, Malone H, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii10.

Genetic changes in radiation-associated meningioma.
Claus EB, Calvocoressi L, Greenhalgh S, Walsh K, et al.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii1.

Temporal and spacial evolution of clones in 400 low grade gliomas in Japan.
Natsume A, Suzuki H, Ogawa S, Wakabayashi T.
Neuro Oncol. 2014 Jul;16 Suppl 3:iii1.

Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions.
Brannon A, Vakiani E, Sylvester BE, Scott SN, et al.
Genome Biol. 2014 Aug 28;15(8):454.

Sequencing of Charcot-Marie-Tooth disease genes in a toxic polyneuropathy.
Beutler AS, Kulkarni AA, Kanwar R, Klein CJ, et al.
Ann Neurol. 2014 Aug 28. [Epub ahead of print]

De novo KCNB1 mutations in epileptic encephalopathy.
Torkamani A, Bersell K, Jorge BS, Bjork RL, et al.
Ann Neurol. 2014 Aug 28. [Epub ahead of print]

Atlas of the clinical genetics of human dilated cardiomyopathy.
Haas J, Frese KS, Peil B, Kloos W, et al.
Eur Heart J. 2014 Aug 27. [Epub ahead of print]

Marked methylation changes in intestinal genes during the perinatal period of preterm neonates.
Gao F, Zhang J, Jiang P, Gong D, et al.
BMC Genomics. 2014 Aug 26;15(1):716.

ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples.
Tian R, Basu MK, Capriotti E.
Bioinformatics. 2014 Sep 1;30(17):i572-i578.

A PGD pregnancy achieved by embryo copy number variation sequencing with confirmation by non-invasive prenatal diagnosis.
Wang H, Wang L, Ma M, Song Z, et al.
J Genet Genomics. 2014 Aug 20;41(8):453-456.

Use of whole-exome sequencing for the diagnosis of atypical Birt-Hogg-Dubé syndrome.
Liu Z, Xu KF, Hu C, Chen R, et al.
Genet Genomics. 2014 Aug 20;41(8):449-451.

Whole exome sequencing hints at a unique mutational profile of paediatric T-cell lymphoblastic lymphoma.
Bonn BR, Huge A, Rohde M, Oschlies I, et al.
Br J Haematol. 2014 Aug 27. [Epub ahead of print]

Diverse modes of genomic alterations in hepatocellular carcinoma.
Jhunjhunwala S, Jiang Z, Stawiski EW, Gnad F, et al.
Genome Biol. 2014 Aug 26;15(8):436.

Genome-wide small nucleolar RNA (snoRNA) expression analysis of lung cancer by next-generation deep sequencing.
Gao L, Ma J, Mannoor K, Guarnera MA, et al.
Int J Cancer. 2014 Aug 27. [Epub ahead of print]

Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution.
Fisher R, Horswell S, Rowan A, Salm MP, et al.
Genome Biol. 2014 Aug 27;15(8):433.

The NF-κB genomic landscape in lymphoblastoid B cells.
Zhao B, Barrera LA, Ersing I, Willox B, et al.
Cell Rep. 2014 Aug 20. [Epub ahead of print]

MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.
Grimes SM, Ji HP.
BMC Bioinformatics. 2014 Aug 27;15(1):290.

High diversity of beta-lactamases in the General Hospital Vienna verified by whole genome sequencing and statistical analysis.
Barišić I, Mitteregger D, Hirschl AM, Noehammer C, Wiesinger-Mayr H.
Infect Genet Evol. 2014 Aug 23. [Epub ahead of print]

Whole exome sequencing of extreme morbid obesity patients: translational implications for obesity and related disorders.
Paz-Filho G, Boguszewski MC, Mastronardi CA, Patel HR, et al.
Genes. 2014 Aug 25;5(3):709-725.

Comprehensive diagnostic testing for stereocilin: an approach for analyzing medically important genes with high homology.
Mandelker D, Amr SS, Pugh T, Gowrisankar S, et al.
J Mol Diagn. 2014 Aug 22. [Epub ahead of print]

Analysis of POFUT1 gene mutation in a Chinese family with Dowling-Degos disease.
Chen M, Li Y, Liu H, Fu X, et al.
PLOS One. 2014 Aug 26;9(8):e104496.

Targeted next-generation sequencing in the diagnosis of neurodevelopmental disorders.
Okamoto N, Miya F, Tsunoda T, Kato M, et al.
Clin Genet. 2014 Aug 25. [Epub ahead of print]

The first mutation in CNGA2 in two brothers with anosmia.
Karstensen HG, Mang Y, Fark T, Hummel T, Tommerup N.
Clin Genet. 2014 Aug 25. [Epub ahead of print]

Clinical pertinence metric enables hypothesis-independent genome-phenome analysis for neurologic diagnosis.
Segal MM, Abdellateef M, El-Hattab AW, Hilbush BS, et al.
J Child Neurol. 2014 Aug 24. [Epub ahead of print]

The somatic genomic landscape of chromophobe renal cell carcinoma.
Davis CF, Ricketts CJ, Wang M, Yang L, et al.
Cancer Cell. 2014 Aug 20. [Epub ahead of print].

PBP2a mutations causing high-level ceftaroline resistance in clinical methicillin-resistant Staphylococcus aureus isolates.
Long SW, Olsen RJ, Mehta SC, Palzkill TG, et al.
Antimicrob Agents Chemother. 2014 Aug 25. [Epub ahead of print]

Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer.
Wyatt AW, Mo F, Wang K, McConeghy B, et al.
Genome Biol. 2014 Aug 26;15(8):426.

Identification of a breast cancer family double heterozygote for RAD51C and BRCA2 gene mutations.
Ahlborn LB, Steffensen AY, Jønson L, Djursby M, et al.
Fam Cancer. 2014 Aug 26. [Epub ahead of print]

Whole-exome sequencing in an extended family with myocardial infarction unmasks familial hypercholesterolemia.
Brænne I, Reiz B, Medack A, Kleinecke M, et al.
BMC Cardiovasc Disord. 2014 Aug 26;14(1):108.

A novel mutation identified in PKHD1 by targeted exome sequencing: guiding prenatal diagnosis for an ARPKD family.
Xu Y, Xiao B, Jiang WT, Wang L, et al.
Gene. 2014 Aug 18. [Epub ahead of print]

RNA-sequencing analysis of HepG2 cells treated with atorvastatin.
Stormo C, Kringen MK, Lyle R, Olstad OK, et al.
PLOS One. 2014 Aug 25;9(8):e105836.

Somatic intronic microsatellite loci differentiate glioblastoma from lower-grade gliomas.
Karunasena E, McIver LJ, Rood BR, Wu X, et al.
Oncotarget. 2014 Aug 15;5(15):6003-6014.

Mutations in GRHL2 result in an autosomal-recessive ectodermal dysplasia syndrome.
Petrof G, Nanda A, Howden J, Takeichi T, et al.
Am J Hum Genet. 2014 Aug 20. [Epub ahead of print]

A mutation of COX6A1 causes a recessive axonal or mixed form of Charcot-Marie-Tooth disease.
Tamiya G, Makino S, Hayashi M, Abe A, et al.
Am J Hum Genet. 2014 Aug 20. [Epub ahead of print]

College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests.
Aziz N, Zhao Q, Bry L, Driscoll DK, et al.
Arch Pathol Lab Med. 2014 Aug 25. [Epub ahead of print]

Genetic landscape of esophageal squamous cell carcinoma.
Gao YB, Chen ZL, Li JG, Hu XD, et al.
Nat Genet. 2014 Aug 24. [Epub ahead of print]

Detection of inherited mutations for hereditary cancer using target enrichment and next generation sequencing.
Guan Y, Hu H, Peng Y, Gong Y, et al.
Fam Cancer. 2014 Aug 24. [Epub ahead of print]

A newborn with complex skeletal abnormalities, joint contractures, and bilateral corneal clouding with sclerocornea.
Sellars EA, Bosanko KA, Lepard T, Garnica A, Schaefer GB.
Semin Pediatr Neurol. 2014 Jun;21(2):84-7.

An unusual cause of peroneal neuropathy.
Ananth AL, Yang Y, Lalani SR, Lotze TB.
Semin Pediatr Neurol. 2014 Jun;21(2):77-81.

Novel EXOSC3 mutation causes complicated hereditary spastic paraplegia.
Halevy A, Lerer I, Cohen R, Kornreich L, et al.
J Neurol. 2014 Aug 23. [Epub ahead of print]

Targeting the JAK/STAT Pathway in Cytotoxic T lymphocytes (CTL) by Next Generation Sequencing (NGS).
Gigante M, Diella S, Ranieri E.
Methods Mol Biol. 2014;1186:253-68.

Personalized Diagnosis and Management of Congenital Cataract by Next-Generation Sequencing.
Gillespie RL, O'Sullivan J, Ashworth J, Bhaskar S, et al.
Ophthalmology. 2014 Jul 29. [Epub ahead of print]

Beyond BRAFV600: clinical mutation panel testing by next-generation sequencing in advanced melanoma.
Siroy AE, Boland GM, Milton DR, Roszik J, et al.
J Invest Dermatol. 2014 Aug 22. [Epub ahead of print]

Targeting Glutathione S-transferase M4 in Ewing sarcoma.
Zhuo R, Kosak KM, Sankar S, Wiles ET, et al.
Front Pediatr. 2014 Aug 6;2:83.

A Novel Missense Mutation of Wilms' Tumor 1 Causes Autosomal Dominant FSGS.
Hall G, Gbadegesin RA, Lavin P, Wu G, et al.
J Am Soc Nephrol. 2014 Aug 21. [Epub ahead of print]

HCN4 Mutations in Multiple Families With Bradycardia and Left Ventricular Noncompaction Cardiomyopathy.
Milano A, Vermeer AM, Lodder EM, Barc J, et al.
J Am Coll Cardiol. 2014 Aug 26;64(8):745-56.