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In Print: Last Week's Clinical Sequencing Papers of Note: Oct 23, 2013


Targeted resequencing of candidate genes reveals novel variants associated with severe Behçet's uveitis.
Kim SJ, Lee S, Park C, Seo JS, et al.
Exp Mol Med. 2013 Oct 18;45:e49.

Can I access my personal genome? The current legal position in the UK.
Kaye J, Kanellopoulou N, Hawkins N, Gowans H, et al.
Med Law Rev.2013 Oct 17. [Epub ahead of print]

EIF2AK4 mutations in pulmonary capillary hemangiomatosis.
Best DH, Sumner KL, Austin ED, Chung WK, et al.
Chest.2013 Oct 17. [Epub ahead of print]

Whole-transcriptome analysis of hepatocellular carcinoma.
Lin L, Wang D, Cao N, Lin Y, et al.
Med Oncol.2013 Dec;30(4):736.

Prenatal detection of fetal triploidy from cell-free DNA testing in maternal blood.
Nicolaides KH, Syngelaki A, Del Mar Gil M, Soledad Quezada M, Zinevich Y.
Fetal Diagn Ther. 2013 Oct 10. [Epub ahead of print]

Tracking the clonal origin of lethal prostate cancer.
Haffner MC, Mosbruger T, Esopi DM, Fedor H, et al.
J Clin Invest. 2013 Oct 25. [Epub ahead of print]

Genetic and clinical characteristics of Korean patients with isolated hypoparathyroidism: from the Korean hypopara registry study.
Park SY, Eom YS, Choi B, Yi HS, et al.
J Korean Med Sci. 2013 Oct;28(10):1489-95.

Mutational landscape and significance across 12 major cancer types.
Kandoth C, McLellan MD, Vandin F, Ye K, et al.
Nature. 2013 Oct 17;502(7471):333-9.

Application of variant-calling algorithms for Mendelian disorders: lessons from whole-exome sequencing in Charcot-Marie-Tooth disease.
Hong Y, Jung J, Jung SC, Chung K, Choi BO.
Clin Genet. 2013 Oct 17. [Epub ahead of print]

Deep bisulfite sequencing of aberrantly methylated loci in a patient with multiple methylation defects.
Beygo J, Ammerpohl O, Gritzan D, Heitmann M, et al.
PLOS One. 2013 Oct 9;8(10):e76953.

Targeted exome sequencing integrated with clinicopathological information reveals novel and rare mutations in atypical, suspected and unknown cases of Alport syndrome or proteinuria.
Chatterjee R, Hoffman M, Cliften P, Seshan S, et al.
PLOS One. 2013 Oct 10;8(10):e76360.

Massively parallel DNA sequencing successfully identifies new causative mutations in deafness genes in patients with cochlear implantation and EAS.
Miyagawa M, Nishio SY, Ikeda T, Fukushima K, Usami SI.
PLOS One. 2013 Oct 9;8(10):e75793.

Variant ATRX syndrome with dysfunction of ATRX and MAGT1 genes.
Qiao Y, Mondal K, Trapani V, Wen J, et al.
Hum Mutat. 2013 Oct 15. [Epub ahead of print]

Identification of differentially expressed microRNAs in human hepatocellular adenoma associated with type I glycogen storage disease: a potential utility as biomarkers.
Chiu LY, Kishnani PS, Chuang TP, Tang CY, et al.
J Gastroenterol. 2013 Oct 16. [Epub ahead of print]

NRAS mutation is the sole recurrent somatic mutation in large congenital melanocytic nevi.
Charbel C, Fontaine RH, Malouf GG, Picard A, et al.
J Invest Dermatol. 2013 Oct 15. [Epub ahead of print]

Whole-genome sequencing analysis identifies a distinctive mutational spectrum in an arsenic-related lung tumor.
Martinez VD, Thu KL, Vucic EA, Hubaux R, et al.
J Thorac Oncol. 2013 Nov;8(11):1451-1455.

Exome sequencing identifies a novel SMCHD1 mutation in facioscapulohumeral muscular dystrophy 2.
Mitsuhashi S, Boyden SE, Estrella EA, Jones TI, et al.
Neuromuscul Disord. 2013 Aug 31. [Epub ahead of print]

Exome sequencing identifies mutations in KIF14 as a novel cause of an autosomal recessive lethal fetal ciliopathy phenotype.
Filges I, Nosova E, Bruder E, Tercanli S, et al.
Clin Genet. 2013 Oct 15. [Epub ahead of print]

Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome.
Fabbri G, Khiabanian H, Holmes AB, Wang J, et al.
J Exp Med. 2013 Oct 14. [Epub ahead of print]

A survey of rare coding variants in candidate genes in schizophrenia by deep sequencing.
Hu X, Zhang B, Liu W, Paciga S, et al.
Mol Psychiatry. 2013 Oct 15. [Epub ahead of print]

Excess of rare novel loss-of-function variants in synaptic genes in schizophrenia and autism spectrum disorders.
Kenny EM, Cormican P, Furlong S, Heron E, et al.
Mol Psychiatry. 2013 Oct 15. [Epub ahead of print]

Mutations in VRK1 associated with complex motor and sensory axonal neuropathy plus microcephaly.
Gonzaga-Jauregui C, Lotze T, Jamal L, Penney S, et al.
JAMA Neurol. 2013 Oct 14. [Epub ahead of print]

Ribosomal protein S6 mRNA is a biomarker upregulated in multiple sclerosis, downregulated by interferon treatment, and affected by season.
Parnell GP, Gatt PN, McKay FC, Schibeci S, et al.
Mult Scler. 2013 Oct 14. [Epub ahead of print]

Profiling the molecular mechanism of fullerene cytotoxicity on tumor cells by RNA-seq.
Lucafò M, Gerdol M, Pallavicini A, Pacor S, et al.
Toxicology. 2013 Oct 11. [Epub ahead of print]

A novel large in-frame deletion within the CACNA1F gene associates with a cone-rod dystrophy 3-like phenotype.
Hauke J, Schild A, Neugebauer A, Lappa A, et al.
PLOS One. 2013 Oct 4;8(10):e76414.

Identification of pathogenic gene variants in small families with intellectually disabled siblings by exome sequencing.
Schuurs-Hoeijmakers JH, Vulto-van Silfhout AT, Vissers LE, van de Vondervoort II , et al.
J Med Genet. 2013 Oct 11. [Epub ahead of print]

A post-hoc comparison of the utility of Sanger sequencing and exome sequencing for the diagnosis of heterogeneous diseases.
Neveling K, Feenstra I, Gilissen C, Hoefsloot LH, et al.
Hum Mutat. 2013 Sep 30. [Epub ahead of print]

Exome sequencing identifies potential risk variants for Mendelian disorders at high prevalence in Qatar.
Rodriguez-Flores JL, Fakhro K, Hackett NR, Salit J, et al.
Hum Mutat. 2013 Oct 10. [Epub ahead of print]

Mutated Ephrin receptor genes in non-small cell lung carcinoma and their occurrence with driver mutations-targeted resequencing study on formalin-fixed, paraffin-embedded tumor material of 81 patients.
Mäki-Nevala S, Kaur Sarhadi V, Tuononen K, Lagström S, et al.
Genes Chromosomes Cancer. 2013 Oct 7. [Epub ahead of print]

Ultra-deep T-cell receptor sequencing reveals the complexity and intratumour heterogeneity of T-cell clones in renal cell carcinomas.
Gerlinger M, Quezada SA, Peggs KS, Furness AJ, et al.
J Pathol. 2013 Oct 1. [Epub ahead of print]

Two novel susceptibility SNPs for ischemic stroke using exome sequencing in Chinese Han population.
Zhang Y, Tong Y, Zhang Y, Ding H, et al.
Mol Neurobiol. 2013 Oct 10. [Epub ahead of print]

Exome sequencing reveals RAG1 mutations in a child with autoimmunity and sterile chronic multifocal osteomyelitis evolving into disseminated granulomatous disease.
Reiff A, Bassuk AG, Church JA, Campbell E, et al.
J Clin Immunol. 2013 Oct 12. [Epub ahead of print]

A novel p.Leu(381)Phe mutation in presenilin 1 is associated with very early onset and unusually fast progressing dementia as well as lysosomal inclusions typically seen in Kufs disease.
Dolzhanskaya N, Gonzalez MA, Sperziani F, Stefl S, et al.
J Alzheimers Dis. 2013 Oct 10. [Epub ahead of print]

High-throughput identification of antigen-specific TCRs by TCR gene capture.
Linnemann C, Heemskerk B, Kvistborg P, Kluin RJ, et al.
Nat Med. 2013 Oct 13. [Epub ahead of print]

Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation.
Guo G, Sun X, Chen C, Wu S, et al.
Nat Genet. 2013 Oct 13. [Epub ahead of print]

Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy.
Balbás-Martínez C, Sagrera A, Carrillo-de-Santa-Pau E, Earl J, Márquez M, et al.
Nat Genet. 2013 Oct 13. [Epub ahead of print]

Identification of a novel de novo p.Phe932Ile KCNT1 mutation in a patient with leukoencephalopathy and severe epilepsy.
Vanderver A, Simons C, Schmidt JL, Pearl PL, et al.
Pediatr Neurol. 2013 Oct 10. [Epub ahead of print]

ERBB4 mutations that disrupt the neuregulin-ErbB4 pathway cause amyotrophic lateral sclerosis type 19.
Takahashi Y, Fukuda Y, Yoshimura J, Toyoda A, et al.
Am J Hum Genet. 2013 Oct 8. [Epub ahead of print]

Macrocytic anemia and mitochondriopathy resulting from a defect in sideroflexin 4.
Hildick-Smith GJ, Cooney JD, Garone C, Kremer LS, et al.
Am J Hum Genet. 2013 Oct 9. [Epub ahead of print]

Informed consent for exome sequencing in diagnostics: exploring first experiences and views of professionals and patients.
Rigter T, van Aart CJ, Elting MW, Waisfisz Q, et al.
Clin Genet.2013 Oct 11. [Epub ahead of print]

Mapping of genotype-phenotype diversity among clinical isolates of Mycobacterium tuberculosis by sequence-based transcriptional profiling.
Rose G, Cortes T, Comas I, Coscolla M, et al.
Genome Biol Evol. 2013 Jan;5(10):1849-1862.

De novo mutations in SLC35A2 encoding a UDP-galactose transporter cause early-onset epileptic encephalopathy.
Kodera H, Nakamura K, Osaka H, Maegaki Y, et al.
Hum Mutat. 2013 Sep 30. [Epub ahead of print]

Isolated X-linked hypertrophic cardiomyopathy caused by a novel mutation of the four-and-a-half LIM domain 1 gene.
Hartmannova H, Kubanek M, Sramko M, Piherova L, et al.
Circ Cardiovasc Genet. 2013 Oct 10. [Epub ahead of print]

Somatic copy number alterations by whole exome sequencing implicates YWHAZ and PTK2 in castration-resistant prostate cancer.
Menon R, Deng M, Rüenauver K, Queisser A, et al.
J Pathol. 2013 Sep 23. doi: 10.1002/path.4274. [Epub ahead of print]

Inferring tumour purity and stromal and immune cell admixture from expression data.
Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, et al.
Nat Commun. 2013 Oct 11;4:2612.

Whole-genome methylation sequencing reveals distinct impact of differential methylations on gene transcription in prostate cancer.
Yu YP, Ding Y, Chen R, Liao SG, et al.
Am J Pathol. 2013 Oct 7. [Epub ahead of print]

The integration of next-generation sequencing panels in the clinical cancer genetics practice: an institutional experience.
Mauer CB, Pirzadeh-Miller SM, Robinson LD, Euhus DM.
Genet Med. 2013 Oct 10. [Epub ahead of print]

Patient decisions for disclosure of secondary findings among the first 200 individuals undergoing clinical diagnostic exome sequencing.
Shahmirzadi L, Chao EC, Palmaer E, Parra MC, et al.
Genet Med. 2013 Oct 10. [Epub ahead of print]

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers.
Wang Q, Jia P, Li F, Chen H, et al.
Genome Med. 2013 Oct 11;5(10):91.

No human virus sequences detected by next generation sequencing in benign verrucous skin tumors occurring in BRAF inhibitor treated patients.
Ganzenmueller T, Hage E, Yakushko Y, Kluba J, et al.
Exp Dermatol. 2013 Sep 23. [Epub ahead of print]