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In Print: Last Week's Clinical Sequencing Papers of Note: Oct 2, 2013


Reporting results from whole-genome and whole-exome sequencing in clinical practice: a proposal for Canada?
Zawati MH, Parry D, Thorogood A, Nguyen MT, et al.
J Med Genet. 2013 Sep 27. [Epub ahead of print]

Characterization of a novel tumorigenic esophageal adenocarcinoma cell line: OANC1.
Clemons NJ, Do H, Fennell C, Deb S, et al.
Dig Dis Sci. 2013 Sep 29. [Epub ahead of print]

Deep sequencing identifies two genotypes and high viral genetic diversity of human pegivirus (GB virus C) among rural Ugandan patients.
Ghai R, Sibley SD, Lauck M, Dinis J, et al.
J Gen Virol. 2013 Sep 28. [Epub ahead of print]

eXtasy: variant prioritization by genomic data fusion.
Sifrim A, Popovic D, Tranchevent LC, Ardeshirdavani A, et al.
Nat Methods. 2013 Sep 29. [Epub ahead of print]

Truncating mutations of MAGEL2 cause Prader-Willi phenotypes and autism.
Schaaf CP, Gonzalez-Garay ML, Xia F, Potocki L, et al.
Nat Genet. 2013 Sep 29. [Epub ahead of print]

A mutation in CALM1 encoding calmodulin in familial idiopathic ventricular fibrillation in childhood and adolescence.
Marsman RF, Barc J, Beekman L, Alders M, et al.
J Am Coll Cardiol. 2013 Sep 16. [Epub ahead of print]

Signaling network assessment of mutations and copy number variations predict breast cancer subtype-specific drug targets.
Zaman N, Li L, Jaramillo ML, Sun Z, et al.
Cell Rep. 2013 Sep 25. [Epub ahead of print]

Detection of variations and identifying genomic breakpoints for large deletions in the LDLR by Ion Torrent semiconductor sequencing.
Faiz F, Allcock RJ, Hooper AJ, van Bockxmeer FM.
Atherosclerosis. 2013 Oct;230(2):249-55.

Recessive and dominant mutations in retinoic acid receptor beta in cases with microphthalmia and diaphragmatic hernia.
Srour M, Chitayat D, Caron V, Chassaing N, et al.
Am J Hum Genet. 2013 Sep 25. [Epub ahead of print]

Mutations in NALCN cause an autosomal-recessive syndrome with severe hypotonia, speech impairment, and cognitive delay.
Al-Sayed MD, Al-Zaidan H, Albakheet A, Hakami H, et al.
Am J Hum Genet. 2013 Sep 25. pii: S0002-9297(13)00346-7. [Epub ahead of print]

Cole disease results from mutations in ENPP1.
Eytan O, Morice-Picard F, Sarig O, Ezzedine K, et al.
Am J Hum Genet. 2013 Sep 25. [Epub ahead of print]

Missense mutation in the MEN1 gene discovered through whole exome sequencing co-segregates with familial hyperparathyroidism.
Isakov O, Rinella ES, Olchovsky D, Shimon I, et al.
Genet Res (Camb) . 2013 Aug;95(4):114-20.

A simple consensus approach improves somatic mutation prediction accuracy.
Goode DL, Hunter SM, Doyle MA, Ma T, et al.
Genome Med. 2013 Sep 30;5(9):90.

Characterization of multi-drug resistant Mycobacterium tuberculosis from immigrants residing in the USA using Ion Torrent full-gene sequencing.
Daum LT, Fischer GW, Sromek J, Khubbar M, Hunter P, Gradus MS, Bhattacharyya S.
Epidemiol Infect. 2013 Sep 27:1-6.

Exome sequencing and directed clinical phenotyping diagnose cholesterol ester storage disease presenting as autosomal recessive hypercholesterolemia.
Stitziel NO, Fouchier SW, Sjouke B, Peloso GM, et al.
Arterioscler Thromb Vasc Biol. 2013 Sep 26. [Epub ahead of print]

Exome sequencing reveals novel and recurrent mutations with clinical impact in blastic plasmacytoid dendritic cell neoplasm.
Menezes J, Acquadro F, Wiseman M, Gómez-López G, et al.
Leukemia. 2013 Sep 27. [Epub ahead of print]

The Cancer Genome Atlas pan-cancer analysis project.
Cancer Genome Atlas Research Network; Genome Characterization Center, Chang K, Creighton CJ, Davis C, Donehower L, Drummond J, et al.
Nat Genet. 2013 Sep 26;45(10):1113-20.

Analysis of microRNA expression profile by small RNA sequencing in Down syndrome fetuses.
Xu Y, Li W, Liu X, Ma H, et al.
Int J Mol Med. 2013 Nov;32(5):1115-1125.

A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record.
Tarczy-Hornoch P, Amendola L, Aronson SJ, Garraway L, et al.
Genet Med. 2013 Sep 26. [Epub ahead of print]

Long insert whole genome sequencing for copy number variant and translocation detection.
Liang WS, Aldrich J, Tembe W, Kurdoglu A, et al.
Nucleic Acids Res. 2013 Sep 25. [Epub ahead of print]

Primary cutaneous carcinosarcoma: insights into its clonal origin and mutational pattern expression analysis through next-generation sequencing.
Paniz Mondolfi AE, Jour G, Johnson M, Reidy J, et al.
Hum Pathol. 2013 Sep 24. [Epub ahead of print]

A missense mutation in the alpha-actinin 1 gene (ACTN1) is the cause of autosomal dominant macrothrombocytopenia in a large French family.
Guéguen P, Rouault K, Chen JM, Raguénès O, et al.
PLOS One. 2013 Sep 17;8(9):e74728.

Identification and characterization of cancer mutations in Japanese lung adenocarcinoma without sequencing of normal tissue counterparts.
Suzuki A, Mimaki S, Yamane Y, Kawase A, et al.
PLOS One. 2013 Sep 12;8(9):e73484.

RNA-seq reveals spliceosome and proteasome genes as most consistent transcripts in human cancer cells.
Macrae T, Sargeant T, Lemieux S, Hébert J, et al.
PLOS One. 2013 Sep 17;8(9):e72884.

Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis.
Beaudoin M, Goyette P, Boucher G, Lo KS, et al.
PLOS Genet. 2013 Sep;9(9):e1003723.

Cryptic FUS-ERG fusion identified by RNA-sequencing in childhood acute myeloid leukemia.
Panagopoulos I, Gorunova L, Zeller B, Tierens A, Heim S.
Oncol Rep. 2013 Sep 25. [Epub ahead of print]

Diverse sources of C. difficile infection identified on whole-genome sequencing.
Eyre DW, Cule ML, Wilson DJ, Griffiths D, et al.
N Engl J Med. 2013 Sep 26;369(13):1195-205.

Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.
Koshimizu E, Miyatake S, Okamoto N, Nakashima M, et al.
PLOS One. 2013 Sep 16;8(9):e74167.

Analysis of fusion gene expression in prostate tumors by using single-end reads.
Xie DD, Li JY, Wang Y, Chen L, Yu DX.
Genet Mol Res. 2013 Aug 12;12(3):2886-94.

Exome sequencing reveals new insights into the progression of abdominal aortic aneurysm.
Wang SM, Zhao G, Peng L, Yang W.
Eur Rev Med Pharmacol Sci. 2013 Sep;17(17):2401-9.

Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination.
Di Giallonardo F, Zagordi O, Duport Y, Leemann C, et al.
PLOS One. 2013 Sep 18;8(9):e74249.

The landscape of somatic mutations in Down syndrome-related myeloid disorders.
Yoshida K, Toki T, Okuno Y, Kanezaki R, et al.
Nat Genet. 2013 Sep 22. [Epub ahead of print]

Periventricular heterotopia in 6q terminal deletion syndrome: role of the C6orf70 gene.
Conti V, Carabalona A, Pallesi-Pocachard E, Parrini E, et al.
Brain. 2013 Sep 20. [Epub ahead of print]

Actionable, pathogenic incidental findings in 1,000 participants' exomes.
Dorschner MO, Amendola LM, Turner EH, Robertson PD, et al.
Am J Hum Genet. 2013 Sep 17. [Epub ahead of print]

Mutations in SPAG1 cause primary ciliary dyskinesia associated with defective outer and inner dynein arms.
Knowles MR, Ostrowski LE, Loges NT, Hurd T, et al.
Am J Hum Genet. 2013 Sep 17. [Epub ahead of print]

Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts.
Li S, Shen D, Shao J, Crowder R, et al.
Cell Rep. 2013 Sep 18. [Epub ahead of print]

Next-generation sequencing of advanced prostate cancer treated with androgen-deprivation therapy.
Rajan P, Sudbery IM, Villasevil ME, Mui E, et al.
Eur Urol. 2013 Aug 14. [Epub ahead of print]

An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer.
Jia J, Parikh H, Xiao W, Hoskins JW, et al.
BMC Med Genomics. 2013 Sep 22;6(1):33.