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Recent Clinical Sequencing Papers of Note: Nov 5, 2014


Tracking a tuberculosis outbreak over 21 years: strain-specific single nucleotide polymorphism-typing combined with targeted whole genome sequencing.
Stucki D, Ballif M, Bodmer T, Coscolla M, et al.
J Infect Dis. 2014 Oct 30. [Epub ahead of print]

A recurrent CEP120 mutation in Jeune asphyxiating thoracic dystrophy expands the role of centriolar proteins in skeletal ciliopathies.
Shaheen R, Schmidts M, Faqeih E, Hashem A, et al.
Hum Mol Genet. 2014 Oct 30. [Epub ahead of print]

Identification of causative mutation in a Korean family with Crouzon syndrome using whole exome sequencing.
Sagong B, Jung da J, Baek JI, Kim MA, et al.
Ann Clin Lab Sci. 2014 Fall;44(4):476-83.

Homozygous splice mutation in CWF19L1 in a Turkish family with recessive ataxia syndrome.
Burns R, Majczenko K, Xu J, Peng W, Yapici Z, et al.
Neurology. 2014 Oct 31. [Epub ahead of print]

A homozygous splice-site mutation in CARS2 is associated with progressive myoclonic epilepsy.
Hallmann K, Zsurka G, Moskau-Hartmann S, Kirschner J, et al.
Neurology. 2014 Oct 31. [Epub ahead of print]

Uveal melanoma hepatic metastases mutation spectrum analysis using targeted next-generation sequencing of 400 cancer genes.
Luscan A, Just PA, Briand A, Burin des Roziers C, et al.
Br J Ophthalmol. 2014 Oct 31. [Epub ahead of print]

Whole exome sequencing identifies novel genes for fetal hemoglobin response to hydroxyurea in children with sickle cell anemia.
Sheehan VA, Crosby JR, Sabo A, Mortier NA, et al.
PLoS One. 2014 Oct 31;9(10):e110740.

BCOR-CCNB3 fusions are frequent in undifferentiated sarcomas of male children.
Peters TL, Kumar V, Polikepahad S, Lin FY, et al.
Pathol. 2014 Oct 31. [Epub ahead of print]

Adult-onset autosomal recessive ataxia associated with neuronal ceroid lipofuscinosis type 5 gene (CLN5) mutations.
Mancini C, Nassani S, Guo Y, Chen Y, Giorgio E, et al.
J Neurol. 2014 Oct 31. [Epub ahead of print]

Genome sequencing identifies a novel mutation in ATP1A3 in a family with dystonia in females only.
Wilcox R, Brænne I, Brüggemann N, Winkler S, et al.
J Neurol. 2014 Oct 31. [Epub ahead of print]

Application of high-throughput sequencing to circulating microRNAs reveals novel biomarkers for drug-induced liver injury.
Krauskopf J, Caiment F, Claessen S, Johnson KJ, et al.
Toxicol Sci. 2014 Oct 29. [Epub ahead of print]

Differential increases of specific FMR1 mRNA isoforms in premutation carriers.
Pretto DI, Eid JS, Yrigollen CM, Tang HT, et al.
J Med Genet. 2014 Oct 30. [Epub ahead of print]

Development of molecular technique for deep sequencing of almost full HIV genome.
Kireev DE, Lopatukhin AE, Neverov AD, Fedonin GG, et al.
AIDS Res Hum Retroviruses. 2014 Oct;30(S1):A182.

gDNA enrichment by a transposase-based technology for NGS analysis of the whole sequence of BRCA1, BRCA2, and 9 genes involved in DNA damage repair.
Chevrier S, Boidot R.
J Vis Exp. 2014 Oct 6;(92).

Genetic analysis of Chinese families reveals a novel truncation allele of the retinitis pigmentosa GTPase regulator gene.
Hu F, Zeng XY, Liu LL, Luo YL, et al.
Int J Ophthalmol. 2014 Oct 18;7(5):753-8.

Validation of a next-generation-sequencing cancer panel for use in the clinical laboratory.
Simen BB, Yin L, Goswami CP, Davis KO, et al.
Arch Pathol Lab Med. 2014 Oct 30. [Epub ahead of print]

Genotype-phenotype correlation and mutation spectrum in a large cohort of patients with inherited retinal dystrophy revealed by next-generation sequencing.
Huang XF, Huang F, Wu KC, Wu J, et al.
Genet Med. 2014 Nov 6. [Epub ahead of print]

Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions.
Farwell KD, Shahmirzadi L, El-Khechen D, Powis Z, et al.
Genet Med. 2014 Nov 6. [Epub ahead of print]

Consanguinity and rare mutations outside of MCCC genes underlie nonspecific phenotypes of MCCD.
Shepard PJ, Barshop BA, Baumgartner MR, Hansen JB, et al.
Genet Med. 2014 Nov 6. [Epub ahead of print]

Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort.
Retterer K, Scuffins J, Schmidt D, Lewis R, et al.
Genet Med. 2014 Nov 6. [Epub ahead of print]

ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing.
Genet Med. 2014 Oct 30. [Epub ahead of print]

De novo mutations in moderate or severe intellectual disability.
Hamdan FF, Srour M, Capo-Chichi JM, Daoud H, et al.
PLoS Genet. 2014 Oct 30;10(10):e1004772.

New mutations in the RAB28 gene in 2 Spanish families with cone-rod dystrophy.
Riveiro-Álvarez R, Xie YA, López-Martínez MA, Gambin T, et al.
JAMA Ophthalmol. 2014 Oct 30. [Epub ahead of print]

High-throughput RNA sequencing based virome analysis of 50 lymphoma cell lines from the cancer cell line encyclopedia project.
Cao S, Strong MJ, Wang X, Moss WN, et al.
J Virol. 2014 Oct 29. [Epub ahead of print]

Mutations in Twinkle primase-helicase cause Perrault syndrome with neurologic features.
Morino H, Pierce SB, Matsuda Y, Walsh T, et al.
Neurology. 2014 Oct 29. [Epub ahead of print]

Small cell lung cancer detection in never-smokers: clinical characteristics and multigene mutation profiling using targeted next-generation sequencing.
Sun JM, Choi YL, Ji JH, Ahn JS, et al.
Ann Oncol. 2014 Oct 29. [Epub ahead of print]

Development of a communication protocol for telephone disclosure of genetic test results for cancer predisposition.
Patrick-Miller LJ, Egleston BL, Fetzer D, Forman A, et al.
JMIR Res Protoc. 2014 Oct 29;3(4):e49.

The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing.
Lindqvist CM, Nordlund J, Ekman D, Johansson A, et al.
Hum Mutat. 2014 Oct 30. [Epub ahead of print]

Exome sequencing and CNV analysis on chromosome 18 in small intestinal neuroendocrine tumors: ruling out a suspect?
Delgado Verdugo A, Crona J, Maharjan R, Hellman P, et al.
Horm Metab Res. 2014 Oct 29. [Epub ahead of print]

Germline CARD11 mutation in a patient with severe congenital B cell lymphocytosis.
Brohl AS, Stinson JR, Su HC, Badgett T, et al.
J Clin Immunol. 2014 Oct 29. [Epub ahead of print]

Mutations in the tricarboxylic acid cycle enzyme, aconitase 2, cause either isolated or syndromic optic neuropathy with encephalopathy and cerebellar atrophy.
Metodiev MD, Gerber S, Hubert L, Delahodde A, et al.
J Med Genet. 2014 Oct 28. [Epub ahead of print]

Mutations in filamin C cause a new form of familial hypertrophic cardiomyopathy.
Valdés-Mas R, Gutiérrez-Fernández A, Gómez J2, Coto E, et al.
Nat Commun. 2014 Oct 29;5:5326.

Detection of TRIM32 deletions in LGMD patients analyzed by a combined strategy of CGH array and massively parallel sequencing.
Nectoux J, de Cid R, Baulande S, Leturcq F, et al.
Eur J Hum Genet. 2014 Oct 29. [Epub ahead of print]

Novel genotype-phenotype associations demonstrated by high-throughput sequencing in patients with hypertrophic cardiomyopathy.
Lopes LR, Syrris P, Guttmann OP, O'Mahony C, et al.
Heart. 2014 Oct 28. [Epub ahead of print]

Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis.
Nones K, Waddell N, Wayte N, Patch AM, et al.
Nat Commun. 2014 Oct 29;5:5224.

Variation in genomic landscape of clear cell renal cell carcinoma across Europe.
Scelo G, Riazalhosseini Y, Greger L, Letourneau L, et al.
Nat Commun. 2014 Oct 29;5:5135.

A single-gene cause in 29.5% of cases of steroid-resistant nephrotic syndrome.
Sadowski CE, Lovric S, Ashraf S, Pabst WL, et al.
J Am Soc Nephrol. 2014 Oct 27. [Epub ahead of print]

A novel recurrent NPM1-TYK2 gene fusion in cutaneous CD30-positive lymphoproliferative disorders.
Velusamy T, Kiel MJ, Sahasrabuddhe AA, Rolland D, et al.
Blood. 2014 Oct 27. [Epub ahead of print]

Prognostic serum miRNA biomarkers associated with Alzheimer's disease shows concordance with neuropsychological and neuroimaging assessment.
Cheng L, Doecke JD, Sharples RA, Villemagne VL, et al.
Mol Psychiatry. 2014 Oct 28. [Epub ahead of print]

An anadysplasia-like, spontaneously remitting spondylometaphyseal dysplasia secondary to lamin B receptor (LBR) gene mutations: Further definition of the phenotypic heterogeneity of LBR-bone dysplasias.
Sobreira N, Modaff P, Steel G, You J, et al.
Am J Med Genet A. 2014 Oct 27. [Epub ahead of print]

Whole exome sequencing identifies a POLRID mutation segregating in a father and two daughters with findings of Klippel-Feil and Treacher Collins syndromes.
Giampietro PF, Armstrong L, Stoddard A, Blank RD, et al.
Am J Med Genet A. 2014 Oct 27. [Epub ahead of print]

Chromosomal instability in cell-free DNA is a serum biomarker for prostate cancer.
Schütz E, Akbari MR, Beck J, Urnovitz H, et al.
Clin Chem. 2014 Oct 27. [Epub ahead of print]

Molecular diagnosis of infantile neuro axonal dystrophy by next generation sequencing.
Goyal M, Bijarnia-Mahay S, Kingsmore S, Farrow E, et al.
Indian J Pediatr. 2014 Oct 29. [Epub ahead of print]

Genetics professionals' opinions of whole-genome sequencing in the newborn period.
Ulm E, Feero WG, Dineen R, Charrow J, Wicklund C.
J Genet Couns. 2014 Oct 28. [Epub ahead of print]

Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations.
Martelotto LG, Ng C, De Filippo MR, Zhang Y, et al.
Genome Biol. 2014 Oct 28;15(10):484.

Finding fault? Exploring legal duties to return incidental findings in genomic research.
Pike ER, Rothenberg KH, Berkman BE.
Georgetown Law J. 2014;102:795-843.

Identification of a new HLA-B*57 allele, HLA-B*57:71, by next-generation sequencing.
Kuranov AB, Steiert I, Goodridge D, Müller CA.
Tissue Antigens. 2014 Oct 27. [Epub ahead of print]

Clinical next-generation sequencing in patients with non-small cell lung cancer.
Hagemann IS, Devarakonda S, Lockwood CM, Spencer DH, et al.
Cancer. 2014 Oct 24. [Epub ahead of print]
(See our coverage of this paper here.)