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Recent Clinical Sequencing Papers of Note: Jun 18, 2014


95 Identification of likely pathogenic variants in patients with bicuspid aortic valve: correlation of complex genotype with a more severe aortic phenotype.
Francis C, Prapa S, Abdulkareem N, John S, et al.
Heart. 2014 Jun;100(Suppl 3):A55-A56.

Differences in BRCA counseling and testing practices based on ordering provider type.
Cragun D, Camperlengo L, Robinson E, Caldwell M, et al.
Genet Med. 2014 Jun 12. [Epub ahead of print]

Investigation of pathogenic genes in peri-implantitis from implant clustering failure patients: a whole-exome sequencing pilot study.
Lee S, Kim JY, Hwang J, Kim S, et al.
PLOS One. 2014 Jun 12;9(6):e99360.

Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing.
Sherrill JD, Kiran KC, Blanchard C, Stucke EM, et al.
Genes Immun. 2014 Jun 12. [Epub ahead of print]

Acquired initiating mutations in early hematopoietic cells of CLL patients.
Damm F, Mylonas E, Cosson A, Yoshida K, et al.
Cancer Discov. 2014 Jun 11. [Epub ahead of print]

Models of consent to return of incidental findings in genomic research.
Appelbaum PS, Parens E, Waldman CR, Klitzman R, et al.
Hastings Cent Rep. 2014 Jun 11. [Epub ahead of print]

Comparison of the performance of Ion Torrent chips in noninvasive prenatal trisomy detection.
Wang Y, Wen Z, Shen J, Cheng W, et al.
J Hum Genet. 2014 Jun 12. [Epub ahead of print]

Recurrent somatic mutations underlie corticotropin-independent Cushing's syndrome.
Sato Y, Maekawa S, Ishii R, Sanada M, et al.
Science. 2014 May 23;344(6186):917-20.

Exome sequencing reveals the likely involvement of SOX10 in uveal melanoma.
Das D, Kaur I, Ali MJ, Biswas NK, et al.
Optom Vis Sci. 2014 Jun 12. [Epub ahead of print]

Whole exome sequencing identifies new causative mutations in Tunisian families with non-syndromic deafness.
Riahi Z, Bonnet C, Zainine R, Louha M, et al.
PLOS One. 2014 Jun 13;9(6):e99797.

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.
Patel AP, Tirosh I, Trombetta JJ, Shalek AK, et al.
Science. 2014 Jun 12. [Epub ahead of print]

A robust molecular pattern for myelodysplastic syndromes in two independent cohorts investigated by next-generation sequencing can be revealed by comparative bioinformatic analyses.
Rose D, Kohlmann A, Nagata Y, Ogawa S, et al.
Br J Haematol. 2014 Jun 12. [Epub ahead of print]

TNNI3K mutation in familial syndrome of conduction system disease, atrial tachyarrhythmia and dilated cardiomyopathy.
Theis JL, Zimmermann MT, Larsen BT, Rybakova IN, et al.
Hum Mol Genet. 2014 Jun 11. [Epub ahead of print]

Application of next generation sequencing to CEPH cell lines to discover variants associated with FDA approved chemotherapeutics.
Hariani GD, Lamm E, Havener T, Kwok P, et al.
BMC Res Notes. 2014 Jun 12;7(1):360.

Isolated trisomy 13 defines a genetically homogenous AML subgroup with high frequency of mutations in spliceosome genes and poor prognosis.
Herold T, Metzeler KH, Vosberg S, Hartmann L, et al.
Blood. 2014 Jun 12. [Epub ahead of print]

Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens.
Jin C, Yang L, Xie M, Lin C, et al.
Proc Natl Acad Sci U S A. 2014 Jun 13. [Epub ahead of print]

Novel recessive myotilin mutation causes severe myofibrillar myopathy.
Schessl J, Bach E, Rost S, Feldkirchner S, et al.
Neurogenetics. 2014 Jun 14. [Epub ahead of print]

Novel BCR-ABL1 fusion identified by targeted next-generation sequencing in a patient with an atypical myeloproliferative neoplasm.
Frederick L, Beardell F, Viswanatha DS.
Hum Pathol. 2014 May 8. [Epub ahead of print]

Recurrent read-through fusion transcripts in breast cancer.
Varley KE, Gertz J, Roberts BS, Davis NS, et al.
Breast Cancer Res Treat. 2014 Jun 15. [Epub ahead of print]

DrugTargetSeqR: a genomics- and CRISPR-Cas9-based method to analyze drug targets.
Kasap C, Elemento O, Kapoor TM.
Nat Chem Biol. 2014 Jun 15. [Epub ahead of print]

PIK3CA and TP53 gene mutations in human breast cancer tumors frequently detected by Ion Torrent DNA sequencing.
Bai X, Zhang E, Ye H, Nandakumar V, et al.
PLOS One. 2014 Jun 11;9(6):e99306.

Characterization of HPV DNA methylation of contiguous CpG sites by bisulfite treatment and massively parallel sequencing-the FRAGMENT approach.
Sun C, McAndrew T, Smith BC, Chen Z, et al.
Front Genet. 2014 Jun 3;5:150.

Novel calmodulin (CALM2) mutations associated with congenital arrhythmia susceptibility.
Makita N, Yagihara N, Crotti L, Johnson CN, et al.
Circ Cardiovasc Genet. 2014 Jun 10. [Epub ahead of print]

Prognostic B-cell signatures using mRNA-seq in patients with subtype-specific breast and ovarian cancer.
Iglesia MD, Vincent BG, Parker JS, Hoadley KA, et al.
Clin Cancer Res. 2014 Jun 10. [Epub ahead of print]

Biallelic germline and somatic mutations in malignant mesothelioma: Multiple mutations in transcription regulators including mSWI/SNF genes.
Yoshikawa Y, Sato A, Tsujimura T, Otsuki T, et al.
Int J Cancer. 2014 Jun 10. [Epub ahead of print]

Missense variant in CCDC22 causes X-linked recessive intellectual disability with features of Ritscher-Schinzel/3C syndrome.
Kolanczyk M, Krawitz P, Hecht J, Hupalowska A, et al.
Eur J Hum Genet. 2014 Jun 11. [Epub ahead of print]

New syndrome with retinitis pigmentosa is caused by nonsense mutations in retinol dehydrogenase RDH11.
Xie YA, Lee W, Cai C, Gambin T, et al.
Hum Mol Genet. 2014 Jun 10. [Epub ahead of print]

Association of a low-frequency variant in HNF1A with type 2 diabetes in a Latino population.
The SIGMA Type 2 Diabetes Consortium, Estrada K, Aukrust I, Bjørkhaug L, et al.
JAMA. 2014 Jun 11;311(22):2305-2314.

Hoyeraal-Hreidarsson syndrome with a DKC1 mutation identified by whole-exome sequencing.
Lim BC, Yoo SK, Lee S, Shin JY, et al.
Gene. 2014 Jun 7. [Epub ahead of print]

Comparative genomics of an IncA/C multidrug resistance plasmid from Escherichia coli and Klebsiella species isolated from ICU patients: the utility of whole genome sequencing in healthcare settings.
Hazen TH, Zhao L, Boutin MA, Stancil A, et al.
Antimicrob Agents Chemother. 2014 Jun 9. [Epub ahead of print]

The mutational burden of acral melanoma revealed by whole genome sequencing and comparative analysis.
Furney SJ, Turajlic S, Stamp G, Meirion Thomas J, et al.
Pigment Cell Melanoma Res. 2014 Jun 10. [Epub ahead of print]

Hennekam syndrome can be caused by FAT4 mutations and be allelic to Van Maldergem syndrome.
Alders M, Al-Gazali L, Cordeiro I, Dallapiccola B, et al.
Hum Genet. 2014 Jun 7. [Epub ahead of print]

Exome sequencing reveals CHM mutations in six families with atypical choroideremia initially diagnosed as retinitis pigmentosa.
Li S, Guan L, Fang S, Jiang H, et al.
Int J Mol Med. 2014 Jun 6. [Epub ahead of print]

Mitochondrial mutations in patients with congenital heart defects by next generation sequencing technology.
Abaci N, Arıkan M, Tansel T, Sahin N, et al.
Cardiol Young. 2014 Jun 10:1-7.

Exome sequencing of hepatoblastoma reveals novel mutations and cancer genes in the Wnt pathway and ubiquitin ligase complex.
Jia D, Dong R, Jing Y, Xu D, et al.
Hepatology. 2014 Jun 9. [Epub ahead of print]

Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour.
Torrezan GT, Ferreira EN, Nakahata AM, Barros BD, et al.
Nat Commun. 2014 Jun 9;5:4039.

Exome sequencing of pleuropulmonary blastoma reveals frequent biallelic loss of TP53 and two hits in DICER1 resulting in retention of 5p-derived miRNA hairpin loop sequences.
Pugh TJ, Yu W, Yang J, Field AL, et al.
Oncogene. 2014 Jun 9;0. [Epub ahead of print]

Targeted resequencing of the microRNAome and 3'UTRome reveals functional germline DNA variants with altered prevalence in epithelial ovarian cancer.
Chen X, Paranjape T, Stahlhut C, McVeigh T, et al.
Oncogene. 2014 Jun 9. [Epub ahead of print]