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Recent Clinical Sequencing Papers of Note: Jul 16, 2014

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Pediatric hepatocellular carcinoma due to somatic CTNNB1 and NFE2L2 mutations in the setting of inherited bi-allelic ABCB11 mutations.
Vilarinho S, Zeynep Erson-Omay E, Harmanci AS, Morotti R, et al.
J Hepatol. 2014 Jul 9. [Epub ahead of print]


Individual exome analysis in diagnosis and management of pediatric liver failure of indeterminate etiology.
Vilarinho S, Choi M, Jain D, Malhotra A, et al.
J Hepatol. 2014 Jul 9. [Epub ahead of print]


Deep sequencing of hepatitis C virus hypervariable region 1 reveals no correlation between genetic heterogeneity and antiviral treatment outcome.
Cortés KC, Zagordi O, Perlejewski K, Laskus T, et al.
BMC Infect Dis. 2014 Jul 13;14(1):389.


High-throughput sequencing to identify miRNA biomarkers in colorectal cancer patients.
Sun Y, Wang L, Guo SC, Wu XB, Xu XH.
Oncol Lett. 2014 Aug;8(2):711-713.


Non-invasive diagnosis of actionable mutations by deep sequencing of circulating-free DNA in non-small cell lung cancer: Findings from BioCAST / IFCT-1002.
Couraud S, Vaca Paniagua F, Villar S, Oliver J, et al.
Clin Cancer Res. 2014 Jul 10. [Epub ahead of print]


Cancer therapy. Ex vivo culture of circulating breast tumor cells for individualized testing of drug susceptibility.
Yu M, Bardia A, Aceto N, Bersani F, et al.
Science. 2014 Jul 11;345(6193):216-20.


Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers.
Akat KM, Moore-McGriff D, Morozov P, Brown M, et al.
Proc Natl Acad Sci U S A. 2014 Jul 10. [Epub ahead of print]


"We don't know her history, her background": adoptive parents' perspectives on whole genome sequencing results.
Crouch J, Yu JH, Shankar AG, Tabor HK.
J Genet Couns. 2014 Jul 12. [Epub ahead of print]


Development and validation of a whole genome amplification long-range PCR sequencing method for ADPKD genotyping of low-level DNA samples.
Liu G, Tan AY, Michaeel A, Blumenfeld J, et al.
Gene. 2014 Jul 7 [Epub ahead of print]


Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing.
Hughes AE, Magrini V, Demeter R, Miller CA, et al.
PLOS Genet. 2014 Jul 10;10(7):e1004462.


Inferring clonal composition from multiple sections of a breast cancer.
Zare H, Wang J, Hu A, Weber K, et al.
PLOS Comput Biol. 2014 Jul 10;10(7):e1003703.


The genomic landscape of the Ewing sarcoma family of tumors reveals recurrent STAG2 mutation.
Brohl AS, Solomon DA, Chang W, Wang J, et al.
PLOS Genet. 2014 Jul 10;10(7):e1004475.


The business of genomic testing: a survey of early adopters.
Crawford JM, Bry L, Pfeifer J, Caughron SK, et al.
Genet Med. 2014 Jul 10. [Epub ahead of print]


Whole-exome sequencing identifies Y1495X of SCN5A to be associated with familial conduction disease and sudden death.
Tan ZP, Xie L, Deng Y, Chen JL, et al.
Sci Rep. 2014 Jul 10;4:5616.


Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study.
Petty TJ, Cordey S, Padioleau I, Docquier M, et al.
J Clin Microbiol. 2014 Jul 9. [Epub ahead of print]


Capturing intra-tumor genetic heterogeneity by de novo mutation profiling of circulating cell-free tumor DNA: a proof-of-principle.
De Mattos-Arruda L, Weigelt B, Cortes J, Won HH, et al.
Ann Oncol. 2014 Jul 9. [Epub ahead of print]


Nanoscale chromatin profiling of gastric adenocarcinoma reveals cancer-associated cryptic promoters and somatically acquired regulatory elements.
Muratani M, Deng N, Ooi WF, Lin SJ, et al.
Nat Commun. 2014 Jul 10;5:4361.


Whole exome sequencing reveals that the majority of schwannomatosis cases remain unexplained after excluding SMARCB1 and LZTR1 germline variants.
Hutter S, Piro RM, Reuss DE, Hovestadt V, et al.
Acta Neuropathol. 2014 Jul 10. [Epub ahead of print]


A preliminary quality control (QC) for next generation sequencing (NGS) library evaluation turns out to be a very useful tool for a rapid detection of BRCA1/2 deleterious mutations.
Concolino P, Costella A, Minucci A, Scaglione GL, et al.
Clin Chim Acta. 2014 Jul 5. [Epub ahead of print]


Ocular phenotype of a family with FAM161A-associated retinal degeneration.
Duncan JL, Biswas P, Kozak I, Navani M, et al.
Ophthalmic Genet. 2014 Jul 9:1-9. [Epub ahead of print]


A novel CIC-FOXO4 gene fusion in undifferentiated small round cell sarcoma: a genetically distinct variant of Ewing-like sarcoma.
Sugita S, Arai Y, Tonooka A, Hama N, et al.
Am J Surg Pathol. 2014 Jul 8. [Epub ahead of print]


Sequencing-based approach identified three new susceptibility loci for psoriasis.
Sheng Y, Jin X, Xu J, Gao J, et al.
Nat Commun. 2014 Jul 9;5:4331.


Very small deletions within the NESP55 gene in pseudohypoparathyroidism type 1b.
Rezwan FI, Poole RL, Prescott T, Walker JM, et al.
Eur J Hum Genet. 2014 Jul 9. [Epub ahead of print]


Comparison of KRAS mutation analysis of colorectal cancer samples by standard testing and next-generation sequencing.
Kothari N, Schell MJ, Teer JK, Yeatman T, et al.
J Clin Pathol. 2014 Jul 8. [Epub ahead of print]


Single-nucleotide polymorphism-based noninvasive prenatal screening in a high-risk and low-risk cohort.
Pergament E, Cuckle H, Zimmermann B, Banjevic M, et al.
Obstet Gynecol. 2014 Jul 7. [Epub ahead of print]


Germline FH mutations presenting with pheochromocytoma.
Clark GR, Sciacovelli M, Gaude E, Walsh DM, et al.
J Clin Endocrinol Metab. 2014 Jul 8 [Epub ahead of print]


Tracking genomic cancer evolution for precision medicine: the lung TRACERx study.
Jamal-Hanjani M, Hackshaw A, Ngai Y, Shaw J, et al.
PLOS Biol. 2014 Jul 8;12(7)


ASXL1 and DNMT3A mutation in a cytogenetically normal B3 thymoma.
Belani R, Oliveira G, Erikson GA, Ra S, et al.
Oncogenesis. 2014 Jul 7;3:e111.


Sequencing of breast cancer stem cell populations indicates a dynamic conversion between differentiation states in vivo.
Klevebring D, Rosin G, Ma R, Lindberg J, et al.
Breast Cancer Res. 2014 Jul 6;16(4):R72.


Linkage mapping and whole exome sequencing identify a shared variant in CX3CR1 in a large multi-generation family.
Feldman GJ, Parvizi J, Sawan H, Erickson JA, Peters CL.
J Arthroplasty. 2014 Jun 2. [Epub ahead of print]


Copy number variation sequencing for comprehensive diagnosis of chromosome disease syndromes.
Liang D, Peng Y, Lv W, Deng L, et al.
J Mol Diagn. 2014 Jul 3. [Epub ahead of print]


Whole-exome and targeted gene sequencing of gallbladder carcinoma identifies recurrent mutations in the ErbB pathway.
Li M, Zhang Z, Li X, Ye J, et al.
Nat Genet. 2014 Jul 6. [Epub ahead of print]


Whole exome sequencing identifies a novel EMD mutation in a Chinese family with dilated cardiomyopathy.
Zhang M, Chen J, Si D, Zheng Y, et al.
BMC Med Genet. 2014 Jul 5;15(1):77.


The expanding MEGDEL phenotype: optic nerve atrophy, microcephaly, and myoclonic epilepsy in a child with SERAC1 mutations.
Lumish HS, Yang Y, Xia F, Wilson A, Chung WK.
JIMD Rep. 2014 Jul 6. [Epub ahead of print]


Kinase genotype analysis of gastric gastrointestinal stromal tumor cytology samples using targeted next-generation sequencing.
Gleeson FC, Kipp BR, Kerr SE, Voss JS, et al.
Clin Gastroenterol Hepatol. 2014 Jul 2. [Epub ahead of print]


Comparative effectiveness of next generation genomic sequencing for disease diagnosis: Design of a randomized controlled trial in patients with colorectal cancer/polyposis syndromes.
Gallego CJ, Bennette CS, Heagerty P, Comstock B, et al.
Contemp Clin Trials. 2014 Jul 2. [Epub ahead of print]


Exome sequencing identifies a CHKB mutation in Spanish patient with megaconial congenital muscular dystrophy and mtDNA depletion.
Castro-Gago M, Dacruz-Alvarez D, Pintos-Martínez E, Beiras-Iglesias A, et al.
Eur J Paediatr Neurol. 2014 Jun 20. [Epub ahead of print]


Whole genome and exome sequencing of monozygotic twins discordant for Crohn's disease.
Petersen BS, Spehlmann ME, Raedler A, Stade B, et al.
BMC Genomics. 2014 Jul 5;15(1):564.


Aicardi-Goutières syndrome is caused by IFIH1 mutations.
Oda H, Nakagawa K, Abe J, Awaya T, et al.
Am J Hum Genet. 2014 Jul 3;95(1):121-5.


Mutations in SLC13A5 cause autosomal-recessive epileptic encephalopathy with seizure onset in the first days of life.
Thevenon J, Milh M, Feillet F, St-Onge J, et al.
Am J Hum Genet. 2014 Jul 3;95(1):113-20.


Identification of an HMGB3 frameshift mutation in a family with an X-linked colobomatous microphthalmia syndrome using whole-genome and X-exome sequencing.
Scott AF, Mohr DW, Kasch LM, Barton JA, et al.
JAMA Ophthalmol. 2014 Jul 3. [Epub ahead of print]


Genomic profiling of thousands of candidate polymorphisms predicts risk of relapse in 778 Danish and German childhood acute lymphoblastic leukemia patients.
Wesołowska-Andersen A, Borst L, Dalgaard MD, Yadav R, et al.
Leukemia. 2014 Jul 3. [Epub ahead of print]


Next-generation sequencing analysis of lung and colon carcinomas reveals a variety of genetic alterations.
Chevrier S, Arnould L, Ghiringhelli F, Coudert B, et al.
Int J Oncol. 2014 Sep;45(3):1167-74.


Microsatellite instability detection by next generation sequencing.
Salipante SJ, Scroggins SM, Hampel HL, Turner EH, Pritchard CC.
Clin Chem. 2014 Jun 30. [Epub ahead of print]


Whole exome sequencing of familial hypercholesterolaemia patients negative for LDLR/APOB/PCSK9 mutations.
Futema M, Plagnol V, Li K, Whittall RA, Neil HA, et al.
J Med Genet. 2014 Jul 1. [Epub ahead of print]


Mutations in COL27A1 cause Steel syndrome and suggest a founder mutation effect in the Puerto Rican population.
Gonzaga-Jauregui C, Gamble CN, Yuan B, Penney S, et al.
Eur J Hum Genet. 2014 Jul 2. [Epub ahead of print]


Using whole-exome sequencing to identify variants inherited from mosaic parents.
Rios JJ, Delgado MR.
Eur J Hum Genet. 2014 Jul 2. [Epub ahead of print]


BCR-ABL1 kinase domain mutational analysis of CD34+ stem/progenitor cells in newly diagnosed CML patients by next-generation sequencing.
Musilova M, Razga F, Jurcek T, Jeziskova I, et al.
Am J Hematol. 2014 Jul 1. [Epub ahead of print]


Whole genome sequencing to identify host genetic risk factors for severe outcomes of hepatitis a virus infection.
Long D, Fix OK, Deng X, Seielstad M, et al.
J Med Virol. 2014 Jun 30. [Epub ahead of print]


Next-generation sequencing reveals frequent consistent genomic alterations in small cell undifferentiated lung cancer.
Ross JS, Wang K, Elkadi OR, Tarasen A, et al.
J Clin Pathol. 2014 Jun 24. [Epub ahead of print]


Integrative DNA, RNA, and protein evidence connects TREML4 to coronary artery calcification.
Sen SK, Boelte KC, Barb JJ, Joehanes R, et al.
Am J Hum Genet. 2014 Jun 24. [Epub ahead of print]


Attitudes of genetics professionals toward the return of incidental results from exome and whole-genome sequencing.
Yu JH, Harrell TM, Jamal SM, Tabor HK, Bamshad MJ.
Am J Hum Genet. 2014 Jun 24. [Epub ahead of print]


A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors.
Petrini I, Meltzer PS, Kim IK, Lucchi M, et al.
Nat Genet. 2014 Jun 29. [Epub ahead of print]


Validation and utilisation of high-coverage next-generation sequencing to deliver the pharmacological audit trail.
Ong M, Carreira S, Goodall J, Mateo J, et al.
Br J Cancer. 2014 Jul 1. [Epub ahead of print]


Do participants in genome sequencing studies of psychiatric disorders wish to be informed of their results? A survey study.
Bui ET, Anderson NK, Kassem L, McMahon FJ.
PLOS One. 2014 Jul 1;9(7):e101111.


Genome sequencing of multiple primary tumors reveals a novel PALB2 variant.
Schrader KA, Stratton KL, Murali R, Laitman Y, et al.
J Clin Oncol. 2014 Jun 30. [Epub ahead of print]


Next generation sequencing challenges in the analysis of cardiac sudden death due to arrhythmogenic disorders.
Brion M, Blanco-Verea A, Sobrino B, Santori M, et al.
Electrophoresis. 2014 Jun 30. [Epub ahead of print]

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.