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Recent Clinical Sequencing Papers of Note: Aug 6, 2014


Novel Compound Heterozygous Mutations in MYO7A Associated with Usher Syndrome 1 in a Chinese Family.
Gao X, Wang GJ, Yuan YY, Xin F, Han MY, Lu JQ, Zhao H, Yu F, et al.
PLoS One. 2014 Jul 31;9(7):e103415.

Comprehensive molecular profiling of lung adenocarcinoma.
The Cancer Genome Atlas Research Network; et al.
Nature. 2014 Jul 31;511(7511):543-550.

Clonal evolution in breast cancer revealed by single nucleus genome sequencing.
Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, et al.
Nature. 2014 Jul 30. [Epub ahead of print]

Translational implications of somatic genomics in acute myeloid leukaemia.
Meyer SC, Levine RL.
Lancet Oncol. 2014 Aug;15(9):e382-e394.

Next-generation sequencing of adrenocortical carcinoma reveals new routes to targeted therapies.
Ross JS, Wang K, Rand JV, Gay L, Presta MJ, Sheehan CE, Ali SM, et al.
J Clin Pathol. 2014 Jul 30.

The impact of reporting incidental findings from exome and whole-genome sequencing: predicted frequencies based on modeling.
Ding LE, Burnett L, Chesher D.
Genet Med. 2014 Jul 31. [Epub ahead of print]

Identification of OSBPL2 as a novel candidate gene for progressive nonsyndromic hearing loss by whole-exome sequencing.
Xing G, Yao J, Wu B, Liu T, Wei Q, Liu C, Lu Y, Chen Z, Zheng H, Yang X, Cao X.
Genet Med. 2014 Jul 31. [Epub ahead of print]

Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis.
den Bakker HC, Allard MW, Bopp D, Brown EW, Fontana J, et al.
Emerg Infect Dis. 2014 Aug;20(8):1306-14.

Personalized oncology: genomic screening in phase 1.
Tuxen IV, Jønson L, Santoni-Rugiu E, Hasselby JP, Nielsen FC, Lassen U.
APMIS. 2014 Aug;122(8):723-33.

Exome sequencing identifies highly recurrent MED12 somatic mutations in breast fibroadenoma.
Lim WK, Ong CK, Tan J, Thike AA, Ng CC, Rajasegaran V, Myint SS, et al.
Nat Genet. 2014 Aug;46(8):877-80.

Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples.
Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, et al.
J Clin Microbiol. 2014 Aug;52(8):3136.

Clinical utilisation of a rapid low-pass whole genome sequencing technique for the diagnosis of aneuploidy in human embryos prior to implantation.
Wells D, Kaur K, Grifo J, Glassner M, Taylor JC, Fragouli E, Munne S.
J Med Genet. 2014 Aug;51(8):553-62.

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.
Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SR, et al.
Nat Genet. 2014 Aug;46(8):912-8.

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.

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 Aug;124(2 Pt 1):210-8.

Whole-exome and targeted gene sequencing of gallbladder carcinoma identifies recurrent mutations in the ErbB pathway.
Li M, Zhang Z, Li X, Ye J, Wu X, Tan Z, Liu C, Shen B, Wang XA, et al.
Nat Genet. 2014 Aug;46(8):872-6.

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 Aug;51(8):537-44.

Whole-genome sequence variation, population structure and demographic history of the Dutch population.
Genome of the Netherlands Consortium; Genome of the Netherlands Consortium.
Nat Genet. 2014 Aug;46(8):818-25.

The genomic landscape of nasopharyngeal carcinoma.
Lin DC, Meng X, Hazawa M, Nagata Y, Varela AM, Xu L, Sato Y, et al.
Nat Genet. 2014 Aug;46(8):866-71.

DrugTargetSeqR: a genomics- and CRISPR-Cas9-based method to analyze drug targets.
Kasap C, Elemento O, Kapoor TM.
Nat Chem Biol. 2014 Aug;10(8):626-8.

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 Aug;45(8):1784-9.

Comparative Genomics of an IncA/C Multidrug Resistance Plasmid from Escherichia coli and Klebsiella Isolates from Intensive Care Unit Patients and the Utility of Whole-Genome Sequencing in Health Care Settings.
Hazen TH, Zhao L, Boutin MA, Stancil A, Robinson G, Harris AD, et al.
Antimicrob Agents Chemother. 2014 Aug;58(8):4814-25

Exome sequencing reveals CHM mutations in six families with atypical choroideremia initially diagnosed as retinitis pigmentosa.
Li S, Guan L, Fang S, Jiang H, Xiao X, Yang J, Wang P, Yin Y, Guo X, et al.
Int J Mol Med. 2014 Aug;34(2):573-7.

Next generation sequencing in cardiomyopathy: towards personalized genomics and medicine.
Biswas A, Rao VR, Seth S, Maulik SK.
Mol Biol Rep. 2014 Aug;41(8):4881-8.

Molecular profiling of soft tissue sarcomas using next-generation sequencing: a pilot study toward precision therapeutics.
Jour G, Scarborough JD, Jones RL, Loggers E, Pollack SM, Pritchard CC, L Hoch B.
Hum Pathol. 2014 Aug;45(8):1563-71.

Deep sequencing reveals complex mechanisms of microRNA deregulation in colorectal cancer.
Liang G, Li J, Sun B, Li S, Lü L, Wang Y, Chen B, Xiao Z.
Int J Oncol. 2014 Aug;45(2):603-10.

Whole exome sequencing identifies three recessive FIG4 mutations in an apparently dominant pedigree with Charcot-Marie-Tooth disease.
Menezes MP, Waddell L, Lenk GM, Kaur S, MacArthur DG, Meisler MH, Clarke NF.
Neuromuscul Disord. 2014 Aug;24(8):666-70.

Next generation sequencing reveals microRNA isoforms in liver cirrhosis and hepatocellular carcinoma.
Wojcicka A, Swierniak M, Kornasiewicz O, Gierlikowski W, et al.
Int J Biochem Cell Biol. 2014 Aug;53:208-17.

Whole-Genome Sequencing for High-Resolution Investigation of Methicillin-Resistant Staphylococcus aureus Epidemiology and Genome Plasticity.
SenGupta DJ, Cummings LA, Hoogestraat DR, Butler-Wu SM, et al.
J Clin Microbiol. 2014 Aug;52(8):2787-96.

Exome sequencing identifies compound heterozygous mutations in C12orf57 in two siblings with severe intellectual disability, hypoplasia of the corpus callosum, chorioretinal coloboma, and intractable seizures.
Platzer K, Hüning I, Obieglo C, Schwarzmayr T, Gabriel R, et al.
Am J Med Genet A. 2014 Aug;164(8):1976-80.

Collaboration of colorado cancer genetic counselors to integrate next generation sequencing panels into clinical practice.
Wolfe Schneider K, Anguiano A, Axell L, Barth C, Crow K, et al.
J Genet Couns. 2014 Aug;23(4):640-6.

The evolution of cancer risk assessment in the era of next generation sequencing.
Fecteau H, Vogel KJ, Hanson K, Morrill-Cornelius S.
J Genet Couns. 2014 Aug;23(4):633-9.

Whole exome sequencing to estimate alloreactivity potential between donors and recipients in stem cell transplantation.
Sampson JK, Sheth NU, Koparde VN, Scalora AF, Serrano MG, Lee V, Roberts CH, Jameson-Lee M, Ferreira-Gonzalez A, Manjili MH, Buck GA, Neale MC, Toor AA.
Br J Haematol. 2014 Aug;166(4):566-70.

An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing.
Simen BB, Braverman MS, Abbate I, Aerssens J, Bidet Y, et al.
J Virol Methods. 2014 Aug;204:31-7.

mtDNA mutations in human aging and longevity: controversies and new perspectives opened by high-throughput technologies.
Sevini F, Giuliani C, Vianello D, Giampieri E, Santoro A, et al.
Exp Gerontol. 2014 Aug;56:234-44.

Antenatal noninvasive DNA testing: clinical experience and impact.
Ferres MA, Hui L, Bianchi DW.
Am J Perinatol. 2014 Aug;31(7):577-82.

Whole transcriptome sequencing of a paediatric case of de novo acute myeloid leukaemia with del(5q) reveals RUNX1-USP42 and PRDM16-SKI fusion transcripts.
Masetti R, Togni M, Astolfi A, Pigazzi M, Indio V, Rivalta B, et al.
Br J Haematol. 2014 Aug;166(3):449-52.

Genetic counselors' views and experiences with the clinical integration of genome sequencing.
Machini K, Douglas J, Braxton A, Tsipis J, Kramer K.
J Genet Couns. 2014 Aug;23(4):496-505.

Genetic counseling practice in next generation sequencing research: implications for the ethical oversight of the informed consent process.
Egalite N, Groisman IJ, Godard B.
J Genet Couns. 2014 Aug;23(4):661-70.

Cancer risk assessment using genetic panel testing: considerations for clinical application.
Hiraki S, Rinella ES, Schnabel F, Oratz R, Ostrer H.
J Genet Couns. 2014 Aug;23(4):604-17.

An Assessment of Time Involved in Pre-test Case Review and Counseling for a Whole Genome Sequencing Clinical Research Program.
Williams JL, Faucett WA, Smith-Packard B, Wagner M, Williams MS.
J Genet Couns. 2014 Aug;23(4):516-21.

Teaching genomic counseling: preparing the genetic counseling workforce for the genomic era.
Hooker GW, Ormond KE, Sweet K, Biesecker BB.
J Genet Couns. 2014 Aug;23(4):445-51.

Lynch syndrome patients' views of and preferences for return of results following whole exome sequencing.
Hitch K, Joseph G, Guiltinan J, Kianmahd J, Youngblom J, Blanco A.
J Genet Couns. 2014 Aug;23(4):539-51.

Next Generation Sequencing is the Impetus for the Next Generation of Laboratory-Based Genetic Counselors.
Swanson A, Ramos E, Snyder H.
J Genet Couns. 2014 Aug;23(4):647-54.

Points to Consider in the Clinical Use of NGS Panels for Mitochondrial Disease: An Analysis of Gene Inclusion and Consent Forms.
Platt J, Cox R, Enns GM.
J Genet Couns. 2014 Aug;23(4):594-603.

The ophthalmic experience: unanticipated primary findings in the era of next generation sequencing.
Huang JT, Heckenlively JR, Jayasundera KT, Branham KE.
J Genet Couns. 2014 Aug;23(4):588-93.

Position statement on opportunistic genomic screening from the Association of Genetic Nurses and Counsellors (UK and Ireland).
Middleton A, Patch C, Wiggins J, Barnes K, et al.
Eur J Hum Genet. 2014 Aug;22(8):955-6.

Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2 and ARID4A in microsatellite unstable colorectal cancer.
Cajuso T, Hänninen UA, Kondelin J, Gylfe AE, et al.
Int J Cancer. 2014 Aug 1;135(3):611-23.

Research participants' attitudes towards the confidentiality of genomic sequence information.
Jamal L, Sapp JC, Lewis K, Yanes T, Facio FM, Biesecker LG, Biesecker BB.
Eur J Hum Genet. 2014 Aug;22(8):964-8.

A Genetic Counselor's Guide to Using Next-Generation Sequencing in Clinical Practice.
Facio FM, Lee K, O'Daniel JM.
J Genet Couns. 2014 Aug;23(4):455-62.

Perspective on how to approach molecular diagnostics in acute myeloid leukemia and myelodysplastic syndromes in the era of next-generation sequencing.
Kohlmann A, Bacher U, Schnittger S, Haferlach T.
Leuk Lymphoma. 2014 Aug;55(8):1725-34.

Whole exome sequencing unravels disease-causing genes in consanguineous families in Qatar.
Fahiminiya S, Almuriekhi M, Nawaz Z, Staffa A, Lepage P, Ali R, Hashim L, Schwartzentruber J, Abu Khadija K, Zaineddin S, Gamal H, Majewski J, Ben-Omran T.
Clin Genet. 2014 Aug;86(2):134-41.

A qualitative study of healthcare providers' perspectives on the implications of genome-wide testing in pediatric clinical practice.
Reiff M, Mueller R, Mulchandani S, Spinner NB, Pyeritz RE, Bernhardt BA.
J Genet Couns. 2014 Aug;23(4):474-88.

Stakeholders' opinions on the implementation of pediatric whole exome sequencing: implications for informed consent.
Levenseller BL, Soucier DJ, Miller VA, Harris D, Conway L, Bernhardt BA.
J Genet Couns. 2014 Aug;23(4):552-65.

Whole-exome sequencing expands the phenotype of Hunter syndrome.
Nikkel SM, Huang L, Lachman R, Beaulieu CL, et al.
Clin Genet. 2014 Aug;86(2):172-6.

Targeted Sequencing of a Pediatric Metabolic Bone Gene Panel Using a Desktop Semiconductor Next-Generation Sequencer.
Rauch F, Lalic L, Glorieux FH, Moffatt P, Roughley P.
Calcif Tissue Int. 2014 Aug 3. [Epub ahead of print]

A framework for the interpretation of de novo mutation in human disease.
Samocha KE, Robinson EB, Sanders SJ, Stevens C, Sabo A, et al.
Nat Genet. 2014 Aug 3. [Epub ahead of print]

Phen-Gen: combining phenotype and genotype to analyze rare disorders.
Javed A, Agrawal S, Ng PC.
Nat Methods. 2014 Aug 3. [Epub ahead of print]