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In Print: Last Week's Clinical Sequencing Papers of Note: Jan 15, 2014


Diagnosis of glycine encephalopathy in a pediatric patient by detection of a GLDC mutation during initial next generation DNA sequencing.
Ezgu F, Ciftci B, Topçu B, Adıyaman G, et al.
Metab Brain Dis. 2014 Jan 11. [Epub ahead of print]

Retinoblastoma gene mutations detected by whole exome sequencing of Merkel cell carcinoma.
Cimino PJ, Robirds DH, Tripp SR, Pfeifer JD, et al.
Mod Pathol. 2014 Jan 10. [Epub ahead of print]

Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory.
Strom SP, Lee H, Das K, Vilain E, et al.
Genet Med. 2014 Jan 9. [Epub ahead of print]

Aberrant CDK4 amplification in refractory rhabdomyosarcoma as identified by genomic profiling.
Park S, Lee J, Do IG, Jang J, et al.
Sci Rep. 2014 Jan 10;4:3623.

Human syndromes of immunodeficiency and dysregulation are characterized by distinct defects in T-cell receptor repertoire development.
Yu X, Almeida J, Darko S, van der Burg M, et al.
J Allergy Clin Immunol. 2014 Jan 7. pii: S0091-6749(13)01782-X. [Epub ahead of print]

Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples.
Lee YK, Jin S, Duan S, Lim YC, et al.
Biol Proced Online. 2014 Jan 9;16(1):1.

Whole-genome sequencing of matched primary and metastatic hepatocellular carcinomas.
Ouyang L, Lee J, Park CK, Mao M, et al.
BMC Med Genomics. 2014 Jan 9;7(1):2.

Tumor evolution and intratumor heterogeneity of an oropharyngeal squamous cell carcinoma revealed by whole-genome sequencing.
Zhang XC, Xu C, Mitchell RM, Zhang B, et al.
Neoplasia. 2013 Dec;15(12):1371-8.

Rapid resistome fingerprinting and clonal lineage profiling of carbapenem-resistant Klebsiella pneumonia by targeted next generation sequencing.
Arena F, Rolfe PA, Doran G, Conte V, et al.
J Clin Microbiol. 2014 Jan 8. [Epub ahead of print]

Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma.
Stacey SN, Sulem P, Gudbjartsson DF, Jonasdottir A, et al.
Hum Mol Genet. 2014 Jan 8. [Epub ahead of print]

Frequency of mitochondrial mutations in non-syndromic hearing loss as well as possibly responsible variants found by whole mitochondrial genome screening.
Yano T, Nishio SY, Usami SI.
J Hum Genet. 2014 Jan 9. [Epub ahead of print]

Second-pandemic strain of Vibrio cholera from the Philadelphia cholera outbreak of 1849.
Devault AM, Golding GB, Waglechner N, Enk JM, et al.
N Engl J Med. 2014 Jan 8. [Epub ahead of print]

Outlier-based identification of copy number variations using targeted resequencing in a small cohort of patients with tetralogy of fallot.
Bansal V, Dorn C, Grunert M, Klaassen S, et al.
PLOS One. 2014 Jan 6;9(1):e85375.

NECAP1 loss of function leads to a severe infantile epileptic encephalopathy.
Alazami AM, Hijazi H, Kentab AY, Alkuraya FS.
J Med Genet. 2014 Jan 7. [Epub ahead of print]

Mutation in ST6GALNAC5 identified in family with coronary artery disease.
Inanloorahatloo K, Parsa AF, Huse K, Rasooli P, et al.
Sci Rep. 2014 Jan 8;4:3595.

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 Jan 8. [Epub ahead of print]

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 Jan 8. [Epub ahead of print]

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 Jan 8. [Epub ahead of print]

Exome sequencing reveals a novel TTC19 mutation in an autosomal recessive spinocerebellar ataxia patient.
Morino H, Miyamoto R, Ohnishi S, Maruyama H, Kawakami H.
BMC Neurol. 2014 Jan 7;14(1):5. [Epub ahead of print]

Mrassf1a-Pap, a novel methylation-based assay for the detection of cell-free fetal DNA in maternal plasma.
van den Oever JM, Balkassmi S, Segboer T, Verweij EJ, et al.
PLOS One. 2013 Dec 31;8(12):e84051.

Landscape of genomic alterations in cervical carcinomas.
Ojesina AI, Lichtenstein L, Freeman SS, Pedamallu CS, et al.
Nature. 2013 Dec 25. [Epub ahead of print]

AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.
Bao L, Pu M, Messer K.
Bioinformatics. 2014 Jan 2. [Epub ahead of print]

Socrates: Identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads.
Schroeder J, Hsu A, Boyle SE, Macintyre G, et al.
Bioinformatics. 2014 Jan 2. [Epub ahead of print]

Primary urethral clear-cell adenocarcinoma: comprehensive analysis by surgical pathology, cytopathology, and next-generation sequencing.
Mehra R, Vats P, Kalyana-Sundaram S, Udager AM, et al.
Am J Pathol. 2014 Jan 2. [Epub ahead of print]

Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster.
Santoni FA, Makrythanasis P, Nikolaev S, Guipponi M, et al.
Genome Res. 2014 Jan 3. [Epub ahead of print]

Loss of association of REEP2 with membranes leads to hereditary spastic paraplegia.
Esteves T1, Durr A2, Mundwiller E3, Loureiro JL4, et al.
Am J Hum Genet. 2013 Dec 31. [Epub ahead of print]

Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol.
Bielinski SJ, Olson JE, Pathak J, Weinshilboum RM, et al.
Mayo Clin Proc. 2014 Jan;89(1):25-33.

Mutations in TBC1D24, a gene associated with epilepsy, also cause nonsyndromic deafness DFNB86.
Rehman AU, Santos-Cortez RL, Morell RJ, Drummond MC, et al.
Am J Hum Genet. 2014 Jan 2;94(1):144-52.

Mutations in POGLUT1, encoding protein O-glucosyltransferase 1, cause autosomal-dominant Dowling-Degos disease.
Basmanav FB, Oprisoreanu AM, Pasternack SM, Thiele H, et al.
Am J Hum Genet. 2014 Jan 2;94(1):135-43.

Mutations in PCYT1A cause spondylometaphyseal dysplasia with cone-rod dystrophy.
Yamamoto GL, Baratela WA, Almeida TF, Lazar M, et al.
Am J Hum Genet. 2014 Jan 2;94(1):113-9.

Ultra-deep sequencing analysis of the hepatitis A virus 5'-untranslated region among cases of the same outbreak from a single source.
Wu S, Nakamoto S, Kanda T, Jiang X, et al.
Int J Med Sci. 2013 Dec 20;11(1):60-4.

FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies.
Yao J, Zhang KX, Kramer M, Pellegrini M, McCombie WR.
Bioinformatics. 2014 Jan 5. [Epub ahead of print]

RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder.
Akula N, Barb J, Jiang X, Wendland JR, et al.
Mol Psychiatry. 2014 Jan 7. [Epub ahead of print]