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In Print: Last Week's Clinical Sequencing Papers of Note: Nov 13, 2013

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Whole exome sequencing identifies a troponin T mutation hot spot in familial dilated cardiomyopathy.
Campbell N, Sinagra G, Jones KL, Slavov D, et al.
PLOS One. 2013 Oct 29;8(10):e78104.


Influence of plasma processing on recovery and analysis of circulating nucleic acids.
Page K, Guttery DS, Zahra N, Primrose L, et al.
PLOS One. 2013 Oct 18;8(10):e77963.


PathogenFinder — distinguishing friend from foe using bacterial whole genome sequence data.
Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O.
PLOS One. 2013 Oct 28;8(10):e77302.


Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-seq.
Borozan I, Watt SN, Ferretti V.
PLOS One. 2013 Oct 30;8(10):e76935.


A pilot study using next-generation sequencing in advanced cancers: feasibility and challenges.
Weiss GJ, Liang WS, Demeure MJ, Kiefer JA, et al.
PLOS One. 2013 Oct 30;8(10):e76438.


Combined exome and whole-genome sequencing identifies mutations in ARMC4 as a cause of primary ciliary dyskinesia with defects in the outer dynein arm.
Onoufriadis A, Shoemark A, Munye MM, James CT, et al.
J Med Genet. 2013 Nov 7. [Epub ahead of print]


Recessive dystonia-ataxia syndrome in a Turkish family caused by a COX20 (FAM36A) mutation.
Doss S, Lohmann K, Seibler P, Arns B, et al.
J Neurol. 2013 Nov 8. [Epub ahead of print]


Targeted exome capture and sequencing identifies novel PRPF31 mutations in autosomal dominant retinitis pigmentosa in Chinese families.
Yang L, Yin X, Wu L, Chen N, et al.
BMJ Open. 2013 Nov 7;3(11):e004030.


Irritable bowel syndrome-diarrhea: characterization of genotype by exome sequencing, and phenotypes of bile acid synthesis and colonic transit.
Camilleri M, Klee EW, Shin A, Carlson P, et al.
Am J Physiol Gastrointest Liver Physiol. 2013 Nov 7. [Epub ahead of print]


Low frequency KRAS mutations in colorectal cancer patients and the presence of multiple mutations in oncogenic drivers in non-small cell lung cancer patients.
Jiang L, Huang J, Morehouse C, Zhu W, et al.
Cancer Genet. 2013 Oct 2. pii: S2210-7762(13)00137-3. [Epub ahead of print]


Novel C12orf65 mutations in patients with axonal neuropathy and optic atrophy.
Tucci A, Liu YT, Preza E, Pitceathly RD, et al.
J Neurol Neurosurg Psychiatry. 2013 Nov 6. [Epub ahead of print]


Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network.
Galhardo M, Sinkkonen L, Berninger P, Lin J, et al.
Nucleic Acids Res. 2013 Nov 5. [Epub ahead of print]


Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium.
Berg JS, Amendola LM, Eng C, Allen EV, et al.
Genet Med. 2013 Nov;15(11):860-7.


Using exome data to identify malignant hyperthermia susceptibility mutations.
Gonsalves SG, Ng D, Johnston JJ, Teer JK, et al.
Anesthesiology. 2013 Nov;119(5):1043-53.


Maternal plasma miRNAs expression in preeclamptic pregnancies.
Li H, Ge Q, Guo L, Lu Z.
Biomed Res Int. 2013;2013:970265. Epub 2013 Sep 9.


Unique transcriptome patterns of the white and grey matter corroborate structural and functional heterogeneity in the human frontal lobe.
Mills JD, Kavanagh T, Kim WS, Chen BJ, et al.
PLOS One. 2013 Oct 23;8(10):e78480.


TMCO1 deficiency causes autosomal recessive cerebrofaciothoracic dysplasia.
Alanay Y, Ergüner B, Utine E, Haçarız O, et al.
Am J Med Genet A. 2013 Nov 5. [Epub ahead of print]


Why we should not use the Affordable Care Act to encourage widespread whole genome sequencing.
Ossorio PN, Kelleher JP.
J Health Polit Policy Law. 2013 Nov 5. [Epub ahead of print]


Coverage of whole genome sequencing in the Affordable Care Act.
Pollack HA.
J Health Polit Policy Law. 2013 Nov 5. [Epub ahead of print]


Should the Affordable Care Act's preventive services coverage provision be used to widely disseminate whole genome sequencing to Americans?
Payne P.
J Health Polit Policy Law. 2013 Nov 5. [Epub ahead of print]


A de novo non-sense mutation in ZBTB18 in a patient with features of the 1q43q44 microdeletion syndrome.
de Munnik SA, García-Miñaúr S, Hoischen A, van Bon BW, et al.
Eur J Hum Genet. 2013 Nov 6. [Epub ahead of print]


Maternal mosaicism is a significant contributor to discordant sex chromosomal aneuploidies associated with noninvasive prenatal testing.
Wang Y, Chen Y, Tian F, Zhang J, et al.
Clin Chem. 2013 Nov 5. [Epub ahead of print]


A comparison of methods for EGFR mutation testing in non-small cell lung cancer.
Young EC, Owens MM, Adebiyi I, Bedenham T, et al.
Diagn Mol Pathol. 2013 Nov 4. [Epub ahead of print]


Pyrosequencing for EGFR mutation detection: diagnostic accuracy and clinical implications.
Sahnane N, Gueli R, Tibiletti MG, Bernasconi B, et al.
Diagn Mol Pathol. 2013 Nov 4. [Epub ahead of print]


A high frequency of activating extracellular domain ERBB2 (HER2) mutation in micropapillary urothelial carcinoma.
Ross JS, Wang K, Gay L, Al-Rohil RN, et al.
Clin Cancer Res. 2013 Nov 5. [Epub ahead of print]


Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing.
Won HH, Scott SN, Brannon AR, Shah RH, Berger MF.
J Vis Exp. 2013 Oct 18;(80).


Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy.
Zhang Z, Pinto AM, Wan L, Wang W, et al.
Proc Natl Acad Sci U S A. 2013 Nov 4. [Epub ahead of print]


Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing.
Chan KC, Jiang P, Chan CW, Sun K, et al.
Proc Natl Acad Sci U S A. 2013 Nov 4. [Epub ahead of print]


A novel SLC6A8 mutation in a large family with X-linked intellectual disability: clinical and proton magnetic resonance spectroscopy data of both hemizygous males and heterozygous females.
Dreha-Kulaczewski S, Kalscheuer V, Tzschach A, Hu H, et al.
JIMD Rep. 2013 Nov 5. [Epub ahead of print]


Non optical semi-conductor next generation sequencing of the main cardiac QT-interval duration genes in pooled DNA samples.
Gómez J, Reguero JR, Morís C, Alvarez V, Coto E.
J Cardiovasc Transl Res. 2013 Nov 5. [Epub ahead of print]


Exomic analysis of myxoid liposarcomas, synovial sarcomas, and osteosarcomas.
Joseph CG, Hwang H, Jiao Y, Wood LD, et al.
Genes Chromosomes Cancer. 2013 Nov 5. [Epub ahead of print]


Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens.
Pritchard CC, Salipante SJ, Koehler K, Smith C, et al.
J Mol Diagn. 2013 Nov 1. [Epub ahead of print]

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.