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In Print: Last Week's Clinical Sequencing Papers of Note: Feb 8, 2012


Severe ALG8-CDG (CDG-Ih) associated with homozygosity for two novel missense mutations detected by exome sequencing of candidate genes.
Sorte H, Mørkrid L, Rødningen O, Kulseth MA, et al.
Eur J Med Genet. 2012 Jan 16. [Epub ahead of print]

Ultra-deep sequencing of HIV-1 reverse transcriptase before start of an NNRTI-based regimen in treatment-naive patients.
Messiaen P, Verhofstede C, Vandenbroucke I, Dinakis S, et al.
Virology. 2012 Feb 3. [Epub ahead of print]

Haploinsufficiency of a spliceosomal GTPase encoded by EFTUD2 causes mandibulofacial dysostosis with microcephaly.
Lines MA, Huang L, Schwartzentruber J, Douglas SL, et al.
Am J Hum Genet. 2012 Feb 1. [Epub ahead of print]

DDOST mutations identified by whole-exome sequencing are implicated in congenital disorders of glycosylation.
Jones MA, Ng BG, Bhide S, Chin E, et al.
Am J Hum Genet. 2012 Feb 1. [Epub ahead of print]

RAD51 haploinsufficiency causes congenital mirror movements in humans.
Depienne C, Bouteiller D, Méneret A, Billot S, et al.
Am J Hum Genet. 2012 Feb 1. [Epub ahead of print]

Diagnosis of mitochondrial disorders applying massive pyrosequencing.
Kauffman MA, González-Morón D, Consalvo D, Westergaard G, et al.
Mol Biol Rep. 2012 Feb 3. [Epub ahead of print]

VAR-MD: A tool to analyze whole exome/genome variants in small human pedigrees with Mendelian inheritance.
Sincan M, Simeonov D, Adams D, Markello TC, et al.
Hum Mutat. 2012 Jan 30. [Epub ahead of print]

Whole genome sequences of a male and female supercentenarian, ages greater than 114 years.
Sebastiani P, Riva A, Montano M, Pham P, et al.
Front Genet. 2011;2:90.

Somatic mutations in the notch, NF-KB, PIK3CA, and hedgehog pathways in human breast cancers.
Jiao X, Wood LD, Lindman M, Jones S, et al.
Genes Chromosomes Cancer. 2012 Feb 3. [Epub ahead of print]

Identification of hepatitis C virus transmission using a next generation sequencing approach.
Escobar-Gutiérrez A, Vazquez-Pichardo M, Cruz-Rivera M, Rivera-Osorio P, et al.
J Clin Microbiol. 2012 Feb 1. [Epub ahead of print]

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing.
Koboldt DC, Zhang Q, Larson DE, Shen D, et al.
Genome Res. 2012 Feb 2. [Epub ahead of print]

Refining noninvasive prenatal diagnosis with single-molecule next-generation sequencing.
Avent ND.
Clin Chem. 2012 Feb 2. [Epub ahead of print]

Multi-locus HLA class I and II allele and haplotype associations with follicular lymphoma.
Skibola CF, Akers NK, Conde L, Ladner M, et al.
Tissue Antigens. 2012 Feb 2. [Epub ahead of print]

Microfluidic amplification as a tool for massive parallel sequencing of familial hypercholesterolemia genes.
Hollants S, Redeker EJ, Matthijs G.
Clin Chem. 2012 Jan 31. [Epub ahead of print]

Inflamed target tissue provides a specific niche for highly expanded T-cell clones in early human autoimmune disease.
Klarenbeek PL, de Hair MJ, Doorenspleet ME, van Schaik BD, et al.
Ann Rheum Dis. 2012 Jan 31. [Epub ahead of print]

Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer.
Wu C, Wyatt AW, Lapuk AV, McPherson A, et al.
J Pathol. 2012 Jan 4. [Epub ahead of print]

Detecting false positive signals in exome sequencing.
Fuentes Fajardo KV, Adams D, Nisc Comparative Sequencing Program, et al.
Hum Mutat. 2012 Jan 31. [Epub ahead of print]

Whole genome sequences of three Treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence.
Cejková D, Zobaníková M, Chen L, Pospíšilová P, et al.
PLoS Negl Trop Dis. 2012 Jan;6(1):e1471.

The viral and cellular microRNA targetome in lymphoblastoid cell lines.
Skalsky RL, Corcoran DL, Gottwein E, Frank CL, et al.
PLoS Pathog. 2012 Jan;8(1):e1002484.

Analysis of DNA sequence variants detected by high throughput sequencing.
Adams DR, Sincan M, Fajardo KF, for the NISC Comparative Sequencing Program et al.
Hum Mutat. 2012 Jan 30. [Epub ahead of print]

Mutation in the AP4B1 gene cause hereditary spastic paraplegia type 47 (SPG47) .
Bauer P, Leshinsky-Silver E, Blumkin L, Schlipf N, et al.
Neurogenetics. 2012 Jan 31. [Epub ahead of print]

Improving bioinformatic pipelines for exome variant calling.
Ji HP.
Genome Med. 2012 Jan 30;4(1):7.

Whole-exome sequencing in a single proband reveals a mutation in the CHST8 gene in autosomal recessive peeling skin syndrome.
Cabral RM, Kurban M, Wajid M, Shimomura Y, et al.
Genomics. 2012 Jan 25. [Epub ahead of print]

The Scan

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.

New Insights Into TP53-Driven Cancer

Researchers examine in Nature how TP53 mutations arise and spark tumor development.

Mapping Single-Cell Genomic, Transcriptomic Landscapes of Colorectal Cancer

In Genome Medicine, researchers present a map of single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer.

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.