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Clinical Sequencing Papers of Note: Aug 3, 2011


Human papillomavirus genotyping by 454 next generation sequencing technology.
Barzon L, Militello V, Lavezzo E, et al.
J Clin Virol. 2011 Jul 28. [Epub ahead of print]

Characterization of a 8q21.11 microdeletion syndrome associated with intellectual disability and a recognizable phenotype.
Palomares M, Delicado A, Mansilla E, et al.
Am J Hum Genet. 2011 Jul 27. [Epub ahead of print]

Corpus callosum abnormalities, mental retardation, speech impairment, and autism in patients with haploinsufficiency of ARID1B.
Halgren C, Kjaergaard S, Bak M, et al.
Clin Genet. 2011 Jul 29. [Epub ahead of print]

SuperSAGE evidence for CD14++CD16+ monocytes as a third monocyte subset.
Zawada AM, Rogacev KS, Rotter B, et al.
Blood. 2011 Jul 29. [Epub ahead of print]

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression.
Prensner JR, Iyer MK, Balbin OA, et al.
Nat Biotechnol. 2011 Jul 31. [Epub ahead of print]

Analysis of the coding genome of diffuse large B-cell lymphoma.
Pasqualucci L, Trifonov V, Fabbri G, et al.
Nat Genet. 2011 Jul 31. [Epub ahead of print]

Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation.
Mild M, Hedskog C, Jernberg J, Albert J.
PLoS One. 2011;6(7):e22741.

ChIP-seq defined genome-wide map of TGFβ/SMAD4 targets: implications with clinical outcome of ovarian cancer.
Kennedy BA, Deatherage DE, Gu F, et al.
PLoS One. 2011;6(7):e22606.

Comparative mRNA and microRNA expression profiling of three genitourinary cancers reveals common hallmarks and cancer-specific molecular events.
Li X, Chen J, Hu X, et al.
PLoS One. 2011;6(7):e22570.

Identification of RNF213 as a susceptibility gene for Moyamoya disease and its possible role in vascular development.
Liu W, Morito D, Takashima S, et al.
PLoS One. 2011;6(7):e22542.

Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates.
Baltrus DA, Nishimura MT, Romanchuk A, et al.
PLoS Pathog. 2011 Jul;7(7):e1002132.

Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1.
Agrawal N, Frederick MJ, Pickering CR, et al.
Science. 2011 Jul 28. [Epub ahead of print]

The mutational landscape of head and neck squamous cell carcinoma.
Stransky N, Egloff AM, Tward AD, et al.
Science. 2011 Jul 28. [Epub ahead of print]

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma.
Morin RD, Mendez-Lago M, Mungall AJ, et al.
Nature. 2011 Jul 27. [Epub ahead of print]

Targeting TLRs expands the antibody repertoire in response to a malaria vaccine.
Wiley SR, Raman VS, Desbien A, et al.
Sci Transl Med. 2011 Jul 27;3(93):93ra69.

Characterization of microRNAs expression profiling in one group of Chinese urothelial cell carcinoma identified by Solexa sequencing.
Chen YH, Wang SQ, Wu XL, et al.
Urol Oncol. 2011 Jul 25. [Epub ahead of print]

A novel mitochondrial DNA deletion producing progressive external ophthalmoplegia associated with multiple sclerosis.
Slee M, Finkemeyer J, Krupa M, et al.
J Clin Neurosci. 2011 Jul 25. [Epub ahead of print]

Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications.
Lyon GJ, Jiang T, Van Wijk R, et al.
Discov Med. 2011 Jul;12(62):41-55.

A mosaic activating mutation in AKT1 associated with the Proteus syndrome.
Lindhurst MJ, Sapp JC, Teer JK, et al.
N Engl J Med. 2011 Jul 27. [Epub ahead of print]

Prediction of functional regulatory SNPs in monogenic and complex disease.
Zhao Y, Clark WT, Mort M, Cooper DN, Radivojac P, Mooney SD.
Hum Mutat. 2011 Jul 27. [Epub ahead of print]

Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities.
Schrader KA, Heravi-Moussavi A, Waters PJ, et al.
J Pathol. 2011 Sep;225(1):12-8.

Comparison between direct sequencing and INNO-LiPA methods for HPV detection and genotyping in Thai women.
Chinchai T, Chansaenroj J, Junyangdikul P, et al.
Asian Pac J Cancer Prev. 2011;12(4):989-94.

Divergent human populations show extensive shared IGK rearrangements in peripheral blood B cells.
Jackson KJ, Wang Y, Gaeta BA, et al.
Immunogenetics. 2011 Jul 26. [Epub ahead of print]

An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing.
Auburn S, Campino S, Clark TG, et al.
PLoS One. 2011;6(7):e22213.

Analysis of mitochondrial genome revealed a rare 50bp deletion and substitutions in a family with hypertension.
Elango S, Govindaraj P, Vishwanadha VP, et al.
Mitochondrion. 2011 Jul 20. [Epub ahead of print]

The Scan

For Better Odds

Bloomberg reports that a child has been born following polygenic risk score screening as an embryo.

Booster Decision Expected

The New York Times reports the US Food and Drug Administration is expected to authorize a booster dose of the Pfizer-BioNTech SARS-CoV-2 vaccine this week for individuals over 65 or at high risk.

Snipping HIV Out

The Philadelphia Inquirer reports Temple University researchers are to test a gene-editing approach for treating HIV.

PLOS Papers on Cancer Risk Scores, Typhoid Fever in Colombia, Streptococcus Protection

In PLOS this week: application of cancer polygenic risk scores across ancestries, genetic diversity of typhoid fever-causing Salmonella, and more.