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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

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.