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In Print: Last Week's Clinical Sequencing Papers of Note: Sep 12, 2012


Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data.
Pfeifer N, Lengauer T.
Bioinformatics. 2012 Sep 15;28(18):i589-i595.

An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis.
Coin LJ, Cao D, Ren J, Zuo X, et al.
Bioinformatics. 2012 Sep 15;28(18):i370-i374.

FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma.
Jiang P, Chan KC, Liao GJ, Zheng YW, et al.
Bioinformatics. 2012 Sep 8. [Epub ahead of print]

GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples.
Cazier JB, Holmes CC, Broxholme J.
Bioinformatics. 2012 Sep 8. [Epub ahead of print]

DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders.
Swaminathan GJ, Bragin E, Chatzimichali EA, Corpas M, et al.
Hum Mol Genet. 2012 Sep 8. [Epub ahead of print]

Loss-of-function mutations in HINT1 cause axonal neuropathy with neuromyotonia.
Zimoń M, Baets J, Almeida-Souza L, De Vriendt E, et al.
Nat Genet. 2012 Sep 9. [Epub ahead of print]

Comprehensive genomic characterization of squamous cell lung cancers.
The Cancer Genome Atlas Research Network
Nature. 2012 Sep 9. [Epub ahead of print]

Segregation of a missense variant in enteric smooth muscle actin γ-2 with autosomal dominant familial visceral myopathy.
Lehtonen HJ, Sipponen T, Tojkander S, Karikoski R, et al.
Gastroenterology. 2012 Sep 6. [Epub ahead of print]

Exome sequencing and functional validation in zebrafish identify GTDC2 mutations as a cause of Walker-Warburg syndrome.
Manzini MC, Tambunan DE, Hill RS, Yu TW, et al.
Am J Hum Genet. 2012 Sep 7;91(3):541-7.

Loss of SUFU function in familial multiple meningioma.
Aavikko M, Li SP, Saarinen S, Alhopuro P, et al.
Am J Hum Genet. 2012 Sep 7;91(3):520-6.

Burden of rare sarcomere gene variants in the Framingham and Jackson Heart Study cohorts.
Bick AG, Flannick J, Ito K, Cheng S, et al.
Am J Hum Genet. 2012 Sep 7;91(3):513-9.

Exome sequencing identifies UPF3B as the causative gene for a Chinese non-syndrome mental retardation pedigree.
Xu X, Zhang L, Tong P, Xun G, et al.
Clin Genet. 2012 Sep 7. [Epub ahead of print]

Two rare human mitofusin 2 mutations alter mitochondrial dynamics and induce retinal and cardiac pathology in Drosophila.
Eschenbacher WH, Song M, Chen Y, Bhandari P, et al.
PLoS One. 2012;7(9):e44296.

Next generation diagnostics in inherited arrhythmia syndromes: a comparison of two approaches.
Ware JS, John S, Roberts AM, Buchan R, et al.
Cardiovasc Transl Res. 2012 Sep 7. [Epub ahead of print]

Improving the efficiency and relevance of evidence-based recommendations in the era of whole-genome sequencing: an EGAPP methods update.
Veenstra DL, Piper M, Haddow JE, Pauker SG, et al.
Genet Med. 2012 Sep 6. [Epub ahead of print]

Exploring bacterial diversity in hospital environments by GS-FLX Titanium pyrosequencing.
Poza M, Gayoso C, Gómez MJ, Rumbo-Feal S, et al.
PLoS One. 2012;7(8):e44105.

Allele-biased expression in differentiating human neurons: implications for neuropsychiatric disorders.
Lin M, Hrabovsky A, Pedrosa E, Wang T, et al.
PLoS One. 2012;7(8):e44017.

Molecular diagnosis of Usher syndrome: application of two different next generation sequencing-based procedures.
Licastro D, Mutarelli M, Peluso I, Neveling K, et al.
PLoS One. 2012;7(8):e43799.

A deletion in the bovine FANCI gene compromises fertility by causing fetal death and brachyspina.
Charlier C, Agerholm JS, Coppieters W, Karlskov-Mortensen P, et al.
PLoS One. 2012;7(8):e43085.

Identification of retinol binding protein 1 promoter hypermethylation in isocitrate dehydrogenase 1 and 2 mutant gliomas.
Chou AP, Chowdhury R, Li S, Chen W, et al.
J Natl Cancer Inst. 2012 Sep 3. [Epub ahead of print]

Myelodysplastic syndrome with a t(2;11)(p21;q23-24) and translocation breakpoint close to miR-125b-1.
Thorsen J, Aamot HV, Roberto R, Tjønnfjord GE, et al.
Cancer Genet. 2012 Aug 31. [Epub ahead of print]

Description of a large family with autosomal dominant hypercholesterolemia associated with the APOE p.Leu167del mutation.
Marduel M, Ouguerram K, Serre V, Bonnefont-Rousselot D, et al.
Hum Mutat. 2012 Sep 4. [Epub ahead of print]

Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial.
Tran B, Brown AM, Bedard PL, Winquist E, et al.
Int J Cancer. 2012 Sep 5. [Epub ahead of print]

High-throughput sequencing reveals the incomplete, short-term, recovery of the infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamycin.
Fouhy F, Guinane CM, Hussey S, Wall R, et al.
Antimicrob Agents Chemother. 2012 Sep 4. [Epub ahead of print]

Large-scale MHC class II genotyping of a wild lemur population by next generation sequencing.
Huchard E, Albrecht C, Schliehe-Diecks S, Baniel A, et al.
Immunogenetics. 2012 Sep 5. [Epub ahead of print]

CDK2-dependent activation of PARP-1 is required for hormonal gene regulation in breast cancer cells.
Wright RH, Castellano G, Bonet J, Le Dily F, et al.
Genes Dev. 2012 Sep 1;26(17):1972-83.

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.