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

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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.

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