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In Print: Last Week's Clinical Sequencing Papers of Note: Sep 19, 2012


Identification of drug resistant mutations in HIV-1 CRF07_BC variants selected by nevirapine in vitro.
Wu H, Zhang HJ, Zhang XM, Xu HF, et al.
PLoS One. 2012;7(9):e44333.

Dynamic population changes in Mycobacterium tuberculosis during acquisition and fixation of drug resistance in patients.
Sun G, Luo T, Yang C, Dong X, et al.
J Infect Dis. 2012 Sep 14. [Epub ahead of print]

Approaches to homozygosity mapping and exome sequencing for the identification of novel types of CDG.
Matthijs G, Rymen D, Millón MB, Souche E, Race V.
Glycoconj J. 2012 Sep 15. [Epub ahead of print]

Exome sequencing identifies MVK mutations in disseminated superficial actinic porokeratosis.
Zhang SQ, Jiang T, Li M, Zhang X, et al.
Nat Genet. 2012 Sep 16. [Epub ahead of print]

Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity.
Beltran H, Yelensky R, Frampton GM, Park K, et al.
Eur Urol. 2012 Sep 5. [Epub ahead of print]

A population-based study of autosomal-recessive disease-causing mutations in a founder population.
Chong JX, Ouwenga R, Anderson RL, Waggoner DJ, Ober C.
Am J Hum Genet. 2012 Sep 12. [Epub ahead of print]

Genomic landscape of non-small cell lung cancer in smokers and never-smokers.
Govindan R, Ding L, Griffith M, Subramanian J, et al.
Cell. 2012 Sep 14;150(6):1121-34.

Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing.
Imielinski M, Berger AH, Hammerman PS, Hernandez B, et al.
Cell. 2012 Sep 14;150(6):1107-20.

Recurrent mutations in DNAJC5 cause autosomal dominant Kufs disease.
Cadieux-Dion M, Andermann E, Lachance-Touchette P, Ansorge O, et al.
Clin Genet. 2012 Sep 14. [Epub ahead of print]

Evaluating rare coding variants as contributing causes to nonsyndromic cleft lip and palate.
Leslie EJ, Murray JC.
Clin Genet. 2012 Sep 14. [Epub ahead of print]

Commonly altered genomic regions in acute myeloid leukemia are enriched for somatic mutations involved in chromatin-remodeling and splicing.
Dolnik A, Engelmann JC, Scharfenberger-Schmeer M, Mauch J, Kelkenberg-Schade S, Blood. 2012 Sep 13. [Epub ahead of print]

Deep sequencing reveals small RNA characterization of invasive micropapillary carcinomas of the breast.
Li S, Yang C, Zhai L, Zhang W, et al.
Breast Cancer Res Treat. 2012 Sep 14. [Epub ahead of print]

The transcriptional landscape and mutational profile of lung adenocarcinoma.
Seo JS, Ju YS, Lee WC, Shin JY, et al.
Genome Res. 2012 Sep 13. [Epub ahead of print]

Prediction of cochlear implant performance by genetic mutation: The spiral ganglion hypothesis.
Eppsteiner RW, Shearer AE, Hildebrand MS, Deluca AP, et al.
Hear Res. 2012 Aug 28. [Epub ahead of print]

Whole exome sequencing reveals a novel mutation in CUL7 in a patient with an undiagnosed growth disorder..
Dauber A, Stoler J, Hechter E, Safer J, Hirschhorn JN.
J Pediatr. 2012 Sep 10. [Epub]

Alterations of microbiota in urine from women with interstitial cystitis.
Siddiqui H, Lagesen K, Nederbragt AJ, Jeansson SL, Jakobsen KS .
BMC Microbiol. 2012 Sep 13;12(1):205.

In depth comparison of an individual's DNA and its lymphoblastoid cell line using whole genome sequencing.
Nickles D, Madireddy L, Yang S, Khankhanian P, et al.
BMC Genomics. 2012 Sep 14;13(1):477.

SDHA loss of function mutations in a subset of young adult wild-type gastrointestinal stromal tumors.
Italiano A, Chen CL, Sung YS, Singer S, et al.
BMC Cancer. 2012 Sep 14;12(1):408.

Genomic inheritances: disclosing individual research results from whole-exome sequencing to deceased participants' relatives.
Chan B, Facio FM, Eidem H, Hull SC, et al.
Am J Bioeth. 2012 Oct;12(10):1-8.

Localization of association signal from risk and protective variants in sequencing studies.
Brisbin A, Jenkins GD, Ellsworth KA, Wang L, Fridley BL.
Front Genet. 2012;3:173.

Exome sequencing identifies a COL14A1 mutation in a large Chinese pedigree with punctate palmoplantar keratoderma.
Guo BR, Zhang X, Chen G, Zhang JG, et al.
J Med Genet. 2012 Sep;49(9):563-8.

Next-generation Ion Torrent sequencing of drug resistance mutations in Mycobacterium tuberculosis strains.
Daum LT, Rodriguez JD, Worthy SA, Ismail NA, et al.
J Clin Microbiol. 2012 Sep 12. [Epub ahead of print]

Analysis and optimal design for association studies using next-generation sequencing with case-control pools.
Liang WE, Thomas DC, Conti DV.
Genet Epidemiol. 2012 Sep 12. [Epub ahead of print]

Genetic predisposing factors to bronchopulmonary dysplasia: preliminary data from a multicentre study.
Somaschini M, Castiglioni E, Volonteri C, Cursi M, et al.
J Matern Fetal Neonatal Med. 2012 Oct;25 Suppl 4:119-22.

Cultivable and pyrosequenced fecal microflora in centenarians and young subjects.
Drago L, Toscano M, Rodighiero V, De Vecchi E, Mogna G.
J Clin Gastroenterol. 2012 Oct;46 Suppl:S81-4.

Genetic characterisation of Malawian pneumococci prior to the roll-out of the PCV13 vaccine using a high-throughput whole genome sequencing approach.
Everett DB, Cornick J, Denis B, Chewapreecha C, et al.
PLoS One. 2012;7(9):e44250.

Extensive somatic L1 retrotransposition in colorectal tumors.
Solyom S, Ewing AD, Rahrmann EP, Doucet TT, et al.
Genome Res. 2012 Sep 11. [Epub ahead of print]

Next-generation sequencing (NGS) as a diagnostic tool for retinal degeneration reveals a much higher detection rate in early-onset disease.
Shanks ME, Downes SM, Copley RR, Lise S, et al.
Eur J Hum Genet. 2012 Sep 12. [Epub ahead of print]

Comparison of genome diversity of Brucella spp. field isolates using universal bio-signature detection array and whole genome sequencing reveals limitations of current diagnostic methods.
Shallom SJ, Tae H, Sarmento L, Preston D, et al.
Gene. 2012 Aug 8. [Epub ahead of print]

Presence of oseltamivir-resistant pandemic A/H1N1 minor variants before drug therapy with subsequent selection and transmission.
Ghedin E, Holmes EC, Depasse JV, Pinilla LT, et al.
J Infect Dis. 2012 Sep 10. [Epub ahead of print]

Not all floating harbor syndrome cases are due to mutations in exon 34 of SRCAP.
Le Goff C, Mahaut C, Bottani A, Doray B, et al.
Hum Mutat. 2012 Sep 10. [Epub ahead of print]

MPV17 mutations causing adult-onset multisystemic disorder with multiple mitochondrial DNA deletions.
Garone C, Rubio JC, Calvo SE, Naini A, et al.
Arch Neurol. 2012 Sep 10:1-4. [Epub ahead of print]

Transcriptional regulation of the GPX1 gene by TFAP2C and aberrant CpG methylation in human breast cancer.
Kulak MV, Cyr AR, Woodfield GW, Bogachek M, et al.
Oncogene. 2012 Sep 10. [Epub ahead of print]

High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic.
Sealfon R, Gire S, Ellis C, Calderwood S, et al.
BMC Genomics. 2012 Sep 11;13(1):468.

Pediatric case report: clinical profile of a patient with PCWH with p.Q377X nonsense mutation in the SOX10 gene.
Oshimo T, Fukai K, Abe Y, Hozumi Y, et al.
J Dermatol. 2012 Sep 11. [Epub ahead of print]