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In Print: Clinical Sequencing Papers of Note of the Last Two Weeks: Sep 5, 2012


Exome enrichment and SOLiD sequencing of formalin fixed paraffin embedded (FFPE) prostate cancer tissue.
Menon R, Deng M, Boehm D, Braun M, et al.
Int J Mol Sci. 2012;13(7):8933-42.

Genome-wide analysis of DNA methylation and expression of microRNAs in breast cancer cells.
Morita S, Takahashi RU, Yamashita R, Toyoda A, et al.
Int J Mol Sci. 2012;13(7):8259-72.

Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer.
Rudin CM, Durinck S, Stawiski EW, Poirier JT, et al.
Nat Genet. 2012 Sep 2. [Epub ahead of print]

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer.
Peifer M, Fernández-Cuesta L, Sos ML, George J, et al.
Nat Genet. 2012 Sep 2. [Epub ahead of print]

Using ERDS to infer copy-number variants in high-coverage genomes.
Zhu M, Need AC, Han Y, Ge D, et al.
Am J Hum Genet. 2012 Aug 29. [Epub ahead of print]

Sequencing and analysis of a South Asian-Indian personal genome.
Gupta R, Ratan A, Rajesh C, Chen R, et al.
BMC Genomics. 2012 Aug 31;13(1):440.

Targeted massive parallel sequencing: the effective detection of novel causative mutations associated with hearing loss in small families.
Baek JI, Oh SK, Kim DB, Choi SY, et al.
Orphanet J Rare Dis. 2012 Sep 3;7(1):60.

Targeted next-generation sequencing identifies a homozygous nonsense mutation in ABHD12, the gene underlying PHARC, in a family clinically diagnosed with Usher syndrome type 3.
Eisenberger T, Slim R, Mansour A, Nauck M, et al.
Orphanet J Rare Dis. 2012 Sep 2;7(1):59.

Targeting the tumor mutanome for personalized vaccination therapy.
Kreiter S, Castle JC, Türeci O, Sahin U.
Oncoimmunology. 2012 Aug 1;1(5):768-769.

Whole-genome sequences and comparative genomics of Salmonella enteric serovar typhi isolates from patients with fatal and nonfatal typhoid fever in Papua New Guinea.
Baddam R, Thong KL, Avasthi TS, Shaik S, et al.
J Bacteriol. 2012 Sep;194(18):5122-3.

Novel microcephalic primordial dwarfism disorder associated with variants in the centrosomal protein ninein.
Dauber A, Lafranchi SH, Maliga Z, Lui JC, et al.
J Clin Endocrinol Metab. 2012 Aug 29. [Epub ahead of print]

Massive evolution of the immunoglobulin heavy chain locus in children with B precursor acute lymphoblastic leukemia.
Gawad C, Pepin F, Carlton V, Klinger M, et al.
Blood. 2012 Aug 28. [Epub ahead of print]

Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia.
Jan M, Snyder TM, Corces-Zimmerman MR, Vyas P, et al.
Sci Transl Med. 2012 Aug 29;4(149):149ra118.

A new phlebovirus associated with severe febrile illness in Missouri.
McMullan LK, Folk SM, Kelly AJ, MacNeil A, et al.
N Engl J Med. 2012 Aug 30;367(9):834-41.

MYD88 L265P somatic mutation in Waldenström's macroglobulinemia.
Treon SP, Xu L, Yang G, Zhou Y, et al.
N Engl J Med. 2012 Aug 30;367(9):826-33.

Whole exome sequencing identifies a novel DFNA9 mutation, C162Y: the first reported DFNA9 mutation in the intervening domain of COCH.
Gao J, Xue J, Chen L, Ke X, et al.
Clin Genet. 2012 Aug 29. [Epub ahead of print]

Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated LncRNAs and novel transcripts.
Lee CS, Ungewickell A, Bhaduri A, Qu K, et al.
Blood. 2012 Aug 30. [Epub ahead of print]

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization.
Sharon I, Morowitz MJ, Thomas BC, Costello EK, et al.
Genome Res. 2012 Aug 30. [Epub ahead of print]

Identifying ChIP-seq enrichment using MACS.
Feng J, Liu T, Qin B, Zhang Y, Liu XS.
Nat Protoc. 2012 Aug 30;7(9):1728-40.

Factors influencing intention to undergo whole genome screening in future healthcare: A single-blind parallel-group randomised trial.
Fisher A, Bonner C, Biankin A, Juraskova I.
Prev Med. 2012 Aug 23. [Epub ahead of print]

Harnessing genomics to identify environmental determinants of heritable disease.
Yauk CL, Argueso JL, Auerbach SS, Awadalla P, et al.
Mutat Res. 2012 Aug 27. [Epub ahead of print]

Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing.
Li H, Stoddard MB, Wang S, Blair LM, et al.
PLoS Pathog. 2012 Aug;8(8):e1002880.

Whole exome sequencing identifies KCNQ2 mutations in Ohtahara syndrome.
Saitsu H, Kato M, Koide A, Goto T, et al.
Ann Neurol. 2012 Aug;72(2):298-300.

Familial cortical myoclonus with a mutation in NOL3.
Russell JF, Steckley JL, Coppola G, G Hahn AF, et al.
Ann Neurol. 2012 Aug;72(2):175-83.

Transcriptional profiling of lncRNAs and novel transcribed regions across a diverse panel of archived human cancers.
Brunner AL, Beck AH, Edris B, Sweeney RT, et al.
Genome Biol. 2012 Aug 28;13(8):R75.

Identification of molecular pathway aberrations in uterine serous carcinoma by genome-wide analyses.
Kuhn E, Wu RC, Guan B, Wu G, et al.
J Natl Cancer Inst. 2012 Aug 23. [Epub ahead of print]

Genome sequencing identifies a basis for everolimus sensitivity.
Iyer G, Hanrahan AJ, Milowsky MI, Al-Ahmadie H, et al.
Science. 2012 Aug 23. [Epub ahead of print]

Pooled DNA re-sequencing of 68 myocardial infaction candidate genes in French Canadians.
Beaudoin M, Lo KS, N'diaye A, Rivas MA, et al.
Circ Cardiovasc Genet. 2012 Aug 25. [Epub ahead of print]

Exome sequencing identifies two rare variants for low HDL-C in an extended family.
Linga Reddy MV, Iatan I, Weissglas-Volkov D, Nikkola E, et al.
Circ Cardiovasc Genet. 2012 Aug 25. [Epub ahead of print]

Mutations in ABCD4 cause a new inborn error of vitamin B(12) metabolism.
Coelho D, Kim JC, Miousse IR, Fung S, et al.
Nat Genet. 2012 Aug 26. [Epub ahead of print]

Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma.
Huang J, Deng Q, Wang Q, Li KY, et al.
Nat Genet. 2012 Aug 26. [Epub ahead of print]

Challenges in medical applications of whole exome/genome sequencing discoveries.
Marian AJ.
Trends Cardiovasc Med. 2012 Aug 23. [Epub ahead of print]

Development of a next-generation sequencing method for BRCA mutation screening: a comparison between a high-throughput and a benchtop platform.
Chan M, Mo Ji S, Yeo ZX, Gan L, et al.
J Mol Diagn. 2012 Aug 22. [Epub ahead of print]

Absence of global hypomethylation in promoter hypermethylated mixed lineage leukaemia-rearranged infant acute lymphoblastic leukaemia.
Stumpel DJ, Schneider P, van Roon EH, Pieters R, Stam RW.
Eur J Cancer. 2012 Aug 23. [Epub ahead of print]

Clinical applications of the latest molecular diagnostics in noninvasive prenatal diagnosis.
Chan KC.
Top Curr Chem. 2012 Aug 24. [Epub ahead of print]

Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns.
Schuh A, Becq J, Humphray S, Alexa A, et al.
Blood. 2012 Aug 22. [Epub ahead of print]

Mutation detection by clonal sequencing of PCR amplicons and grouped read typing is applicable to clinical diagnostics.
Chambers PA, Stead LF, Morgan JE, Carr IMet al.
Hum Mutat. 2012 Aug 22. [Epub ahead of print]

Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumonia with whole-genome sequencing.
Snitkin ES, Zelazny AM, Thomas PJ, Stock F; et al.
Sci Transl Med. 2012 Aug 22;4(148):148ra116.

Rate of de novo mutations and the importance of father's age to disease risk.
Kong A, Frigge ML, Masson G, Besenbacher S, et al.
Nature. 2012 Aug 23;488(7412):471-5.

Rare variants in TMEM132D in a case-control sample for panic disorder.
Quast C, Altmann A, Weber P, Arloth J, et al.
Am J Med Genet B Neuropsychiatr Genet. 2012 Aug 22.

Next-generation sequencing reveals the secrets of the chronic lymphocytic leukemia genome.
Ramsay AJ, Martínez-Trillos A, Jares P, Rodríguez D, et al.
Clin Transl Oncol. 2012 Aug 22. [Epub ahead of print]

BRAFL597 mutations in melanoma are associated with sensitivity to MEK inhibitors.
Dahlman KB, Xia J, Hutchinson K, Ng C, et al.
Cancer Discov. 2012 Aug 23. [Epub ahead of print]

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.