期刊论文详细信息
BMC Genetics
Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations
Madhuri Hegde1  Cristina da Silva1  Ephrem LH Chin1 
[1]Department of Human Genetics, Emory University, Michael Street, Atlanta, GA, USA
关键词: Detection;    Mutation;    Sequencing;    Next-generation;    Enrichment;    Targeted;   
Others  :  1087366
DOI  :  10.1186/1471-2156-14-6
 received in 2012-02-01, accepted in 2013-02-08,  发布年份 2013
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2013 Chin et al; licensee BioMed Central Ltd.

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【 参考文献 】
  • [1]Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Guo Y: The diploid genome sequence of an Asian individual. Nature 2008, 456:60-65.
  • [2]Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT: The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452:872-876.
  • [3]Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR: Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59.
  • [4]Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
  • [5]Voelkerding KV, Dames SA, Durtschi JD: Next-generation sequencing: from basic research to diagnostics. Clin Chem 2009, 55:641-658.
  • [6]Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B: Real-time DNA sequencing from single polymerase molecules. Science 2009, 323:133-138.
  • [7]Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M: An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475:348-352.
  • [8]Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977, 74:5463-5467.
  • [9]Oetting WS: Impact of next generation sequencing: the 2009 Human Genome Variation Society Scientific Meeting. Hum Mutat 2010, 31:500-503.
  • [10]Saah AJ, Hoover DR: "Sensitivity" and "specificity" reconsidered: the meaning of these terms in analytical and diagnostic settings. Ann Intern Med 1997, 126:91-94.
  • [11]Huang T: Next generation sequencing to characterize mitochondrial genomic DNA heteroplasmy. Curr Protoc Hum Genet 2011, 71:19.8.1-19.8.12.
  • [12]Association for Molecular Pathology Clinical Practice Committee: Molecular Diagnostic Assay Validation. 2009.
  • [13]Koenig M, Hoffman EP, Bertelson CJ, Monaco AP, Feener C, Kunkel LM: Complete cloning of the Duchenne muscular dystrophy (DMD) cDNA and preliminary genomic organization of the DMD gene in normal and affected individuals. Cell 1987, 50:509-517.
  • [14]Mehler MF: Brain dystrophin, neurogenetics and mental retardation. Brain Res Brain Res Rev 2000, 32:277-307.
  • [15]Horowitz M, Wilder S, Horowitz Z, Reiner O, Gelbart T, Beutler E: The human glucocerebrosidase gene and pseudogene: structure and evolution. Genomics 1989, 4:87-96.
  • [16]Martinez-Arias R, Calafell F, Mateu E, Comas D, Andres A, Bertranpetit J: Sequence variability of a human pseudogene. Genome Res 2001, 11:1071-1085.
  • [17]Kitao S, Lindor NM, Shiratori M, Furuichi Y, Shimamoto A: Rothmund-thomson syndrome responsible gene, RECQL4: genomic structure and products. Genomics 1999, 61:268-276.
  • [18]Kitao S, Shimamoto A, Goto M, Miller RW, Smithson WA, Lindor NM, Furuichi Y: Mutations in RECQL4 cause a subset of cases of Rothmund-Thomson syndrome. Nat Genet 1999, 22:82-84.
  • [19]Hjelm LN, Chin EL, Hegde MR, Coffee BW, Bean LJ: A simple method to confirm and size deletion, duplication, and insertion mutations detected by sequence analysis. JMD 2010, 12:607-610.
  • [20]Jones MA, Bhide S, Chin E, Ng BG, Rhodenizer D, Zhang VW, Sun JJ, Tanner A, Freeze HH, Hegde MR: Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation. Genet Med 2011, 13:921-932.
  • [21]Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP: Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res 2008, 18(10):1638-1642.
  • [22]Besaratinia A, Li H, Yoon JI, Zheng A, Gao H, Tommasi S: A high-throughput next-generation sequencing-based method for detecting the mutational fingerprint of carcinogens. Nucleic Acids Res 2012, 40(15):e116.
  • [23]Mokry M, Nijman IJ, van Dijken A, Benjamins R, Heidstra R, Scheres B, Cuppen E: Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach. BMC Genomics 2011, 12:256. BioMed Central Full Text
  • [24]De Leeneer K, De Schrijver J, Clement L, Baetens M, Lefever S, De Keulenaer S, Van Criekinge W, Deforce D, Van Nieuwerburgh F, Bekaert S: Practical tools to implement massive parallel pyrosequencing of PCR products in next generation molecular diagnostics. PLoS One 2011, 6(9):25531.
  • [25]Dohm Juliane C, Lattaz C, Borodina T, Himmelbauer H: Substantial biases in ultra short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36(16):e105.
  • [26]Reducing Error in Next Generation Sequencing Data with NextGENe™ Software’s Condensation Tool™ Application Note. http://www.softgenetics.com/ReducingError_NextGenerationSequencing_AppNote.pdf webcite
  • [27]Clark MJ, Chen R, Lam HY, Karczewski KJ, Euskirchen G, Butte AJ, Snyder M: Performance comparison of exome DNA sequencing technologies. Nat Biotechnol 2011, 29:908-914.
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