Clinical Integration of Next-Generation Sequencing Technology

被引：41
作者：
Gullapalli, R. R.
Lyons-Weiler, M. [3 ]
Petrosko, P. [3 ]
Dhir, R. [2 ,3 ]
Becich, M. J. [2 ,3 ]
LaFramboise, W. A. [1 ,2 ,3 ]
机构：
[1] Univ Pittsburgh, Sch Med, Shadyside Hosp, Dept Pathol, Pittsburgh, PA 15232 USA
[2] Univ Pittsburgh, Sch Med, Dept Biomed Informat, Pittsburgh, PA 15206 USA
[3] Univ Pittsburgh, Inst Canc, Pittsburgh, PA USA
来源：
CLINICS IN LABORATORY MEDICINE | 2012年 / 32卷 / 04期
关键词：
Clinical pathology; Computational pathology; Genomics; Genomic sequencing; Molecular diagnostics; Next generation sequencing; Tumor diagnostics; CANCER GENOME; IDENTIFICATION; PLATFORMS; MUTATIONS; LANDSCAPE; DISCOVERY; EGFR;
D O I：
10.1016/j.cll.2012.07.005
中图分类号：
R446 [实验室诊断]; R-33 [实验医学、医学实验];
学科分类号：
1001 ;
摘要：
Recent advances in next-generation sequencing (NGS) methods and technology have substantially reduced costs and operational complexity leading to production of benchtop sequencers and commercial software solutions for implementation in small research and clinical laboratories. This article addresses requirements and limitations to successful implementation of these systems, including (1) calibration and validation of the instrumentation, experimental paradigm, and primary readout, (2) secure data transfer, storage, and secondary processing, (3) implementation of software tools for targeted analysis, and (4) training of research and clinical personnel to evaluate data fidelity and interpret the molecular significance of the genomic output.
引用
收藏
页码：585 / +
页数：16
相关论文
共 56 条
  • [1] A map of human genome variation from population-scale sequencing
    Altshuler, David
    Durbin, Richard M.
    Abecasis, Goncalo R.
    Bentley, David R.
    Chakravarti, Aravinda
    Clark, Andrew G.
    Collins, Francis S.
    De la Vega, Francisco M.
    Donnelly, Peter
    Egholm, Michael
    Flicek, Paul
    Gabriel, Stacey B.
    Gibbs, Richard A.
    Knoppers, Bartha M.
    Lander, Eric S.
    Lehrach, Hans
    Mardis, Elaine R.
    McVean, Gil A.
    Nickerson, DebbieA.
    Peltonen, Leena
    Schafer, Alan J.
    Sherry, Stephen T.
    Wang, Jun
    Wilson, Richard K.
    Gibbs, Richard A.
    Deiros, David
    Metzker, Mike
    Muzny, Donna
    Reid, Jeff
    Wheeler, David
    Wang, Jun
    Li, Jingxiang
    Jian, Min
    Li, Guoqing
    Li, Ruiqiang
    Liang, Huiqing
    Tian, Geng
    Wang, Bo
    Wang, Jian
    Wang, Wei
    Yang, Huanming
    Zhang, Xiuqing
    Zheng, Huisong
    Lander, Eric S.
    Altshuler, David L.
    Ambrogio, Lauren
    Bloom, Toby
    Cibulskis, Kristian
    Fennell, Tim J.
    Gabriel, Stacey B.
    [J]. NATURE, 2010, 467 (7319) : 1061 - 1073
  • [2] Integrating common and rare genetic variation in diverse human populations
    Altshuler, David M.
    Gibbs, Richard A.
    Peltonen, Leena
    Dermitzakis, Emmanouil
    Schaffner, Stephen F.
    Yu, Fuli
    Bonnen, Penelope E.
    de Bakker, Paul I. W.
    Deloukas, Panos
    Gabriel, Stacey B.
    Gwilliam, Rhian
    Hunt, Sarah
    Inouye, Michael
    Jia, Xiaoming
    Palotie, Aarno
    Parkin, Melissa
    Whittaker, Pamela
    Chang, Kyle
    Hawes, Alicia
    Lewis, Lora R.
    Ren, Yanru
    Wheeler, David
    Muzny, Donna Marie
    Barnes, Chris
    Darvishi, Katayoon
    Hurles, Matthew
    Korn, Joshua M.
    Kristiansson, Kati
    Lee, Charles
    McCarroll, Steven A.
    Nemesh, James
    Keinan, Alon
    Montgomery, Stephen B.
    Pollack, Samuela
    Price, Alkes L.
    Soranzo, Nicole
    Gonzaga-Jauregui, Claudia
    Anttila, Verneri
    Brodeur, Wendy
    Daly, Mark J.
    Leslie, Stephen
    McVean, Gil
    Moutsianas, Loukas
    Nguyen, Huy
    Zhang, Qingrun
    Ghori, Mohammed J. R.
    McGinnis, Ralph
    McLaren, William
    Takeuchi, Fumihiko
    Grossman, Sharon R.
    [J]. NATURE, 2010, 467 (7311) : 52 - 58
  • [3] [Anonymous], CURR PROTOC BIOINFOR
  • [4] RETRACTED: Evaluation of next-generation sequencing software in mapping and assembly (Retracted article. See vol. 56, pg. 687, 2011)
    Bao, Suying
    Jiang, Rui
    Kwan, WingKeung
    Wang, BinBin
    Ma, Xu
    Song, You-Qiang
    [J]. JOURNAL OF HUMAN GENETICS, 2011, 56 (06) : 406 - 414
  • [5] Integrative analysis of the melanoma transcriptome
    Berger, Michael F.
    Levin, Joshua Z.
    Vijayendran, Krishna
    Sivachenko, Andrey
    Adiconis, Xian
    Maguire, Jared
    Johnson, Laura A.
    Robinson, James
    Verhaak, Roel G.
    Sougnez, Carrie
    Onofrio, Robert C.
    Ziaugra, Liuda
    Cibulskis, Kristian
    Laine, Elisabeth
    Barretina, Jordi
    Winckler, Wendy
    Fisher, David E.
    Getz, Gad
    Meyerson, Matthew
    Jaffe, David B.
    Gabriel, Stacey B.
    Lander, Eric S.
    Dummer, Reinhard
    Gnirke, Andreas
    Nusbaum, Chad
    Garraway, Levi A.
    [J]. GENOME RESEARCH, 2010, 20 (04) : 413 - 427
  • [6] QSRA - a quality-value guided de novo short read assembler
    Bryant, Douglas W., Jr.
    Wong, Weng-Keen
    Mockler, Todd C.
    [J]. BMC BIOINFORMATICS, 2009, 10
  • [7] Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
    Campbell, Peter J.
    Stephens, Philip J.
    Pleasance, Erin D.
    O'Meara, Sarah
    Li, Heng
    Santarius, Thomas
    Stebbings, Lucy A.
    Leroy, Catherine
    Edkins, Sarah
    Hardy, Claire
    Teague, Jon W.
    Menzies, Andrew
    Goodhead, Ian
    Turner, Daniel J.
    Clee, Christopher M.
    Quail, Michael A.
    Cox, Antony
    Brown, Clive
    Durbin, Richard
    Hurles, Matthew E.
    Edwards, Paul A. W.
    Bignell, Graham R.
    Stratton, Michael R.
    Futreal, P. Andrew
    [J]. NATURE GENETICS, 2008, 40 (06) : 722 - 729
  • [8] The patterns and dynamics of genomic instability in metastatic pancreatic cancer
    Campbell, Peter J.
    Yachida, Shinichi
    Mudie, Laura J.
    Stephens, Philip J.
    Pleasance, Erin D.
    Stebbings, Lucy A.
    Morsberger, Laura A.
    Latimer, Calli
    McLaren, Stuart
    Lin, Meng-Lay
    McBride, David J.
    Varela, Ignacio
    Nik-Zainal, Serena A.
    Leroy, Catherine
    Jia, Mingming
    Menzies, Andrew
    Butler, Adam P.
    Teague, Jon W.
    Griffin, Constance A.
    Burton, John
    Swerdlow, Harold
    Quail, Michael A.
    Stratton, Michael R.
    Iacobuzio-Donahue, Christine
    Futreal, P. Andrew
    [J]. NATURE, 2010, 467 (7319) : 1109 - 1113
  • [9] Short read fragment assembly of bacterial genomes
    Chaisson, Mark J.
    Pevzner, Pavel A.
    [J]. GENOME RESEARCH, 2008, 18 (02) : 324 - 330
  • [10] Chen K, 2009, NAT METHODS, V6, P677, DOI [10.1038/NMETH.1363, 10.1038/nmeth.1363]
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