Genome sequencing guide: An introductory toolbox to whole-genome analysis methods

被引:10
作者
Burian, Alexis N. [1 ]
Zhao, Wufan [2 ]
Lo, Te-Wen [1 ]
Thurtle-Schmidt, Deborah M. [2 ]
机构
[1] Ithaca Coll, Dept Biol, Ithaca, NY 14850 USA
[2] Davidson Coll, Dept Biol, Box 7118, Davidson, NC 28035 USA
关键词
bioinformatics; ethics; genomics; sequencing; MOLECULAR-STRUCTURE; DNA; QUANTIFICATION;
D O I
10.1002/bmb.21561
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
To fully appreciate genetics, one must understand the link between genotype (DNA sequence) and phenotype (observable characteristics). Advances in high-throughput genomic sequencing technologies and applications, so-called "-omics," have made genetic sequencing readily available across fields in biology from applications in non-traditional study organisms to precision medicine. Thus, understanding these tools is critical for any biologist, especially those early in their career. This comprehensive review discusses the chronological development of different sequencing methods, the bioinformatics steps to analyzing this data, and social and ethical issues raised by these techniques that must be discussed and evaluated, including anticipatory guides and discussion questions for active engagement in the classroom. Additionally, the Supporting Information includes a case study to apply technical and ethical concepts from the text.
引用
收藏
页码:815 / 825
页数:11
相关论文
共 42 条
[1]  
[Anonymous], 2020, GENOME WIDE ASS STUD
[2]   ENZYMATIC SYNTHESIS OF DEOXYRIBONUCLEIC ACID .34. TERMINATION OF CHAIN GROWTH BY A 2',3'-DIDEOXYRIBONUCLEOTIDE [J].
ATKINSON, MR ;
DEUTSCHER, MP ;
KORNBERG, A ;
RUSSELL, AF ;
MOFFATT, JG .
BIOCHEMISTRY, 1969, 8 (12) :4897-+
[3]   Accurate whole human genome sequencing using reversible terminator chemistry [J].
Bentley, David R. ;
Balasubramanian, Shankar ;
Swerdlow, Harold P. ;
Smith, Geoffrey P. ;
Milton, John ;
Brown, Clive G. ;
Hall, Kevin P. ;
Evers, Dirk J. ;
Barnes, Colin L. ;
Bignell, Helen R. ;
Boutell, Jonathan M. ;
Bryant, Jason ;
Carter, Richard J. ;
Cheetham, R. Keira ;
Cox, Anthony J. ;
Ellis, Darren J. ;
Flatbush, Michael R. ;
Gormley, Niall A. ;
Humphray, Sean J. ;
Irving, Leslie J. ;
Karbelashvili, Mirian S. ;
Kirk, Scott M. ;
Li, Heng ;
Liu, Xiaohai ;
Maisinger, Klaus S. ;
Murray, Lisa J. ;
Obradovic, Bojan ;
Ost, Tobias ;
Parkinson, Michael L. ;
Pratt, Mark R. ;
Rasolonjatovo, Isabelle M. J. ;
Reed, Mark T. ;
Rigatti, Roberto ;
Rodighiero, Chiara ;
Ross, Mark T. ;
Sabot, Andrea ;
Sankar, Subramanian V. ;
Scally, Aylwyn ;
Schroth, Gary P. ;
Smith, Mark E. ;
Smith, Vincent P. ;
Spiridou, Anastassia ;
Torrance, Peta E. ;
Tzonev, Svilen S. ;
Vermaas, Eric H. ;
Walter, Klaudia ;
Wu, Xiaolin ;
Zhang, Lu ;
Alam, Mohammed D. ;
Anastasi, Carole .
NATURE, 2008, 456 (7218) :53-59
[4]   Near-optimal probabilistic RNA-seq quantification (vol 34, pg 525, 2016) [J].
Bray, Nicolas L. ;
Pimentel, Harold ;
Melsted, Pall ;
Pachter, Lior .
NATURE BIOTECHNOLOGY, 2016, 34 (08) :888-888
[5]   Single-molecule DNA detection with an engineered MspA protein nanopore [J].
Butler, Tom Z. ;
Pavlenok, Mikhail ;
Derrington, Ian M. ;
Niederweis, Michael ;
Gundlach, Jens H. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (52) :20647-20652
[6]   Genome sequence of the nematode C-elegans:: A platform for investigating biology [J].
不详 .
SCIENCE, 1998, 282 (5396) :2012-2018
[7]   Accessing genetic information with high-density DNA arrays [J].
Chee, M ;
Yang, R ;
Hubbell, E ;
Berno, A ;
Huang, XC ;
Stern, D ;
Winkler, J ;
Lockhart, DJ ;
Morris, MS ;
Fodor, SPA .
SCIENCE, 1996, 274 (5287) :610-614
[8]   The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants [J].
Cock, Peter J. A. ;
Fields, Christopher J. ;
Goto, Naohisa ;
Heuer, Michael L. ;
Rice, Peter M. .
NUCLEIC ACIDS RESEARCH, 2010, 38 (06) :1767-1771
[9]   Nanopore DNA sequencing with MspA [J].
Derrington, Ian M. ;
Butler, Tom Z. ;
Collins, Marcus D. ;
Manrao, Elizabeth ;
Pavlenok, Mikhail ;
Niederweis, Michael ;
Gundlach, Jens H. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (37) :16060-16065
[10]   Real-Time DNA Sequencing from Single Polymerase Molecules [J].
Eid, John ;
Fehr, Adrian ;
Gray, Jeremy ;
Luong, Khai ;
Lyle, John ;
Otto, Geoff ;
Peluso, Paul ;
Rank, David ;
Baybayan, Primo ;
Bettman, Brad ;
Bibillo, Arkadiusz ;
Bjornson, Keith ;
Chaudhuri, Bidhan ;
Christians, Frederick ;
Cicero, Ronald ;
Clark, Sonya ;
Dalal, Ravindra ;
deWinter, Alex ;
Dixon, John ;
Foquet, Mathieu ;
Gaertner, Alfred ;
Hardenbol, Paul ;
Heiner, Cheryl ;
Hester, Kevin ;
Holden, David ;
Kearns, Gregory ;
Kong, Xiangxu ;
Kuse, Ronald ;
Lacroix, Yves ;
Lin, Steven ;
Lundquist, Paul ;
Ma, Congcong ;
Marks, Patrick ;
Maxham, Mark ;
Murphy, Devon ;
Park, Insil ;
Pham, Thang ;
Phillips, Michael ;
Roy, Joy ;
Sebra, Robert ;
Shen, Gene ;
Sorenson, Jon ;
Tomaney, Austin ;
Travers, Kevin ;
Trulson, Mark ;
Vieceli, John ;
Wegener, Jeffrey ;
Wu, Dawn ;
Yang, Alicia ;
Zaccarin, Denis .
SCIENCE, 2009, 323 (5910) :133-138