Is it time to change the reference genome?

被引：117

作者：

Ballouz, Sara ^{[1
]}

Dobin, Alexander ^{[1
]}

Gillis, Jesse A. ^{[1
]}

机构：

[1] Cold Spring Harbor Lab, Stanley Inst Cognit Genom, POB 100, Cold Spring Harbor, NY 11724 USA

来源：

GENOME BIOLOGY | 2019年 / 20卷 / 01期

基金：

美国国家卫生研究院;

关键词：

SEQUENCE; GENE; MAP; VARIANTS; GRAPHS; GRCH38; READ; TOOL;

D O I：

10.1186/s13059-019-1774-4

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

The use of the human reference genome has shaped methods and data across modern genomics. This has offered many benefits while creating a few constraints. In the following opinion, we outline the history, properties, and pitfalls of the current human reference genome. In a few illustrative analyses, we focus on its use for variant-calling, highlighting its nearness to a 'type specimen'. We suggest that switching to a consensus reference would offer important advantages over the continued use of the current reference with few disadvantages.

引用

页数：9

共 82 条

[1] A map of human genome variation from population-scale sequencing [J].

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. .

NATURE, 2010, 467 (7319) :1061-1073

[2] E pluribus unum [J].

不详 .

NATURE METHODS, 2010, 7 (05) :331-331

[3] Characterizing the Major Structural Variant Alleles of the Human Genome [J].

Audano, Peter A. ;

Sulovari, Arvis ;

Graves-Lindsay, Tina A. ;

Cantsilieris, Stuart ;

Sorensen, Melanie ;

Welch, AnneMarie E. ;

Dougherty, Max L. ;

Nelson, Bradley J. ;

Shah, Ankeeta ;

Dutcher, Susan K. ;

Warren, Wesley C. ;

Magrini, Vincent ;

McGrath, Sean D. ;

Li, Yang I. ;

Wilson, Richard K. ;

Eichler, Evan E. .

CELL, 2019, 176 (03) :663-+

[4] Gene inactivation and its implications for annotation in the era of personal genomics [J].

Balasubramanian, Suganthi ;

Habegger, Lukas ;

Frankish, Adam ;

MacArthur, Daniel G. ;

Harte, Rachel ;

Tyler-Smith, Chris ;

Harrow, Jennifer ;

Gerstein, Mark .

GENES & DEVELOPMENT, 2011, 25 (01) :1-10

[5] Catching hidden variation: systematic correction of reference minor allele annotation in clinical variant calling [J].

Barbitoff, Yury A. ;

Bezdvornykh, Igor V. ;

Polev, Dmitrii E. ;

Serebryakova, Elena A. ;

Glotov, Andrey S. ;

Glotov, Oleg S. ;

Predeus, Alexander V. .

GENETICS IN MEDICINE, 2018, 20 (03) :360-364

[6] 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

[7] Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci [J].

Buchkovich, Martin L. ;

Eklund, Karl ;

Duan, Qing ;

Li, Yun ;

Mohlke, Karen L. ;

Furey, Terrence S. .

BMC MEDICAL GENOMICS, 2015, 8

[8]

Bureau International des Poids et Mesures, INT PROT KIL

[9] Tools and best practices for data processing in allelic expression analysis [J].

Castel, Stephane E. ;

Levy-Moonshine, Ami ;

Mohammadii, Pejman ;

Banks, Eric ;

Lappalainenii, Tuuli .

GENOME BIOLOGY, 2015, 16

[10] Resolving the complexity of the human genome using single-molecule sequencing [J].

Chaisson, Mark J. P. ;

Huddleston, John ;

Dennis, Megan Y. ;

Sudmant, Peter H. ;

Malig, Maika ;

Hormozdiari, Fereydoun ;

Antonacci, Francesca ;

Surti, Urvashi ;

Sandstrom, Richard ;

Boitano, Matthew ;

Landolin, Jane M. ;

Stamatoyannopoulos, John A. ;

Hunkapiller, Michael W. ;

Korlach, Jonas ;

Eichler, Evan E. .

NATURE, 2015, 517 (7536) :608-U163

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