Is it time to change the reference genome?

被引：110
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
收藏
页数：9
相关论文
共 82 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] E pluribus unum
    不详
    [J]. NATURE METHODS, 2010, 7 (05) : 331 - 331
  • [3] Characterizing the Major Structural Variant Alleles of the Human Genome
    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.
    [J]. CELL, 2019, 176 (03) : 663 - +
  • [4] Gene inactivation and its implications for annotation in the era of personal genomics
    Balasubramanian, Suganthi
    Habegger, Lukas
    Frankish, Adam
    MacArthur, Daniel G.
    Harte, Rachel
    Tyler-Smith, Chris
    Harrow, Jennifer
    Gerstein, Mark
    [J]. GENES & DEVELOPMENT, 2011, 25 (01) : 1 - 10
  • [5] Catching hidden variation: systematic correction of reference minor allele annotation in clinical variant calling
    Barbitoff, Yury A.
    Bezdvornykh, Igor V.
    Polev, Dmitrii E.
    Serebryakova, Elena A.
    Glotov, Andrey S.
    Glotov, Oleg S.
    Predeus, Alexander V.
    [J]. GENETICS IN MEDICINE, 2018, 20 (03) : 360 - 364
  • [6] Accurate whole human genome sequencing using reversible terminator chemistry
    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
    [J]. 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
    Buchkovich, Martin L.
    Eklund, Karl
    Duan, Qing
    Li, Yun
    Mohlke, Karen L.
    Furey, Terrence S.
    [J]. 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
    Castel, Stephane E.
    Levy-Moonshine, Ami
    Mohammadii, Pejman
    Banks, Eric
    Lappalainenii, Tuuli
    [J]. GENOME BIOLOGY, 2015, 16
  • [10] Resolving the complexity of the human genome using single-molecule sequencing
    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.
    [J]. NATURE, 2015, 517 (7536) : 608 - U163
123456789