Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

被引：0
|
作者：
Ziller M.J. [1 ,2 ,3 ]
Hansen K.D. [4 ,5 ]
Meissner A. [1 ,2 ,3 ]
Aryee M.J. [1 ,6 ,7 ,8 ]
机构：
[1] Broad Institute of MIT and Harvard, Cambridge, MA
[2] Harvard Stem Cell Institute, Cambridge, MA
[3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
[4] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD
[5] Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
[6] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA
[7] Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
[8] Department of Pathology, Harvard Medical School, Boston, MA
来源：
Nature Methods | 2015年 / 12卷 / 3期
基金：
美国国家卫生研究院;
关键词：
D O I：
10.1038/nmeth.3152
中图分类号：
学科分类号：
摘要：
Whole-genome bisulfite sequencing (WGBS) allows genome-wide DNA methylation profiling, but the associated high sequencing costs continue to limit its widespread application. We used several high-coverage reference data sets to experimentally determine minimal sequencing requirements. We present data-derived recommendations for minimum sequencing depth for WGBS libraries, highlight what is gained with increasing coverage and discuss the trade-off between sequencing depth and number of assayed replicates. © 2015 Nature America, Inc.
引用
收藏
页码：230 / 232
页数：2
相关论文
共 50 条
  • [1] Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing
    Ziller, Michael J.
    Hansen, Kasper D.
    Meissner, Alexander
    Aryee, Martin J.
    [J]. NATURE METHODS, 2015, 12 (03) : 230 - +
  • [2] Information recovery from low coverage whole-genome bisulfite sequencing
    Libertini, Emanuele
    Heath, Simon C.
    Hamoudi, Rifat A.
    Gut, Marta
    Ziller, Michael J.
    Czyz, Agata
    Ruotti, Victor
    Stunnenberg, Hendrik G.
    Frontini, Mattia
    Ouwehand, Willem H.
    Meissner, Alexander
    Gut, Ivo G.
    Beck, Stephan
    [J]. NATURE COMMUNICATIONS, 2016, 7
  • [3] Information recovery from low coverage whole-genome bisulfite sequencing
    Emanuele Libertini
    Simon C. Heath
    Rifat A. Hamoudi
    Marta Gut
    Michael J. Ziller
    Agata Czyz
    Victor Ruotti
    Hendrik G. Stunnenberg
    Mattia Frontini
    Willem H. Ouwehand
    Alexander Meissner
    Ivo G. Gut
    Stephan Beck
    [J]. Nature Communications, 7
  • [4] Saturation analysis for whole-genome bisulfite sequencing data
    Emanuele Libertini
    Simon C Heath
    Rifat A Hamoudi
    Marta Gut
    Michael J Ziller
    Javier Herrero
    Agata Czyz
    Victor Ruotti
    Hendrik G Stunnenberg
    Mattia Frontini
    Willem H Ouwehand
    Alexander Meissner
    Ivo G Gut
    Stephan Beck
    [J]. Nature Biotechnology, 2016, 34 : 691 - 693
  • [5] Methodological aspects of whole-genome bisulfite sequencing analysis
    Adusumalli, Swarnaseetha
    Omar, Mohd Feroz Mohd
    Soong, Richie
    Benoukraf, Touati
    [J]. BRIEFINGS IN BIOINFORMATICS, 2015, 16 (03) : 369 - 379
  • [6] Saturation analysis for whole-genome bisulfite sequencing data
    Libertini, Emanuele
    Heath, Simon C.
    Hamoudi, Rifat A.
    Gut, Marta
    Ziller, Michael J.
    Herrero, Javier
    Czyz, Agata
    Ruotti, Victor
    Stunnenberg, Hendrik G.
    Frontini, Mattia
    Ouwehand, Willem H.
    Meissner, Alexander
    Gut, Ivo G.
    Beck, Stephan
    [J]. NATURE BIOTECHNOLOGY, 2016, 34 (07) : 691 - 693
  • [7] Global analysis of DNA methylation in hepatocellular carcinoma via a whole-genome bisulfite sequencing approach
    Yan, Qian
    Tang, Ying
    He, Fan
    Xue, Jiao
    Zhou, Ruisheng
    Zhang, Xiaoying
    Luo, Huiyan
    Zhou, Daihan
    Wang, Xiongwen
    [J]. GENOMICS, 2021, 113 (05) : 3618 - 3634
  • [8] A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies
    Crary-Dooley, Florence K.
    Tam, Mitchell E.
    Dunaway, Keith W.
    Hertz-Picciotto, Irva
    Schmidt, Rebecca J.
    LaSalle, Janine M.
    [J]. EPIGENETICS, 2017, 12 (03) : 206 - 214
  • [9] msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data
    Heesun Kim
    Mikang Sim
    Nayoung Park
    Kisang Kwon
    Junyoung Kim
    Jaebum Kim
    [J]. BMC Bioinformatics, 23
  • [10] msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data
    Kim, Heesun
    Sim, Mikang
    Park, Nayoung
    Kwon, Kisang
    Kim, Junyoung
    Kim, Jaebum
    [J]. BMC BIOINFORMATICS, 2022, 23 (01)
12345