A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip

Zhenxing Wang; Yanshuo Chu; Yongtian Wang; Yadong Wang

doi:10.1109/BIBM.2017.8217914

A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip

Zhenxing Wang
, Yanshuo Chu
, Yongtian Wang
, Yadong Wang^*

^*Corresponding author for this work

Harbin Institute of Technology

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has been accepted as one of the most efficient technologies. However, challenges exist in analysis of DNA methylation data generated by this technology due to widespread biases. Here we proposed a generalized framework for evaluating data analysis methods for Illumina 450K array. This framework considers the following steps towards a successful analysis: importing data, quality control, within-array normalization, correcting type bias, detecting differentially methylated probes or regions and biological interpretation. We evaluated five methods using three real datasets, and proposed outperform methods for the Illumina 450K array data analysis.

Original language	English
Title of host publication	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Editors	Illhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1688-1693
Number of pages	6
ISBN (Electronic)	9781509030491
DOIs	https://doi.org/10.1109/BIBM.2017.8217914
Publication status	Published - 15 Dec 2017
Externally published	Yes
Event	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States Duration: 13 Nov 2017 → 16 Nov 2017

Publication series

Name	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Volume	2017-January

Conference

Conference	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Country/Territory	United States
City	Kansas City
Period	13/11/17 → 16/11/17

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

DNA methylation
Illumina 450K
ontology interpretation

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10.1109/BIBM.2017.8217914

Cite this

Wang, Z., Chu, Y., Wang, Y., & Wang, Y. (2017). A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip. In I. Yoo, J. H. Zheng, Y. Gong, X. T. Hu, C.-R. Shyu, Y. Bromberg, J. Gao, & D. Korkin (Eds.), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 (pp. 1688-1693). (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2017.8217914

Wang, Zhenxing ; Chu, Yanshuo ; Wang, Yongtian et al. / A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. editor / Illhoi Yoo ; Jane Huiru Zheng ; Yang Gong ; Xiaohua Tony Hu ; Chi-Ren Shyu ; Yana Bromberg ; Jean Gao ; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 1688-1693 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017).

@inproceedings{914d37a43f9846429816ecda26f1d937,

title = "A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip",

abstract = "DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has been accepted as one of the most efficient technologies. However, challenges exist in analysis of DNA methylation data generated by this technology due to widespread biases. Here we proposed a generalized framework for evaluating data analysis methods for Illumina 450K array. This framework considers the following steps towards a successful analysis: importing data, quality control, within-array normalization, correcting type bias, detecting differentially methylated probes or regions and biological interpretation. We evaluated five methods using three real datasets, and proposed outperform methods for the Illumina 450K array data analysis.",

keywords = "DNA methylation, Illumina 450K, ontology interpretation",

author = "Zhenxing Wang and Yanshuo Chu and Yongtian Wang and Yadong Wang",

note = "Publisher Copyright: {\textcopyright} 2017 IEEE.; 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 ; Conference date: 13-11-2017 Through 16-11-2017",

year = "2017",

month = dec,

day = "15",

doi = "10.1109/BIBM.2017.8217914",

language = "English",

series = "Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "1688--1693",

editor = "Illhoi Yoo and Zheng, \{Jane Huiru\} and Yang Gong and Hu, \{Xiaohua Tony\} and Chi-Ren Shyu and Yana Bromberg and Jean Gao and Dmitry Korkin",

booktitle = "Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017",

address = "United States",

}

Wang, Z, Chu, Y, Wang, Y & Wang, Y 2017, A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip. in I Yoo, JH Zheng, Y Gong, XT Hu, C-R Shyu, Y Bromberg, J Gao & D Korkin (eds), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, vol. 2017-January, Institute of Electrical and Electronics Engineers Inc., pp. 1688-1693, 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, Kansas City, United States, 13/11/17. https://doi.org/10.1109/BIBM.2017.8217914

A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip. / Wang, Zhenxing; Chu, Yanshuo; Wang, Yongtian et al.
Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. ed. / Illhoi Yoo; Jane Huiru Zheng; Yang Gong; Xiaohua Tony Hu; Chi-Ren Shyu; Yana Bromberg; Jean Gao; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. p. 1688-1693 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip

AU - Wang, Zhenxing

AU - Chu, Yanshuo

AU - Wang, Yongtian

AU - Wang, Yadong

PY - 2017/12/15

Y1 - 2017/12/15

N2 - DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has been accepted as one of the most efficient technologies. However, challenges exist in analysis of DNA methylation data generated by this technology due to widespread biases. Here we proposed a generalized framework for evaluating data analysis methods for Illumina 450K array. This framework considers the following steps towards a successful analysis: importing data, quality control, within-array normalization, correcting type bias, detecting differentially methylated probes or regions and biological interpretation. We evaluated five methods using three real datasets, and proposed outperform methods for the Illumina 450K array data analysis.

AB - DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has been accepted as one of the most efficient technologies. However, challenges exist in analysis of DNA methylation data generated by this technology due to widespread biases. Here we proposed a generalized framework for evaluating data analysis methods for Illumina 450K array. This framework considers the following steps towards a successful analysis: importing data, quality control, within-array normalization, correcting type bias, detecting differentially methylated probes or regions and biological interpretation. We evaluated five methods using three real datasets, and proposed outperform methods for the Illumina 450K array data analysis.

KW - DNA methylation

KW - Illumina 450K

KW - ontology interpretation

UR - https://www.scopus.com/pages/publications/85045971012

U2 - 10.1109/BIBM.2017.8217914

DO - 10.1109/BIBM.2017.8217914

M3 - Conference contribution

AN - SCOPUS:85045971012

T3 - Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017

SP - 1688

EP - 1693

BT - Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017

A2 - Yoo, Illhoi

A2 - Zheng, Jane Huiru

A2 - Gong, Yang

A2 - Hu, Xiaohua Tony

A2 - Shyu, Chi-Ren

A2 - Bromberg, Yana

A2 - Gao, Jean

A2 - Korkin, Dmitry

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017

Y2 - 13 November 2017 through 16 November 2017

ER -

Wang Z, Chu Y, Wang Y, Wang Y. A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip. In Yoo I, Zheng JH, Gong Y, Hu XT, Shyu CR, Bromberg Y, Gao J, Korkin D, editors, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc. 2017. p. 1688-1693. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017). doi: 10.1109/BIBM.2017.8217914

A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip

Abstract

Publication series

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UN SDGs

Keywords

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