CloudAssoc: A pipeline for imputation based genome wide association study on cloud

Weidi Dai; Qiuwen Wang; Meng Gao; Lu Zhang

doi:10.1109/ICCSNT.2012.6526190

CloudAssoc: A pipeline for imputation based genome wide association study on cloud

Weidi Dai
, Qiuwen Wang
, Meng Gao
, Lu Zhang

Department of Computer Science

Research output: Chapter in book/report/conference proceeding › Conference proceeding › peer-review

1 Citation (Scopus)

Abstract

Genome wide association study (GWAS) has been proved to be an efficient approach to identify susceptibility genes for complex diseases. In order to increase the power for detecting the disease causal variants, imputation has been used to predict genotype dosages of untyped variants on the basis of linkage disequilibrium evaluated by public data. However, as the volume of data grows, time-consuming of imputation based association study becomes extremely large. We developed a cloud based pipeline to implement data format conversion, imputation, quality control and association study based on Map/Reduce framework which can aid biologists to accelerate the identification and evaluation of susceptibility genes for complex diseases and make it easier to combine GWAS data from worldwide for meta analysis.

Original language	English
Title of host publication	Proceedings of 2012 2nd International Conference on Computer Science and Network Technology
Publisher	IEEE
Pages	1435-1438
Number of pages	4
ISBN (Electronic)	9781467329644
ISBN (Print)	9781467329637
DOIs	https://doi.org/10.1109/ICCSNT.2012.6526190
Publication status	Published - Dec 2012
Event	2nd International Conference on Computer Science and Network Technology, ICCSNT 2012 - Changchun, China Duration: 29 Dec 2012 → 31 Dec 2012 https://ieeexplore.ieee.org/xpl/conhome/6519162/proceeding (Conference Proceeding)

Publication series

Name	Proceedings of the International Conference on Computer Science and Network Technology, ICCSNT

Conference

Conference	2nd International Conference on Computer Science and Network Technology, ICCSNT 2012
Country/Territory	China
City	Changchun
Period	29/12/12 → 31/12/12
Internet address	https://ieeexplore.ieee.org/xpl/conhome/6519162/proceeding (Conference Proceeding)

UN SDGs

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

SDG 3 Good Health and Well-being

User-Defined Keywords

GWAS
Cloud Computing
Imputation

Access to Document

10.1109/ICCSNT.2012.6526190

Cite this

Dai, W., Wang, Q., Gao, M., & Zhang, L. (2012). CloudAssoc: A pipeline for imputation based genome wide association study on cloud. In Proceedings of 2012 2nd International Conference on Computer Science and Network Technology (pp. 1435-1438). (Proceedings of the International Conference on Computer Science and Network Technology, ICCSNT). IEEE. https://doi.org/10.1109/ICCSNT.2012.6526190

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title = "CloudAssoc: A pipeline for imputation based genome wide association study on cloud",

abstract = "Genome wide association study (GWAS) has been proved to be an efficient approach to identify susceptibility genes for complex diseases. In order to increase the power for detecting the disease causal variants, imputation has been used to predict genotype dosages of untyped variants on the basis of linkage disequilibrium evaluated by public data. However, as the volume of data grows, time-consuming of imputation based association study becomes extremely large. We developed a cloud based pipeline to implement data format conversion, imputation, quality control and association study based on Map/Reduce framework which can aid biologists to accelerate the identification and evaluation of susceptibility genes for complex diseases and make it easier to combine GWAS data from worldwide for meta analysis.",

keywords = "GWAS, Cloud Computing, Imputation",

author = "Weidi Dai and Qiuwen Wang and Meng Gao and Lu Zhang",

note = "Publisher Copyright: {\textcopyright} 2012 IEEE.; 2nd International Conference on Computer Science and Network Technology, ICCSNT 2012 ; Conference date: 29-12-2012 Through 31-12-2012",

year = "2012",

month = dec,

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language = "English",

isbn = "9781467329637",

series = "Proceedings of the International Conference on Computer Science and Network Technology, ICCSNT",

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Dai, W, Wang, Q, Gao, M & Zhang, L 2012, CloudAssoc: A pipeline for imputation based genome wide association study on cloud. in Proceedings of 2012 2nd International Conference on Computer Science and Network Technology. Proceedings of the International Conference on Computer Science and Network Technology, ICCSNT, IEEE, pp. 1435-1438, 2nd International Conference on Computer Science and Network Technology, ICCSNT 2012, Changchun, China, 29/12/12. https://doi.org/10.1109/ICCSNT.2012.6526190

CloudAssoc: A pipeline for imputation based genome wide association study on cloud. / Dai, Weidi; Wang, Qiuwen; Gao, Meng et al.
Proceedings of 2012 2nd International Conference on Computer Science and Network Technology. IEEE, 2012. p. 1435-1438 (Proceedings of the International Conference on Computer Science and Network Technology, ICCSNT).

Research output: Chapter in book/report/conference proceeding › Conference proceeding › peer-review

TY - GEN

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AU - Dai, Weidi

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AU - Gao, Meng

AU - Zhang, Lu

PY - 2012/12

Y1 - 2012/12

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AB - Genome wide association study (GWAS) has been proved to be an efficient approach to identify susceptibility genes for complex diseases. In order to increase the power for detecting the disease causal variants, imputation has been used to predict genotype dosages of untyped variants on the basis of linkage disequilibrium evaluated by public data. However, as the volume of data grows, time-consuming of imputation based association study becomes extremely large. We developed a cloud based pipeline to implement data format conversion, imputation, quality control and association study based on Map/Reduce framework which can aid biologists to accelerate the identification and evaluation of susceptibility genes for complex diseases and make it easier to combine GWAS data from worldwide for meta analysis.

KW - GWAS

KW - Cloud Computing

KW - Imputation

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U2 - 10.1109/ICCSNT.2012.6526190

DO - 10.1109/ICCSNT.2012.6526190

M3 - Conference proceeding

AN - SCOPUS:84880247305

SN - 9781467329637

T3 - Proceedings of the International Conference on Computer Science and Network Technology, ICCSNT

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EP - 1438

BT - Proceedings of 2012 2nd International Conference on Computer Science and Network Technology

PB - IEEE

Y2 - 29 December 2012 through 31 December 2012

ER -

CloudAssoc: A pipeline for imputation based genome wide association study on cloud

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