A hybrid framework for genome wide epistasis discovery

Zehao Tan; Zhuo Zhang; Jiang Liu; Chee Keong Kwoh; Sim Heng Ong; Yik Ying Teo; Chiea Chuen Khor; E. Shyong Tai; Tin Aung; Eranga Vithana; Tien Yin Wong

doi:10.1109/IEMBS.2011.6091599

A hybrid framework for genome wide epistasis discovery

Zehao Tan^*
, Zhuo Zhang
, Jiang Liu
, Chee Keong Kwoh
, Sim Heng Ong
, Yik Ying Teo
, Chiea Chuen Khor
, E. Shyong Tai
, Tin Aung
, Eranga Vithana
, Tien Yin Wong

^*Corresponding author for this work

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

Abstract

A hybrid framework integrating Random Forest and Logistic Regression is proposed and implemented for genome-wide epistasis study. The two-stage approach first uses random forest model to capture a pool of epistasis-prone single nucleotide polymorphisms (SNPs), followed by using logistic regression to identify the significant pair-wise epistasis SNPs. We tested the proposed framework on data obtained from Singapore Malay Eye Study (SiMES), in which, 3280 subjects were genotyped on Illumina 610 quad arrays and optic nerve parameters were measured in ocular examination. Case-control data set is labeled by choosing the high/low end of vertical Cup-to-Disc ratio (vCDR) values which is a measure of optic nerve degeneration. Our method identified 230 pairs of interacting SNPs with P-values below 5×10 ⁸. A preliminary search identified a protein interaction network at a high confidence score of 0.9. The proteins are known to participate in the WNT pathway with involvement in the survival and differentiation of the retina ganglion cells, inferring a strong association with vCDR. The experimental results demonstrate that the proposed framework is valid and efficient for large scale epistatsis study.

Original language	English
Title of host publication	33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011
Pages	6479-6482
Number of pages	4
DOIs	https://doi.org/10.1109/IEMBS.2011.6091599
Publication status	Published - 2011
Externally published	Yes
Event	33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011 - Boston, MA, United States Duration: 30 Aug 2011 → 3 Sept 2011

Publication series

Name	Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
ISSN (Print)	1557-170X

Conference

Conference	33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011
Country/Territory	United States
City	Boston, MA
Period	30/08/11 → 3/09/11

UN SDGs

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

SDG 3 Good Health and Well-being
SDG 15 Life on Land

ASJC Scopus subject areas

Signal Processing
Biomedical Engineering
Computer Vision and Pattern Recognition
Health Informatics

Access to Document

10.1109/IEMBS.2011.6091599

Cite this

Tan, Z., Zhang, Z., Liu, J., Kwoh, C. K., Ong, S. H., Teo, Y. Y., Khor, C. C., Tai, E. S., Aung, T., Vithana, E., & Wong, T. Y. (2011). A hybrid framework for genome wide epistasis discovery. In 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011 (pp. 6479-6482). Article 6091599 (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS). https://doi.org/10.1109/IEMBS.2011.6091599

@inproceedings{0b6177366b644630a97c733702f26d03,

title = "A hybrid framework for genome wide epistasis discovery",

abstract = "A hybrid framework integrating Random Forest and Logistic Regression is proposed and implemented for genome-wide epistasis study. The two-stage approach first uses random forest model to capture a pool of epistasis-prone single nucleotide polymorphisms (SNPs), followed by using logistic regression to identify the significant pair-wise epistasis SNPs. We tested the proposed framework on data obtained from Singapore Malay Eye Study (SiMES), in which, 3280 subjects were genotyped on Illumina 610 quad arrays and optic nerve parameters were measured in ocular examination. Case-control data set is labeled by choosing the high/low end of vertical Cup-to-Disc ratio (vCDR) values which is a measure of optic nerve degeneration. Our method identified 230 pairs of interacting SNPs with P-values below 5×10 8. A preliminary search identified a protein interaction network at a high confidence score of 0.9. The proteins are known to participate in the WNT pathway with involvement in the survival and differentiation of the retina ganglion cells, inferring a strong association with vCDR. The experimental results demonstrate that the proposed framework is valid and efficient for large scale epistatsis study.",

author = "Zehao Tan and Zhuo Zhang and Jiang Liu and Kwoh, \{Chee Keong\} and Ong, \{Sim Heng\} and Teo, \{Yik Ying\} and Khor, \{Chiea Chuen\} and Tai, \{E. Shyong\} and Tin Aung and Eranga Vithana and Wong, \{Tien Yin\}",

note = "Copyright: Copyright 2012 Elsevier B.V., All rights reserved.; 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011 ; Conference date: 30-08-2011 Through 03-09-2011",

year = "2011",

doi = "10.1109/IEMBS.2011.6091599",

language = "English",

isbn = "9781424441211",

series = "Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS",

pages = "6479--6482",

booktitle = "33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011",

}

Tan, Z, Zhang, Z, Liu, J, Kwoh, CK, Ong, SH, Teo, YY, Khor, CC, Tai, ES, Aung, T, Vithana, E & Wong, TY 2011, A hybrid framework for genome wide epistasis discovery. in 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011., 6091599, Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, pp. 6479-6482, 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011, Boston, MA, United States, 30/08/11. https://doi.org/10.1109/IEMBS.2011.6091599

A hybrid framework for genome wide epistasis discovery. / Tan, Zehao; Zhang, Zhuo; Liu, Jiang et al.
33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011. 2011. p. 6479-6482 6091599 (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

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

TY - GEN

T1 - A hybrid framework for genome wide epistasis discovery

AU - Tan, Zehao

AU - Zhang, Zhuo

AU - Liu, Jiang

AU - Kwoh, Chee Keong

AU - Ong, Sim Heng

AU - Teo, Yik Ying

AU - Khor, Chiea Chuen

AU - Tai, E. Shyong

AU - Aung, Tin

AU - Vithana, Eranga

AU - Wong, Tien Yin

PY - 2011

Y1 - 2011

N2 - A hybrid framework integrating Random Forest and Logistic Regression is proposed and implemented for genome-wide epistasis study. The two-stage approach first uses random forest model to capture a pool of epistasis-prone single nucleotide polymorphisms (SNPs), followed by using logistic regression to identify the significant pair-wise epistasis SNPs. We tested the proposed framework on data obtained from Singapore Malay Eye Study (SiMES), in which, 3280 subjects were genotyped on Illumina 610 quad arrays and optic nerve parameters were measured in ocular examination. Case-control data set is labeled by choosing the high/low end of vertical Cup-to-Disc ratio (vCDR) values which is a measure of optic nerve degeneration. Our method identified 230 pairs of interacting SNPs with P-values below 5×10 8. A preliminary search identified a protein interaction network at a high confidence score of 0.9. The proteins are known to participate in the WNT pathway with involvement in the survival and differentiation of the retina ganglion cells, inferring a strong association with vCDR. The experimental results demonstrate that the proposed framework is valid and efficient for large scale epistatsis study.

AB - A hybrid framework integrating Random Forest and Logistic Regression is proposed and implemented for genome-wide epistasis study. The two-stage approach first uses random forest model to capture a pool of epistasis-prone single nucleotide polymorphisms (SNPs), followed by using logistic regression to identify the significant pair-wise epistasis SNPs. We tested the proposed framework on data obtained from Singapore Malay Eye Study (SiMES), in which, 3280 subjects were genotyped on Illumina 610 quad arrays and optic nerve parameters were measured in ocular examination. Case-control data set is labeled by choosing the high/low end of vertical Cup-to-Disc ratio (vCDR) values which is a measure of optic nerve degeneration. Our method identified 230 pairs of interacting SNPs with P-values below 5×10 8. A preliminary search identified a protein interaction network at a high confidence score of 0.9. The proteins are known to participate in the WNT pathway with involvement in the survival and differentiation of the retina ganglion cells, inferring a strong association with vCDR. The experimental results demonstrate that the proposed framework is valid and efficient for large scale epistatsis study.

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DO - 10.1109/IEMBS.2011.6091599

M3 - Conference contribution

C2 - 22255822

AN - SCOPUS:84864618061

SN - 9781424441211

T3 - Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS

SP - 6479

EP - 6482

BT - 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011

T2 - 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011

Y2 - 30 August 2011 through 3 September 2011

ER -

Tan Z, Zhang Z, Liu J, Kwoh CK, Ong SH, Teo YY et al. A hybrid framework for genome wide epistasis discovery. In 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011. 2011. p. 6479-6482. 6091599. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS). doi: 10.1109/IEMBS.2011.6091599

A hybrid framework for genome wide epistasis discovery

Abstract

Publication series

Conference

UN SDGs

ASJC Scopus subject areas

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