BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data

Xi Chen; Xu Shi; Ayesha N. Shajahan; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan

doi:10.1109/EMBC.2014.6944485

BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data

Xi Chen, Xu Shi, Ayesha N. Shajahan, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan

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

2 Scopus citations

Abstract

High coverage whole genome DNA-sequencing enables identification of somatic structural variation (SSV) more evident in paired tumor and normal samples. Recent studies show that simultaneous analysis of paired samples provides a better resolution of SSV detection than subtracting shared SVs. However, available tools can neither identify all types of SSVs nor provide any rank information regarding their somatic features. In this paper, we have developed a Bayesian framework, by integrating read alignment information from both tumor and normal samples, called BSSV, to calculate the significance of each SSV. Tested by simulated data, the precision of BSSV is comparable to that of available tools and the false negative rate is significantly lowered. We have also applied this approach to The Cancer Genome Atlas breast cancer data for SSV detection. Many known breast cancer specific mutated genes like RAD51, BRIP1, ER, PGR and PTPRD have been successfully identified.

Original language	English (US)
Title of host publication	2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	3937-3940
Number of pages	4
ISBN (Electronic)	9781424479290
DOIs	https://doi.org/10.1109/EMBC.2014.6944485
State	Published - Nov 2 2014
Externally published	Yes
Event	2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014 - Chicago, United States Duration: Aug 26 2014 → Aug 30 2014

Publication series

Name	2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014

Other

Other	2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014
Country/Territory	United States
City	Chicago
Period	8/26/14 → 8/30/14

Bibliographical note

Publisher Copyright:
© 2014 IEEE.

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

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10.1109/EMBC.2014.6944485

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Chen, X., Shi, X., Shajahan, A. N., Hilakivi-Clarke, L., Clarke, R., & Xuan, J. (2014). BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data. In 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014 (pp. 3937-3940). Article 6944485 (2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/EMBC.2014.6944485

BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data. / Chen, Xi; Shi, Xu; Shajahan, Ayesha N. et al.
2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014. Institute of Electrical and Electronics Engineers Inc., 2014. p. 3937-3940 6944485 (2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014).

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

Chen, X, Shi, X, Shajahan, AN, Hilakivi-Clarke, L , Clarke, R & Xuan, J 2014, BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data. in 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014., 6944485, 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014, Institute of Electrical and Electronics Engineers Inc., pp. 3937-3940, 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014, Chicago, United States, 8/26/14. https://doi.org/10.1109/EMBC.2014.6944485

Chen X, Shi X, Shajahan AN, Hilakivi-Clarke L , Clarke R, Xuan J. BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data. In 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014. Institute of Electrical and Electronics Engineers Inc. 2014. p. 3937-3940. 6944485. (2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014). doi: 10.1109/EMBC.2014.6944485

Chen, Xi ; Shi, Xu ; Shajahan, Ayesha N. et al. / BSSV : Bayesian based somatic structural variation identification with whole genome DNA-seq data. 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014. Institute of Electrical and Electronics Engineers Inc., 2014. pp. 3937-3940 (2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014).

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BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data

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