Building a Research-Quality Copy Number Variation Data Repository for Translational Research

Chen Wang; Raymond M. Moore; Jared M. Evans; Xiaonan Hou; S. John Weroha; Guoqian Jiang

doi:10.1007/978-3-030-14177-6_12

Building a Research-Quality Copy Number Variation Data Repository for Translational Research

Chen Wang, Raymond M. Moore, Jared M. Evans, Xiaonan Hou, S. John Weroha, Guoqian Jiang

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

Abstract

Copy number variation (CNV) has known associations with population diversities and disease conditions. However, research communities face great challenges in reusing the CNV data due to the heterogeneity of existing CNV data sources. The objective of the study is to design, develop and evaluate a scalable CNV data repository based on a proposed common data schema for facilitating research-quality CNV data integration and reuse. We created a proposal for a CNV common data schema through analyzing multiple existing CNV data sources. We designed a collection of the CNV quality metrics and demonstrated its usefulness using the CNV data from a study of ovarian cancer xenograft models. We implemented a CNV data repository using a MongoDB database backend and established the CNV genomic data services that enable reusing of the curated CNV data and answering CNV-relevant research questions. The critical issues and future plan for the system enhancement and community engagement were discussed.

Original language	English (US)
Title of host publication	Heterogeneous Data Management, Polystores, and Analytics for Healthcare - VLDB 2018 Workshops, Poly and DMAH, 2018, Revised Selected Papers
Editors	Timothy Mattson, Fusheng Wang, George Teodoro, Michael Stonebraker, Vijay Gadepally, Gang Luo
Publisher	Springer Verlag
Pages	148-161
Number of pages	14
ISBN (Print)	9783030141769
DOIs	https://doi.org/10.1007/978-3-030-14177-6_12
State	Published - 2019
Event	International Workshop on Polystores and other Systems for Heterogeneous Data, Poly 2018 and 4th International Workshop on Data Management and Analytics for Medicine and Health Care, DMAH 2019 held in conjunction with 44th International Conference on Very Large Data Bases, VLDB 2018 - Rio de Janeiro, Brazil Duration: Aug 27 2018 → Aug 31 2018

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	11470 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	International Workshop on Polystores and other Systems for Heterogeneous Data, Poly 2018 and 4th International Workshop on Data Management and Analytics for Medicine and Health Care, DMAH 2019 held in conjunction with 44th International Conference on Very Large Data Bases, VLDB 2018
Country/Territory	Brazil
City	Rio de Janeiro
Period	8/27/18 → 8/31/18

Keywords

Copy number variation
Integrated data repository
Quality assurance
Standardization

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-030-14177-6_12

Cite this

Wang, C., Moore, R. M., Evans, J. M., Hou, X., John Weroha, S., & Jiang, G. (2019). Building a Research-Quality Copy Number Variation Data Repository for Translational Research. In T. Mattson, F. Wang, G. Teodoro, M. Stonebraker, V. Gadepally, & G. Luo (Eds.), Heterogeneous Data Management, Polystores, and Analytics for Healthcare - VLDB 2018 Workshops, Poly and DMAH, 2018, Revised Selected Papers (pp. 148-161). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11470 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-030-14177-6_12

Building a Research-Quality Copy Number Variation Data Repository for Translational Research. / Wang, Chen; Moore, Raymond M.; Evans, Jared M. et al.
Heterogeneous Data Management, Polystores, and Analytics for Healthcare - VLDB 2018 Workshops, Poly and DMAH, 2018, Revised Selected Papers. ed. / Timothy Mattson; Fusheng Wang; George Teodoro; Michael Stonebraker; Vijay Gadepally; Gang Luo. Springer Verlag, 2019. p. 148-161 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11470 LNCS).

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

Wang, C, Moore, RM, Evans, JM, Hou, X, John Weroha, S & Jiang, G 2019, Building a Research-Quality Copy Number Variation Data Repository for Translational Research. in T Mattson, F Wang, G Teodoro, M Stonebraker, V Gadepally & G Luo (eds), Heterogeneous Data Management, Polystores, and Analytics for Healthcare - VLDB 2018 Workshops, Poly and DMAH, 2018, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 11470 LNCS, Springer Verlag, pp. 148-161, International Workshop on Polystores and other Systems for Heterogeneous Data, Poly 2018 and 4th International Workshop on Data Management and Analytics for Medicine and Health Care, DMAH 2019 held in conjunction with 44th International Conference on Very Large Data Bases, VLDB 2018, Rio de Janeiro, Brazil, 8/27/18. https://doi.org/10.1007/978-3-030-14177-6_12

Wang C, Moore RM, Evans JM, Hou X, John Weroha S , Jiang G. Building a Research-Quality Copy Number Variation Data Repository for Translational Research. In Mattson T, Wang F, Teodoro G, Stonebraker M, Gadepally V, Luo G, editors, Heterogeneous Data Management, Polystores, and Analytics for Healthcare - VLDB 2018 Workshops, Poly and DMAH, 2018, Revised Selected Papers. Springer Verlag. 2019. p. 148-161. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-030-14177-6_12

Wang, Chen ; Moore, Raymond M. ; Evans, Jared M. et al. / Building a Research-Quality Copy Number Variation Data Repository for Translational Research. Heterogeneous Data Management, Polystores, and Analytics for Healthcare - VLDB 2018 Workshops, Poly and DMAH, 2018, Revised Selected Papers. editor / Timothy Mattson ; Fusheng Wang ; George Teodoro ; Michael Stonebraker ; Vijay Gadepally ; Gang Luo. Springer Verlag, 2019. pp. 148-161 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "Copy number variation (CNV) has known associations with population diversities and disease conditions. However, research communities face great challenges in reusing the CNV data due to the heterogeneity of existing CNV data sources. The objective of the study is to design, develop and evaluate a scalable CNV data repository based on a proposed common data schema for facilitating research-quality CNV data integration and reuse. We created a proposal for a CNV common data schema through analyzing multiple existing CNV data sources. We designed a collection of the CNV quality metrics and demonstrated its usefulness using the CNV data from a study of ovarian cancer xenograft models. We implemented a CNV data repository using a MongoDB database backend and established the CNV genomic data services that enable reusing of the curated CNV data and answering CNV-relevant research questions. The critical issues and future plan for the system enhancement and community engagement were discussed.",

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author = "Chen Wang and Moore, {Raymond M.} and Evans, {Jared M.} and Xiaonan Hou and {John Weroha}, S. and Guoqian Jiang",

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AB - Copy number variation (CNV) has known associations with population diversities and disease conditions. However, research communities face great challenges in reusing the CNV data due to the heterogeneity of existing CNV data sources. The objective of the study is to design, develop and evaluate a scalable CNV data repository based on a proposed common data schema for facilitating research-quality CNV data integration and reuse. We created a proposal for a CNV common data schema through analyzing multiple existing CNV data sources. We designed a collection of the CNV quality metrics and demonstrated its usefulness using the CNV data from a study of ovarian cancer xenograft models. We implemented a CNV data repository using a MongoDB database backend and established the CNV genomic data services that enable reusing of the curated CNV data and answering CNV-relevant research questions. The critical issues and future plan for the system enhancement and community engagement were discussed.

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Building a Research-Quality Copy Number Variation Data Repository for Translational Research

Abstract

Publication series

Conference

Keywords

ASJC Scopus subject areas

Access to Document

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Cite this