Binary time-series query framework for efficient quantitative trait association study

Hongfei Wang, Xiang Zhang

Research output: Contribution to journalConference article

Abstract

Quantitative trait association study examines the association between quantitative traits and genetic variants. As a promising tool, it has been widely applied to dissect the genetic basis of complex diseases. However, such study usually involves testing trillions of variant-trait pairs and demands intensive computational resources. Recently, several algorithms have been developed to improve its efficiency. In this paper, we propose a framework, Fabrique, which models quantitative trait association study as querying binary time-series and bridges the two seemly different problems. Specifically, in the proposed framework, genetic variants are treated as a database consisting of binary time-series. Finding trait-associated variants is equivalent to finding the nearest neighbors of the trait. For efficient query process, Fabrique partitions and normalizes the binary time-series, and estimates a tight upper bound for each group of time-series to prune the search space. Extensive experimental results demonstrate that Fabrique only needs to search a very small portion of the database to locate the target variants and significantly outperforms the state-of-the-art method. We also show that Fabrique can be applied to other binary time-series query problem in addition to the genetic association study.

Original languageEnglish (US)
Article number6729562
Pages (from-to)777-786
Number of pages10
JournalProceedings - IEEE International Conference on Data Mining, ICDM
DOIs
StatePublished - Dec 1 2013
Event13th IEEE International Conference on Data Mining, ICDM 2013 - Dallas, TX, United States
Duration: Dec 7 2013Dec 10 2013

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Time series
Testing

All Science Journal Classification (ASJC) codes

  • Engineering(all)

Cite this

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title = "Binary time-series query framework for efficient quantitative trait association study",
abstract = "Quantitative trait association study examines the association between quantitative traits and genetic variants. As a promising tool, it has been widely applied to dissect the genetic basis of complex diseases. However, such study usually involves testing trillions of variant-trait pairs and demands intensive computational resources. Recently, several algorithms have been developed to improve its efficiency. In this paper, we propose a framework, Fabrique, which models quantitative trait association study as querying binary time-series and bridges the two seemly different problems. Specifically, in the proposed framework, genetic variants are treated as a database consisting of binary time-series. Finding trait-associated variants is equivalent to finding the nearest neighbors of the trait. For efficient query process, Fabrique partitions and normalizes the binary time-series, and estimates a tight upper bound for each group of time-series to prune the search space. Extensive experimental results demonstrate that Fabrique only needs to search a very small portion of the database to locate the target variants and significantly outperforms the state-of-the-art method. We also show that Fabrique can be applied to other binary time-series query problem in addition to the genetic association study.",
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Binary time-series query framework for efficient quantitative trait association study. / Wang, Hongfei; Zhang, Xiang.

In: Proceedings - IEEE International Conference on Data Mining, ICDM, 01.12.2013, p. 777-786.

Research output: Contribution to journalConference article

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