RVTESTS

An efficient and comprehensive tool for rare variant association analysis using sequence data

Xiaowei Zhan, Youna Hu, Bingshan Li, Goncalo R. Abecasis, Dajiang Liu

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

Motivation: Next-generation sequencing technologies have enabled the large-scale assessment of the impact of rare and low-frequency genetic variants for complex human diseases. Gene-level association tests are often performed to analyze rare variants, where multiple rare variants in a gene region are analyzed jointly. Applying gene-level association tests to analyze sequence data often requires integrating multiple heterogeneous sources of information (e.g. annotations, functional prediction scores, allele frequencies, genotypes and phenotypes) to determine the optimal analysis unit and prioritize causal variants. Given the complexity and scale of current sequence datasets and bioinformatics databases, there is a compelling need for more efficient software tools to facilitate these analyses. To answer this challenge, we developed RVTESTS, which implements a broad set of rare variant association statistics and supports the analysis of autosomal and X-linked variants for both unrelated and related individuals. RVTESTS also provides useful companion features for annotating sequence variants, integrating bioinformatics databases, performing data quality control and sample selection. We illustrate the advantages of RVTESTS in functionality and efficiency using the 1000 Genomes Project data.

Original languageEnglish (US)
Pages (from-to)1423-1426
Number of pages4
JournalBioinformatics
Volume32
Issue number9
DOIs
StatePublished - May 1 2016

Fingerprint

Sequence Analysis
Genes
Gene
Computational Biology
Bioinformatics
Databases
Sample Selection
Data Quality
Quality Control
Genotype
Software Tools
Gene Frequency
Phenotype
Sequencing
Annotation
Low Frequency
Genome
Software
Statistics
Technology

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Zhan, Xiaowei ; Hu, Youna ; Li, Bingshan ; Abecasis, Goncalo R. ; Liu, Dajiang. / RVTESTS : An efficient and comprehensive tool for rare variant association analysis using sequence data. In: Bioinformatics. 2016 ; Vol. 32, No. 9. pp. 1423-1426.
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RVTESTS : An efficient and comprehensive tool for rare variant association analysis using sequence data. / Zhan, Xiaowei; Hu, Youna; Li, Bingshan; Abecasis, Goncalo R.; Liu, Dajiang.

In: Bioinformatics, Vol. 32, No. 9, 01.05.2016, p. 1423-1426.

Research output: Contribution to journalArticle

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