rareSurvival: rare variant association analysis for “time-to-event” outcomes

Abstract

AbstractSummaryRare variants have been proposed as contributing to the “missing heritability” of complex human traits. There has been much recent development of methodology to investigate association of complex traits with multiple rare variants within pre-defined “units” from sequence and array-based studies of the exome or genome. However, software for modelling time to event outcomes for rare variant associations has been under developed in comparison with binary and quantitative traits. We introduce a new command line application, rareSurvival, used for the analysis of rare variants with time to event outcomes. The program is compatible with high performance computing (HPC) clusters for batch processing. rareSurvival implements statistical methodology, which are a combination of widely used survival and gene-based analysis techniques such as the Cox proportional hazards model and the burden test. We introduce a novel piece of software that will be at the forefront of efforts to discover rare variants associated with a variety of complex diseases with survival endpoints.Availability & ImplementationrareSurvival is implemented in C#, available on Linux, Windows and Mac OS X operating systems. It is freely available (GNU General Public License, version 3) to download from https://www.liverpool.ac.uk/translational-medicine/research/statistical-genetics/software/. Download Mono for Linux or Mac OS X to run software.Contacthamzah.syed@liverpool.ac.ukSupplementary informationLinks to additional figures and tables are available at Bioinformatics online.