General Information
| Description | Secure quality control for meta-analysis of genome-wide association studies |
| Homepage | https://github.com/acs6610987/secureqc |
Publications
SQC: secure quality control for meta-analysis of genome-wide association studies
Motivation:
Due to the limited power of small-scale genome-wide association studies (GWAS), researchers tend to collaborate and establish a larger consortium in order to perform large-scale GWAS. Genome-wide association meta-analysis (GWAMA) is a statistical tool that aims to synthesize results from multiple independent studies to increase the statistical power and reduce false-positive findings of GWAS. However, it has been demonstrated that the aggregate data of individual studies are subject to inference attacks, hence privacy concerns arise when researchers share study data in GWAMA.
Results:
In this article, we propose a secure quality control (SQC) protocol, which enables checking the quality of data in a privacy-preserving way without revealing sensitive information to a potential adversary. SQC employs state-of-the-art cryptographic and statistical techniques for privacy protection. We implement the solution in a meta-analysis pipeline with real data to demonstrate the efficiency and scalability on commodity machines. The distributed execution of SQC on a cluster of 128 cores for one million genetic variants takes less than one hour, which is a modest cost considering the 10-month time span usually observed for the completion of the QC procedure that includes timing of logistics.
Availability and Implementation:
SQC is implemented in Java and is publicly available at https://github.com/acs6610987/secureqc
Contact:
jean-pierre.hubaux@epfl.ch
Supplementary information:
Supplementary data are available at Bioinformatics online.
Related Tools
GWAtoolbox
Published December 2011
An R package for fast quality control and handling of genome-wide association studies meta-analysis data
Gencrypt
Published February 2012
One-way cryptographic hashes to detect overlapping individuals across samples
GRASP
Published June 2014
Analysis of genotype–phenotype results from 1390 genome-wide association studies and corresponding open access database
METAINTER
Published September 2014
Meta-analysis of multiple regression models in genome-wide association studies
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