title: SQC: secure quality control for meta-analysis of genome-wide association studies.
abstract: BACKGROUND
  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.
  
  
  METHODS
  SQC is implemented in Java and is publicly available at https://github.com/acs6610987/secureqc.
  
  
  BACKGROUND
  jean-pierre.hubaux@epfl.ch.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Zhicong
authors.initials: Z
authors.lastname: Huang
authors.affiliation: School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Huang
authors.initials: H
authors.lastname: Lin
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.|Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
authors.forename: Jacques
authors.initials: J
authors.lastname: Fellay
authors.affiliation: Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.|Institute of Social and Preventive Medicine, University Hospital Lausanne (CHUV), 1011 Lausanne, Switzerland.
authors.forename: Zoltán
authors.initials: Z
authors.lastname: Kutalik
authors.affiliation: School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Hubaux
mesh_terms: D003219:Confidentiality; D055106:Genome-Wide Association Study / Q000379:methods* / Q000592:standards; D006801:Humans; D015201:Meta-Analysis as Topic; D011786:Quality Control