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Secure-GWAS specifications


Unique identifier OMICS_29737
Name Secure-GWAS
Alternative name Secure-Genome-Wide Association Study
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++
License MIT License
Computer skills Advanced
Stability Stable
clang++ compiler, GMP library, libssl-dev, NTL
Maintained Yes




No version available


  • person_outline Bonnie Berger
  • person_outline Hoon Cho

Publication for Secure-Genome-Wide Association Study

Secure-GWAS citations


The development of large scale de identified biomedical databases in the age of genomics—principles and challenges

Hum Genomics
PMCID: 5894154
PMID: 29636096
DOI: 10.1186/s40246-018-0147-5

[…] y to support data sharing without fear of privacy abuse. In [, ], the authors designed a secure linear regression using homomorphic encryption for a multi-hospital quality improvement study. In [], a secure genome-wide association study (GWAS) was designed using homomorphic encryption, and in [], a GWAS protocol was designed using secret sharing. In [], the authors use garbled circuits to perform […]


Protecting genomic data analytics in the cloud: state of the art and opportunities

BMC Med Genomics
PMCID: 5062944
PMID: 27733153
DOI: 10.1186/s12920-016-0224-3

[…] enome computation using HME techniques (Application 1), and (2) secure collaboration on human genome computation by using SMC techniques (Application 2). For each challenge, we devised two tasks: (1) secure GWAS, and (2) secure genome sequence comparison. To evaluate the performance of the submitted algorithms, we provided template virtual machines (VMs) for the participating teams to train and co […]


FORESEE: Fully Outsourced secuRe gEnome Study basEd on homomorphic Encryption

BMC Med Inform Decis Mak
PMCID: 4698942
PMID: 26733391
DOI: 10.1186/1472-6947-15-S5-S5

[…] omplexity and accuracy by using the group-based computation and binary tree product with improved efficiency. In comparison to existing HME-based schemes [,,], both protocols enabled fully outsourced secure GWAS in an untrusted public cloud and could directly release study results to authorized users for decryption. Experimental results show that the secure approximation division protocol can capt […]


Secure distributed genome analysis for GWAS and sequence comparison computation

BMC Med Inform Decis Mak
PMCID: 4699166
PMID: 26733307
DOI: 10.1186/1472-6947-15-S5-S4

[…] ponds to the bitlength of secret shared values.Our implementation incorporates all optimizations and uses parameters ℓ 1 = 11 and ℓ 2 = 21 computed as described in the optimizations subsection of the secure GWAS computation section (ℓ 2 = 35 + |k| would be required for integer division, but a lower parameter is requested precision). We can see from the table that sufficient with floating point ope […]


A new way to protect privacy in large scale genome wide association studies

PMCID: 3605601
PMID: 23413435
DOI: 10.1093/bioinformatics/btt066

[…] Although the results prove the practical feasibility of cryptographically secure GWAS, the solution is also notably more resource demanding than the alternatives. We have to analyze further whether potential benefits outweigh costs. We consider three potential application s […]


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Secure-GWAS institution(s)
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Computer Science, Stanford University, Stanford, California, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Secure-GWAS funding source(s)
Supported by the US National Institutes of Health GM108348, by Kwanjeong Educational Foundation and by fellowships from the Simons and National Science Foundations.

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