Privately computing set-maximal matches in genomic data.

BMC Medical Genomics
Katerina SotirakiHao Chen

Abstract

Finding long matches in deoxyribonucleic acid (DNA) sequences in large aligned genetic sequences is a problem of great interest. A paradigmatic application is the identification of distant relatives via large common subsequences in DNA data. However, because of the sensitive nature of genomic data such computations without security consideration might compromise the privacy of the individuals involved. The secret sharing technique enables the computation of matches while respecting the privacy of the inputs of the parties involved. This method requires interaction that depends on the circuit depth needed for the computation. We design a new depth-optimized algorithm for computing set-maximal matches between a database of aligned genetic sequences and the DNA of an individual while respecting the privacy of both the database owner and the individual. We then implement and evaluate our protocol. Using modern cryptographic techniques, difficult genomic computations are performed in a privacy-preserving way. We enrich this research area by proposing a privacy-preserving protocol for set-maximal matches.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Mar 22, 1985·Science·D J Lipman, W R Pearson
Apr 5, 2002·Genome Research·W James Kent
Apr 6, 2002·Bioinformatics·Bin MaMing Li
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
May 13, 2010·Briefings in Bioinformatics·Heng Li, Nils Homer
Mar 13, 2014·Genome Research·Dan HeEleazar Eskin
May 7, 2016·Bioinformatics·Kana ShimizuGunnar Rätsch

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Software Mentioned

ABY

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

© 2021 Meta ULC. All rights reserved