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2015 ; 97
(5
): 631-46
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Privacy Risks from Genomic Data-Sharing Beacons
#MMPMID26522470
Shringarpure SS
; Bustamante CD
Am J Hum Genet
2015[Nov]; 97
(5
): 631-46
PMID26522470
show ga
The human genetics community needs robust protocols that enable secure sharing of
genomic data from participants in genetic research. Beacons are web servers that
answer allele-presence queries--such as "Do you have a genome that has a specific
nucleotide (e.g., A) at a specific genomic position (e.g., position 11,272 on
chromosome 1)?"--with either "yes" or "no." Here, we show that individuals in a
beacon are susceptible to re-identification even if the only data shared include
presence or absence information about alleles in a beacon. Specifically, we
propose a likelihood-ratio test of whether a given individual is present in a
given genetic beacon. Our test is not dependent on allele frequencies and is the
most powerful test for a specified false-positive rate. Through simulations, we
showed that in a beacon with 1,000 individuals, re-identification is possible
with just 5,000 queries. Relatives can also be identified in the beacon.
Re-identification is possible even in the presence of sequencing errors and
variant-calling differences. In a beacon constructed with 65 European individuals
from the 1000 Genomes Project, we demonstrated that it is possible to detect
membership in the beacon with just 250 SNPs. With just 1,000 SNP queries, we were
able to detect the presence of an individual genome from the Personal Genome
Project in an existing beacon. Our results show that beacons can disclose
membership and implied phenotypic information about participants and do not
protect privacy a priori. We discuss risk mitigation through policies and
standards such as not allowing anonymous pings of genetic beacons and requiring
minimum beacon sizes.
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