Identification of individuals by trait prediction using whole-genome sequencing data

Abstract

Prediction of human physical traits and demographic information from genomic data challenges privacy and data deidentification in personalized medicine. To explore the current capabilities of phenotype-based genomic identification, we applied whole-genome sequencing, detailed phenotyping, and statistical modeling to predict biometric traits in a cohort of 1,061 participants of diverse ancestry. Individually, for a large fraction of the traits, their predictive accuracy beyond ancestry and demographic information is limited. However, we have developed a maximum entropy algorithm that integrates multiple predictions to determine which genomic samples and phenotype measurements originate from the same person. Using this algorithm, we have reidentified an average of >8 of 10 held-out individuals in an ethnically mixed cohort and an average of 5 of either 10 African Americans or 10 Europeans. This work challenges current conceptions of personal privacy and may have far-reaching ethical and legal implications.

Clinical sequencing: From raw data to diagnosis with lifetime value

“…Although cloud environments enable high‐capacity data storage (eg, Amazon Web Services, https://aws.amazon.com/), there are legitimate concerns about the privacy and security of sensitive cloud‐stored genetic data, indicating the need for more secure and decentralized solutions (eg, UnLynx) . Data sharing, which facilitates genotype‐phenotype correlation, is subject to further discussions as it has been shown that even after de‐identification, re‐identification of a single person is at least partially possible by either STR or SNP genotyping …”

“…99 Data sharing, which facilitates genotype-phenotype correlation, is subject to further discussions as it has been shown that even after de-identification, re-identification of a single person is at least partially possible by either STR 100 or SNP genotyping. 101…”

Biodata Risks and Synthetic Biology: A Critical Juncture

“…The ability to identify individuals based on portions of their DNA is possible [13]. Individuals can be identified through health records and physical samples provided to their health practitioners.…”

The Future of Forensic Biology

“…For smartphones, the algorithms must be scaled down, which makes them less effective, but in future with more sophistication of mobile phones it may become a handy tool for police officers/forensic scientists to recognize the accused/victim from a crowd [28]. A recent report has analyzed whole genomic sequencing data from different ethnic community around the world (#1061) which is able to identify people according to their physical traits and demography [29]. Morphometrics (the measurement of body shapes) may be used to identify the skeletal remains of missing children, something which is extremely challenging for current forensic experts.…”