Reconstruction of private genomes through reference-based genotype imputation.

BACKGROUND: Genotype imputation is an essential step in genetic studies to improve data quality and statistical power. Public imputation servers are widely used by researchers to impute their data using otherwise access-controlled reference panels of high-fidelity genomes held by these servers. RESULTS: We report evidence against the prevailing assumption that providing access to panels only indirectly via imputation servers poses a negligible privacy risk to individuals in the panels. To this end, we present algorithmic strategies for adaptively constructing artificial input samples and interpreting their imputation results that lead to the accurate reconstruction of reference panel haplotypes. We illustrate this possibility on three reference panels of real genomes for a range of imputation tools and output settings. Moreover, we demonstrate that reconstructed haplotypes from the same individual could be linked via their genetic relatives using our Bayesian linking algorithm, which allows a substantial portion of the individual's diploid genome to be reassembled. We also provide population genetic estimates of the proportion of a panel that could be linked when an adversary holds a varying number of genomes from the same population. CONCLUSIONS: Our results show that genomes in imputation server reference panels can be vulnerable to reconstruction, implying that additional safeguards may need to be considered. We suggest possible mitigation measures based on our findings. Our work illustrates the value of adversarial algorithms in uncovering new privacy risks to help inform the genomics community towards secure data sharing practices.

Greater Compliance With Early Sepsis Management is Associated With Safer Care and Shorter Hospital Stay.

ABSTRACT: This retrospective, cross-sectional study of U.S. hospitals in Medicare's Inpatient Quality Reporting Program aimed to determine whether variation in Sepsis/Septic Shock (Bundle SEP-1) compliance is linked to hospital size and measures of safety and operational efficiency. Two thousand six hundred and fifty-three acute care hospitals in Medicare's Hospital Compare online database were included in the study. Relationships between SEP-1 bundle compliance, hospital size, and indices of operational excellence (including Patient Safety Index [PSI-90], average length of stay [ALOS] and readmission rate) were analyzed. SEP-1 compliance score was inversely associated with staffed bed number (r = -.14, p < .001), PSI-90 (r = -.01, p < .001), and ALOS (r = -.13, p < .001) in a multivariate analysis. Hospitals in the lowest versus highest quartile by bed number had SEP-1 compliance score of 49.8 ± 20.2% versus 46.9 ± 16.8%, p < .001. Hospitals in the lowest versus highest quartile for SEP-1 score had an ALOS of 5.0 ± 1.2 days versus 4.7 ± 1.1 days and PSI-90 rate of 1.03 ± 0.22 versus 0.98 ± 0.16, p < .001 for both. Although this does not establish a causal relationship, it supports the hypothesis that the ability of hospitals to successfully implement SEP-1 is associated with superior performance in key measures of operational excellence.