Human microbiome privacy risks associated with summary statistics.
Ontology highlight
ABSTRACT:
SUBMITTER: Cho JC
PROVIDER: S-EPMC8018636 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Sensory signals are transduced at high resolution, but their structure must be stored in a more compact format. Here we provide evidence that the auditory system summarizes the temporal details of sounds using time-averaged statistics. We measured discrimination of 'sound textures' that were characterized by particular statistical properties, as normally result from the superposition of many acoustic features in auditory scenes. When listeners discriminated examples of different textures, performance improved with excerpt duration. In contrast, when listeners discriminated different examples of the same texture, performance declined with duration, a paradoxical result given that the information available for discrimination grows with duration. These results indicate that once these sounds are of moderate length, the brain's representation is limited to time-averaged statistics, which, for different examples of the same texture, converge to the same values with increasing duration. Such statistical representations produce good categorical discrimination, but limit the ability to discern temporal detail.
| S-EPMC4143328 | biostudies-literature
Project description:ImportancePatient portals can help caregivers better manage care for patients, but how caregivers access the patient portal could threaten patient security and privacy.ObjectiveTo identify the proportions of hospitals that provide proxy accounts to caregivers of adult patients, endorse password sharing with caregivers, and enable patients to restrict the types of information seen by their caregivers.Design, setting, and participantsThis national cross-sectional study included a telephone survey and was conducted from May 21, 2018, to December 20, 2018. The randomly selected sample comprised 1 independent hospital and 1 health system-affiliated general medical hospital from every US state and the District of Columbia. Specialty hospitals and those that did not have a patient portal in place were excluded. An interviewer posing as the daughter of an older adult patient called each hospital to ask about the hospital's patient portal practices. The interviewer used a structured questionnaire to obtain information on proxy account availability, password sharing, and patient control of their own information.Main outcomes and measuresThe primary outcome was the proportion of hospitals that provided proxy accounts to caregivers of adult patients. Secondary outcomes were the proportion of hospitals with personnel who endorsed password sharing and the proportion that allowed adult patients to limit the types of information available to caregivers.ResultsAfter exclusions, a total of 102 (51 health system-affiliated and 51 independent) hospitals were included in the study. Of these hospitals, 69 (68%) provided proxy accounts to caregivers of adult patients and 26 (25%) did not. In 7 of 102 hospitals (7%), the surveyed personnel did not know if proxy accounts were available. In the 94 hospitals asked about password sharing between the patient and caregiver, personnel in 42 hospitals (45%) endorsed the practice. Among hospitals that provided proxy accounts, only 13 of the 69 hospitals (19%) offered controls that enabled patients to restrict the types of information their proxies could see.Conclusions and relevanceThis study found that almost half of surveyed hospital personnel recommended password sharing and that few hospitals enabled patients to limit the types of information seen by those with proxy access. These findings suggest that hospitals and electronic health record (HER) vendors need to improve the availability and setup process of proxy accounts in a way that allows caregivers to care for patients without violating their privacy.
| S-EPMC7199170 | biostudies-literature
Project description: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.
| S-EPMC4667107 | biostudies-literature
Project description:The increasing number of genetic association studies conducted in multiple populations provides an unprecedented opportunity to study how the genetic architecture of complex phenotypes varies between populations, a problem important for both medical and population genetics. Here, we have developed a method for estimating the transethnic genetic correlation: the correlation of causal-variant effect sizes at SNPs common in populations. This methods takes advantage of the entire spectrum of SNP associations and uses only summary-level data from genome-wide association studies. This avoids the computational costs and privacy concerns associated with genotype-level information while remaining scalable to hundreds of thousands of individuals and millions of SNPs. We applied our method to data on gene expression, rheumatoid arthritis, and type 2 diabetes and overwhelmingly found that the genetic correlation was significantly less than 1. Our method is implemented in a Python package called Popcorn.
| S-EPMC5005434 | biostudies-literature
Project description:We examine the ability of observers to extract summary statistics (such as the mean and the relative-variance) from rapid numerical sequences of two digit numbers presented at a rate of 4/s. In four experiments (total N = 100), we find that the participants show a remarkable ability to extract such summary statistics and that their precision in the estimation of the sequence-mean improves with the sequence-length (subject to individual differences). Using model selection for individual participants we find that, when only the sequence-average is estimated, most participants rely on a holistic process of frequency based estimation with a minority who rely on a (rule-based and capacity limited) mid-range strategy. When both the sequence-average and the relative variance are estimated, about half of the participants rely on these two strategies. Importantly, the holistic strategy appears more efficient in terms of its precision. We discuss implications for the domains of two pathways numerical processing and decision-making.
| S-EPMC8517333 | biostudies-literature
Project description:BackgroundColocalization is a statistical method used in genetics to determine whether the same variant is causal for multiple phenotypes, for example, complex traits and gene expression. It provides stronger mechanistic evidence than shared significance, which can be produced through separate causal variants in linkage disequilibrium. Current colocalization methods require full summary statistics for both traits, limiting their use with the majority of reported GWAS associations (e.g. GWAS Catalog). We propose a new approximation to the popular coloc method that can be applied when limited summary statistics are available. Our method (POint EstiMation of Colocalization, POEMColoc) imputes missing summary statistics for one or both traits using LD structure in a reference panel, and performs colocalization using the imputed summary statistics.ResultsWe evaluate the performance of POEMColoc using real (UK Biobank phenotypes and GTEx eQTL) and simulated datasets. We show good correlation between posterior probabilities of colocalization computed from imputed and observed datasets and similar accuracy in simulation. We evaluate scenarios that might reduce performance and show that multiple independent causal variants in a region and imputation from a limited subset of typed variants have a larger effect while mismatched ancestry in the reference panel has a modest effect. Further, we find that POEMColoc is a better approximation of coloc when the imputed association statistics are from a well powered study (e.g., relatively larger sample size or effect size). Applying POEMColoc to estimate colocalization of GWAS Catalog entries and GTEx eQTL, we find evidence for colocalization of 150,000 trait-gene-tissue triplets.ConclusionsWe find that colocalization analysis performed with full summary statistics can be closely approximated when only the summary statistics of the top SNP are available for one or both traits. When applied to the full GWAS Catalog and GTEx eQTL, we find that colocalized trait-gene pairs are enriched in tissues relevant to disease etiology and for matches to approved drug mechanisms. POEMColoc R package is available at https://github.com/AbbVie-ComputationalGenomics/POEMColoc .
| S-EPMC8130535 | biostudies-literature
Project description:MOTIVATION:Multi-trait analyses using public summary statistics from genome-wide association studies (GWASs) are becoming increasingly popular. A constraint of multi-trait methods is that they require complete summary data for all traits. Although methods for the imputation of summary statistics exist, they lack precision for genetic variants with small effect size. This is benign for univariate analyses where only variants with large effect size are selected a posteriori. However, it can lead to strong p-value inflation in multi-trait testing. Here we present a new approach that improve the existing imputation methods and reach a precision suitable for multi-trait analyses. RESULTS:We fine-tuned parameters to obtain a very high accuracy imputation from summary statistics. We demonstrate this accuracy for variants of all effect sizes on real data of 28 GWAS. We implemented the resulting methodology in a python package specially designed to efficiently impute multiple GWAS in parallel. AVAILABILITY AND IMPLEMENTATION:The python package is available at: https://gitlab.pasteur.fr/statistical-genetics/raiss, its accompanying documentation is accessible here http://statistical-genetics.pages.pasteur.fr/raiss/. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.
| S-EPMC6853677 | biostudies-literature
Project description:Strong genetic associations in the region containing human leukocyte antigen (HLA) genes have been well-documented in various human immune disorders. Imputation methods to infer HLA variants from single nucleotide polymorphism (SNP) genotypes are currently used to understand HLA associations with a trait of interest. However, it is challenging for some researchers to obtain individual-level SNP genotype data or reference haplotype data. In this study, we developed and evaluated a new method, DISH (direct imputing summary association statistics of HLA variants), for imputing summary association statistics of HLA variants from SNP summary association statistics based on linkage disequilibria in Asian and European populations. Disease association Z scores in DISH were highly correlated with those from imputed HLA genotypes in null model datasets (r?=?0.934 in Asians; r?=?0.960 in Europeans). We applied DISH to two previous GWAS datasets in Asian systemic lupus erythematosus and European rheumatoid arthritis populations. There was a high correlation between Z scores in the DISH and HLA genotype imputations, showing the same disease-susceptible and protective alleles. This study illustrated the usefulness of the DISH method in understanding and identifying disease-associated HLA variants in human diseases while maintaining individual-level data security.
| S-EPMC6362191 | biostudies-literature
Project description:BackgroundImputation of individual level genotypes at untyped markers using an external reference panel of genotyped or sequenced individuals has become standard practice in genetic association studies. Direct imputation of summary statistics can also be valuable, for example in meta-analyses where individual level genotype data are not available. Two methods (DIST and ImpG-Summary/LD), that assume a multivariate Gaussian distribution for the association summary statistics, have been proposed for imputing association summary statistics. However, both methods assume that the correlations between association summary statistics are the same as the correlations between the corresponding genotypes. This assumption can be violated in the presence of confounding covariates.MethodsWe analytically show that in the absence of covariates, correlation among association summary statistics is indeed the same as that among the corresponding genotypes, thus serving as a theoretical justification for the recently proposed methods. We continue to prove that in the presence of covariates, correlation among association summary statistics becomes the partial correlation of the corresponding genotypes controlling for covariates. We therefore develop direct imputation of summary statistics allowing covariates (DISSCO).ResultsWe consider two real-life scenarios where the correlation and partial correlation likely make practical difference: (i) association studies in admixed populations; (ii) association studies in presence of other confounding covariate(s). Application of DISSCO to real datasets under both scenarios shows at least comparable, if not better, performance compared with existing correlation-based methods, particularly for lower frequency variants. For example, DISSCO can reduce the absolute deviation from the truth by 3.9-15.2% for variants with minor allele frequency <5%.
| S-EPMC4514926 | biostudies-literature
Project description:We describe an importance-sampling method for approximating likelihoods of population parameters based on multiple summary statistics. In this first application, we address the demographic history of closely related members of the Drosophila pseudoobscura group. We base the maximum-likelihood estimation of the time since speciation and the effective population sizes of the extant and ancestral populations on the pattern of nucleotide variation at DPS2002, a noncoding region tightly linked to a paracentric inversion that strongly contributes to reproductive isolation. Consideration of summary statistics rather than entire nucleotide sequences permits a compact description of the genealogy of the sample. We use importance sampling first to propose a genealogical and mutational history consistent with the observed array of summary statistics and then to correct the likelihood with the exact probability of the history determined from a system of recursions. Analysis of a subset of the data, for which recursive computation of the exact likelihood was feasible, indicated close agreement between the approximate and exact likelihoods. Our results for the complete data set also compare well with those obtained through Metropolis-Hastings sampling of fully resolved genealogies of entire nucleotide sequences.
| S-EPMC1456855 | biostudies-literature