Topics

A Unifying Framework for Imputing Summary Statistics in Genome-Wide Association Studies.

07:00 EST 13th February 2020 | BioPortfolio

Summary of "A Unifying Framework for Imputing Summary Statistics in Genome-Wide Association Studies."

Methods to impute missing data are routinely used to increase power in genome-wide association studies. There are two broad classes of imputation methods. The first class imputes genotypes at the untyped variants, given those at the typed variants, and then performs a statistical test of association at the imputed variants. The second class, summary statistic imputation (SSI), directly imputes association statistics at the untyped variants, given the association statistics observed at the typed variants. The second class is appealing as it tends to be computationally efficient while only requiring the summary statistics from a study, while the former class requires access to individual-level data that can be difficult to obtain. The statistical properties of these two classes of imputation methods have not been fully understood. In this study, we show that the two classes of imputation methods yield association statistics with similar distributions for sufficiently large sample sizes. Using this relationship, we can understand the effect of the imputation method on power. We show that a commonly used approach to SSI that we term SSI with variance reweighting generally leads to a loss in power. On the contrary, our proposed method for SSI that does not perform variance reweighting fully accounts for imputation uncertainty, while achieving better power.

Affiliation

Journal Details

This article was published in the following journal.

Name: Journal of computational biology : a journal of computational molecular cell biology
ISSN: 1557-8666
Pages:

Links

DeepDyve research library

PubMed Articles [20997 Associated PubMed Articles listed on BioPortfolio]

CoMM-S2: a collaborative mixed model using summary statistics in transcriptome-wide association studies.

Although genome-wide association studies (GWAS) have deepened our understanding of the genetic architecture of complex traits, the mechanistic links that underlie how genetic variants cause complex tr...

Causal assessment of sleep on coronary heart disease.

Sleep is an essential physiological process that protects our physical and mental health. However, the causality of the association between sleep and coronary heart disease (CHD) is unknown. Mendelian...

bWGR: Bayesian Whole-Genome Regression.

Whole-genome regressions methods represent a key framework for genome-wide prediction, cross-validation studies, and association analysis. The bWGR offers a compendium of Bayesian methods with various...

Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies.

Genetic risk prediction is an important problem in human genetics, and accurate prediction can facilitate disease prevention and treatment. Calculating polygenic risk score (PRS) has become widely use...

Summary statistic analyses can mistake confounding bias for heritability.

Linkage disequilibrium SCore regression (LDSC) has become a popular approach to estimate confounding bias, heritability, and genetic correlation using only genome-wide association study (GWAS) test st...

Clinical Trials [4100 Associated Clinical Trials listed on BioPortfolio]

A Genome-Wide Association Study for Neonatal Diseases

This is an observational study to identify genetic risks for neonatal diseases, necrotizing enterocolitis (NEC) using genome-wide association study (GWAS) and enterotype investigation. We ...

Genome-Wide Association Study in Patients With Nontuberculous Mycobacterial Lung Disease

The aim of this study was to elucidate genetic susceptibility of patients with nontuberculous mycobacterial lung disease using genome-wide association study.

PheWAS of a Polygenic Predictor of Thyroid Function

Performing a phenome-wide association study (PheWAS) identifying clinical diagnoses associated with a polygenic predictor of Thyroid stimulating hormone (TSH) levels identified by a previo...

Uro-DNA Collection for Expanded Genome-Wide Association Study (GWAS) of Renal Cell Carcinoma (RCC)

In the last decade, investigators from the Department of Cancer Epidemiology and Genetics (National Cancer Institute, USA) have conducted genome-wide association (GWAS) studies of renal ce...

Identification of Genetic Polymorphism Related to Acute Kidney Injury After Liver Transplantation Through Genome-wide Association Study (GWAS) in Korean Population

Some of the liver transplantation recipients experience postoperative acute kidney injury due to various causes including genetic factors. Prevention of postoperative acute kidney injury i...

Medical and Biotech [MESH] Definitions

An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.

Used for general articles concerning statistics of births, deaths, marriages, etc.

A center in the PUBLIC HEALTH SERVICE which is primarily concerned with the collection, analysis, and dissemination of health statistics on vital events and health activities to reflect the health status of people, health needs, and health resources.

Component of the NATIONAL INSTITUTES OF HEALTH. It conducts and supports research into the mapping of the human genome and other organism genomes. The National Center for Human Genome Research was established in 1989 and re-named the National Human Genome Research Institute in 1997.

Techniques to determine the entire sequence of the GENOME of an organism or individual.

Quick Search


DeepDyve research library

Relevant Topic

Bioinformatics
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...


Searches Linking to this Article