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Subtle stratification confounds estimates of heritability from rare variants

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/bf01067367openalex-snapshot

The estimation of genetic variance from twin data

inferredcites →https://doi.org/10.1016/j.ajhg.2010.11.011openalex-snapshot

GCTA: A Tool for Genome-wide Complex Trait Analysis

inferredcites →https://doi.org/10.1016/j.ajhg.2011.02.002openalex-snapshot

Estimating Missing Heritability for Disease from Genome-wide Association Studies

inferredcites →https://doi.org/10.1016/j.ajhg.2011.05.022openalex-snapshot

Response to Browning and Browning

inferredcites →https://doi.org/10.1016/j.ajhg.2011.05.025openalex-snapshot

Population Structure Can Inflate SNP-Based Heritability Estimates

inferredcites →https://doi.org/10.1016/j.ajhg.2011.11.029openalex-snapshot

Five Years of GWAS Discovery

inferredcites →https://doi.org/10.1016/j.ajhg.2012.06.013openalex-snapshot

Phasing of Many Thousands of Genotyped Samples

inferredcites →https://doi.org/10.1016/j.ajhg.2012.10.010openalex-snapshot

Improved Heritability Estimation from Genome-wide SNPs

inferredcites →https://doi.org/10.1016/j.ajhg.2013.10.015openalex-snapshot

Estimation of SNP Heritability from Dense Genotype Data

inferredcites →https://doi.org/10.1016/j.ajhg.2013.10.016openalex-snapshot

Response to Lee et al.: SNP-Based Heritability Analysis with Dense Data

inferredcites →https://doi.org/10.1016/j.ajhg.2014.10.004openalex-snapshot

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

inferredcites →https://doi.org/10.1023/b:bege.0000013734.39266.a3openalex-snapshot

Haplotype Association Analysis of Discrete and Continuous Traits Using Mixture of Regression Models

inferredcites →https://doi.org/10.1038/ejhg.2011.39openalex-snapshot

Genomic inflation factors under polygenic inheritance

inferredcites →https://doi.org/10.1038/nature08494openalex-snapshot

Finding the missing heritability of complex diseases

inferredcites →https://doi.org/10.1038/nature10251openalex-snapshot

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis

inferredcites →https://doi.org/10.1038/nature11632openalex-snapshot

An integrated map of genetic variation from 1,092 human genomes

inferredcites →https://doi.org/10.1038/nature13595openalex-snapshot

Biological insights from 108 schizophrenia-associated genetic loci

inferredcites →https://doi.org/10.1038/nature14962openalex-snapshot

The UK10K project identifies rare variants in health and disease

inferredcites →https://doi.org/10.1038/ng.1074openalex-snapshot

Differential confounding of rare and common variants in spatially structured populations

inferredcites →https://doi.org/10.1038/ng.1108openalex-snapshot

Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs

inferredcites →https://doi.org/10.1038/ng.2711openalex-snapshot

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs

inferredcites →https://doi.org/10.1038/ng.2876openalex-snapshot

Advantages and pitfalls in the application of mixed-model association methods

inferredcites →https://doi.org/10.1038/ng.314openalex-snapshot

Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease

inferredcites →https://doi.org/10.1038/ng.3211openalex-snapshot

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

inferredcites →https://doi.org/10.1038/ng.3285openalex-snapshot

Meta-analysis of the heritability of human traits based on fifty years of twin studies

inferredcites →https://doi.org/10.1038/ng.3390openalex-snapshot

Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index

inferredcites →https://doi.org/10.1038/ng.3404openalex-snapshot

Partitioning heritability by functional annotation using genome-wide association summary statistics

inferredcites →https://doi.org/10.1038/ng.3406openalex-snapshot

An atlas of genetic correlations across human diseases and traits

inferredcites →https://doi.org/10.1038/ng.3431openalex-snapshot

Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis

inferredcites →https://doi.org/10.1038/ng.3446openalex-snapshot

The contribution of rare variation to prostate cancer heritability

inferredcites →https://doi.org/10.1038/ng.608openalex-snapshot

Common SNPs explain a large proportion of the heritability for human height

inferredcites →https://doi.org/10.1038/ng.823openalex-snapshot

Genome partitioning of genetic variation for complex traits using common SNPs

inferredcites →https://doi.org/10.1038/ng1847openalex-snapshot

Principal components analysis corrects for stratification in genome-wide association studies

inferredcites →https://doi.org/10.1038/nrg2796openalex-snapshot

Genotype imputation for genome-wide association studies

inferredcites →https://doi.org/10.1038/nrg3118openalex-snapshot

Rare and common variants: twenty arguments

inferredcites →https://doi.org/10.1038/nrg3472openalex-snapshot

Meta-analysis methods for genome-wide association studies and beyond

inferredcites →https://doi.org/10.1073/pnas.1419064111openalex-snapshot

Measuring missing heritability: Inferring the contribution of common variants

inferredcites →https://doi.org/10.1073/pnas.1520109113openalex-snapshot

Limitations of GCTA as a solution to the missing heritability problem

inferredcites →https://doi.org/10.1093/bioinformatics/btl580openalex-snapshot

WHAP: haplotype-based association analysis

inferredcites →https://doi.org/10.1093/genetics/111.1.147openalex-snapshot

STATISTICAL PROPERTIES OF THE NUMBER OF RECOMBINATION EVENTS IN THE HISTORY OF A SAMPLE OF DNA SEQUENCES

inferredcites →https://doi.org/10.1093/hmg/dds491openalex-snapshot

Estimation and partitioning of polygenic variation captured by common SNPs for Alzheimer's disease, multiple sclerosis and endometriosis

inferredcites →https://doi.org/10.1101/gr.117259.110openalex-snapshot

Low-coverage sequencing: Implications for design of complex trait association studies

inferredcites →https://doi.org/10.1186/1471-2156-7-38openalex-snapshot

A graphical assessment of p-values from sliding window haplotype tests of association to identify asthma susceptibility loci on chromosome 11q

inferredcites →https://doi.org/10.1186/s13742-015-0047-8openalex-snapshot

Second-generation PLINK: rising to the challenge of larger and richer datasets

inferredcites →https://doi.org/10.1371/journal.pgen.1000529openalex-snapshot

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

inferredcites →https://doi.org/10.1371/journal.pgen.1002453openalex-snapshot

Inference of Population Structure using Dense Haplotype Data

inferredcites →https://doi.org/10.1371/journal.pgen.1003993openalex-snapshot

Quantifying Missing Heritability at Known GWAS Loci

inferredcites →https://doi.org/10.1371/journal.pgen.1005622openalex-snapshot

Disproportionate Contributions of Select Genomic Compartments and Cell Types to Genetic Risk for Coronary Artery Disease

inferredcites →https://doi.org/10.1371/journal.pone.0024945openalex-snapshot

Performance of Genotype Imputation for Rare Variants Identified in Exons and Flanking Regions of Genes

inferredcites →https://doi.org/10.1534/genetics.115.178616openalex-snapshot

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/cphg.48openalex-snapshot

Population Stratification in Genetic Association Studies

inferred← citeshttps://doi.org/10.1002/gepi.22459openalex-snapshot

Clarifying the causes of consistent and inconsistent findings in genetics

inferred← citeshttps://doi.org/10.1016/j.ajhg.2017.03.004openalex-snapshot

Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations

inferred← citeshttps://doi.org/10.1016/j.ajhg.2018.06.002openalex-snapshot

Estimating SNP-Based Heritability and Genetic Correlation in Case-Control Studies Directly and with Summary Statistics

inferred← citeshttps://doi.org/10.1016/j.ajhg.2022.02.012openalex-snapshot

Partitioning gene-level contributions to complex-trait heritability by allele frequency identifies disease-relevant genes

inferred← citeshttps://doi.org/10.1038/ng.3761openalex-snapshot

Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7

inferred← citeshttps://doi.org/10.1038/s41437-018-0067-0openalex-snapshot

Narrow-sense heritability estimation of complex traits using identity-by-descent information

inferred← citeshttps://doi.org/10.1038/s41576-018-0018-xopenalex-snapshot

The personal and clinical utility of polygenic risk scores

inferred← citeshttps://doi.org/10.1038/s41588-018-0178-9openalex-snapshot

Relatedness disequilibrium regression estimates heritability without environmental bias

inferred← citeshttps://doi.org/10.1038/s41588-018-0286-6openalex-snapshot

Discovery of common and rare genetic risk variants for colorectal cancer

inferred← citeshttps://doi.org/10.1038/s41588-020-00735-5openalex-snapshot

Functionally informed fine-mapping and polygenic localization of complex trait heritability

inferred← citeshttps://doi.org/10.1101/076133openalex-snapshot

Correcting subtle stratification in summary association statistics

inferred← citeshttps://doi.org/10.1101/2024.02.16.580613openalex-snapshot

Secure Discovery of Genetic Relatives across Large-Scale and Distributed Genomic Datasets

inferred← citeshttps://doi.org/10.1101/gr.279057.124openalex-snapshot

Secure discovery of genetic relatives across large-scale and distributed genomic data sets

inferred← citeshttps://doi.org/10.1371/journal.pbio.3002847openalex-snapshot

Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations

inferred← citeshttps://doi.org/10.1371/journal.pgen.1008222openalex-snapshot

Solving the missing heritability problem

inferred← citeshttps://doi.org/10.3390/genes12070991openalex-snapshot

Machine Learning Prediction of Biomarkers from SNPs and of Disease Risk from Biomarkers in the UK Biobank

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