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Reconciling S-LDSC and LDAK models and functional enrichment estimates

https://doi.org/10.1101/256412
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What this work says

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

inferredcites →https://doi.org/10.1002/gepi.22161openalex-snapshot
The accuracy of LD Score regression as an estimator of confounding and genetic correlations in genome‐wide association studies
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.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.2016.09.014openalex-snapshot
Population Structure of UK Biobank and Ancient Eurasians Reveals Adaptation at Genes Influencing Blood Pressure
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature12787openalex-snapshot
An atlas of active enhancers across human cell types and tissues
inferredcites →https://doi.org/10.1038/nature13835openalex-snapshot
Genetic and epigenetic fine mapping of causal autoimmune disease variants
inferredcites →https://doi.org/10.1038/nature14248openalex-snapshot
Integrative analysis of 111 reference human epigenomes
inferredcites →https://doi.org/10.1038/nature14962openalex-snapshot
The UK10K project identifies rare variants in health and disease
inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot
A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/nature22969openalex-snapshot
Fine-mapping inflammatory bowel disease loci to single-variant resolution
inferredcites →https://doi.org/10.1038/ng.3190openalex-snapshot
Efficient Bayesian mixed-model analysis increases association power in large cohorts
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.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.3643openalex-snapshot
A reference panel of 64,976 haplotypes for genotype imputation
inferredcites →https://doi.org/10.1038/ng.3865openalex-snapshot
Reevaluation of SNP heritability in complex human traits
inferredcites →https://doi.org/10.1038/ng.3954openalex-snapshot
Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection
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/nrg2322openalex-snapshot
Heritability in the genomics era — concepts and misconceptions
inferredcites →https://doi.org/10.1038/nrg2796openalex-snapshot
Genotype imputation for genome-wide association studies
inferredcites →https://doi.org/10.1038/s41467-019-08424-6openalex-snapshot
Quantification of frequency-dependent genetic architectures in 25 UK Biobank traits reveals action of negative selection
inferredcites →https://doi.org/10.1038/s41586-018-0579-zopenalex-snapshot
The UK Biobank resource with deep phenotyping and genomic data
inferredcites →https://doi.org/10.1038/s41588-018-0101-4openalex-snapshot
Signatures of negative selection in the genetic architecture of human complex traits
inferredcites →https://doi.org/10.1038/s41588-018-0108-xopenalex-snapshot
Comparison of methods that use whole genome data to estimate the heritability and genetic architecture of complex traits
inferredcites →https://doi.org/10.1038/s41588-018-0144-6openalex-snapshot
Mixed-model association for biobank-scale datasets
inferredcites →https://doi.org/10.1038/s41588-018-0148-2openalex-snapshot
Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits
inferredcites →https://doi.org/10.1038/s41588-018-0231-8openalex-snapshot
Functional architecture of low-frequency variants highlights strength of negative selection across coding and non-coding annotations
inferredcites →https://doi.org/10.1038/s41588-018-0279-5openalex-snapshot
SumHer better estimates the SNP heritability of complex traits from summary statistics
inferredcites →https://doi.org/10.1073/pnas.0903103106openalex-snapshot
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
inferredcites →https://doi.org/10.1101/166298openalex-snapshot
Genome-wide genetic data on ~500,000 UK Biobank participants
inferredcites →https://doi.org/10.1101/280784openalex-snapshot
Exposing flaws in S-LDSC; reply to Gazal et al .
inferredcites →https://doi.org/10.1101/375337openalex-snapshot
LDpred-funct: incorporating functional priors improves polygenic prediction accuracy in UK Biobank and 23andMe data sets
inferredcites →https://doi.org/10.1371/journal.pmed.1001779openalex-snapshot
UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age
inferredcites →https://doi.org/10.2307/2532051openalex-snapshot
A Concordance Correlation Coefficient to Evaluate Reproducibility

What points at this work

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

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.2019.02.008openalex-snapshot
Disease Heritability Enrichment of Regulatory Elements Is Concentrated in Elements with Ancient Sequence Age and Conserved Function across Species
inferred← citeshttps://doi.org/10.1016/j.ajhg.2019.03.020openalex-snapshot
Genes with High Network Connectivity Are Enriched for Disease Heritability
inferred← citeshttps://doi.org/10.1016/j.ajhg.2019.07.003openalex-snapshot
Extreme Polygenicity of Complex Traits Is Explained by Negative Selection
inferred← citeshttps://doi.org/10.1016/j.ajhg.2022.01.005openalex-snapshot
Leveraging gene co-regulation to identify gene sets enriched for disease heritability
inferred← citeshttps://doi.org/10.1038/s41467-019-11957-5openalex-snapshot
Functional disease architectures reveal unique biological role of transposable elements
inferred← citeshttps://doi.org/10.1038/s41467-020-18515-4openalex-snapshot
Evaluating the informativeness of deep learning annotations for human complex diseases
inferred← citeshttps://doi.org/10.1038/s41467-023-40913-7openalex-snapshot
A versatile, fast and unbiased method for estimation of gene-by-environment interaction effects on biobank-scale datasets
inferred← citeshttps://doi.org/10.1038/s41576-019-0137-zopenalex-snapshot
Genetic correlations of polygenic disease traits: from theory to practice
inferred← citeshttps://doi.org/10.1038/s41588-018-0148-2openalex-snapshot
Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits
inferred← citeshttps://doi.org/10.1038/s41588-018-0231-8openalex-snapshot
Functional architecture of low-frequency variants highlights strength of negative selection across coding and non-coding annotations
inferred← citeshttps://doi.org/10.1038/s41588-019-0465-0openalex-snapshot
Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture
inferred← citeshttps://doi.org/10.1038/s41588-020-0600-yopenalex-snapshot
Evaluating and improving heritability models using summary statistics
inferred← citeshttps://doi.org/10.1093/brain/awz295openalex-snapshot
Informing disease modelling with brain-relevant functional genomic annotations
inferred← citeshttps://doi.org/10.1093/hmg/ddz226openalex-snapshot
Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability
inferred← citeshttps://doi.org/10.1101/2020.09.08.288563openalex-snapshot
Integrative approaches to improve the informativeness of deep learning models for human complex diseases
inferred← citeshttps://doi.org/10.1101/2021.04.24.21255884openalex-snapshot
A versatile, fast and unbiased method for estimation of gene-by-environment interaction effects on biobank-scale datasets
inferred← citeshttps://doi.org/10.1101/420497openalex-snapshot
Polygenicity of complex traits is explained by negative selection
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