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Ultra-rare variants drive substantial cis -heritability of human gene expression

https://doi.org/10.1101/219238

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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.21866openalex-snapshot

Population Genetic Simulations of Complex Phenotypes with Implications for Rare Variant Association Tests

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.2015.12.023openalex-snapshot

A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood

inferredcites →https://doi.org/10.1016/j.cell.2017.01.038openalex-snapshot

Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression

inferredcites →https://doi.org/10.1016/j.cell.2017.05.038openalex-snapshot

An Expanded View of Complex Traits: From Polygenic to Omnigenic

inferredcites →https://doi.org/10.1038/nature12531openalex-snapshot

Transcriptome and genome sequencing uncovers functional variation in humans

inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot

A global reference for human genetic variation

inferredcites →https://doi.org/10.1038/nature18642openalex-snapshot

The genetic architecture of type 2 diabetes

inferredcites →https://doi.org/10.1038/nature24267openalex-snapshot

The impact of rare variation on gene expression across tissues

inferredcites →https://doi.org/10.1038/nature24277openalex-snapshot

Genetic effects on gene expression across human tissues

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.2394openalex-snapshot

Mapping cis- and trans-regulatory effects across multiple tissues in twins

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.2896openalex-snapshot

The deleterious mutation load is insensitive to recent population history

inferredcites →https://doi.org/10.1038/ng.3039openalex-snapshot

Most genetic risk for autism resides with common variation

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.3446openalex-snapshot

The contribution of rare variation to prostate cancer heritability

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.3656openalex-snapshot

Next-generation genotype imputation service and methods

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/nrg3031openalex-snapshot

Exome sequencing as a tool for Mendelian disease gene discovery

inferredcites →https://doi.org/10.1038/s41467-018-07276-wopenalex-snapshot

Detecting heritable phenotypes without a model using fast permutation testing for heritability and set-tests

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/s41586-021-03205-yopenalex-snapshot

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

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/10.1073/pnas.0906182107openalex-snapshot

Genetic architecture of a complex trait and its implications for fitness and genome-wide association studies

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

Measuring missing heritability: Inferring the contribution of common variants

inferredcites →https://doi.org/10.1086/321272openalex-snapshot

Are Rare Variants Responsible for Susceptibility to Complex Diseases?

inferredcites →https://doi.org/10.1093/bioinformatics/btn522openalex-snapshot

A flexible forward simulator for populations subject to selection and demography

inferredcites →https://doi.org/10.1093/genetics/145.2.505openalex-snapshot

Inferring Coalescence Times From DNA Sequence Data

inferredcites →https://doi.org/10.1101/345801openalex-snapshot

Measurement of selective constraint on human gene expression

inferredcites →https://doi.org/10.1101/gr.126540.111openalex-snapshot

Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent

inferredcites →https://doi.org/10.1101/gr.202440.115openalex-snapshot

Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants

inferredcites →https://doi.org/10.1126/science.1142430openalex-snapshot

Human Genome Ultraconserved Elements Are Ultraselected

inferredcites →https://doi.org/10.1126/science.1217283openalex-snapshot

Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants

inferredcites →https://doi.org/10.1126/science.1219240openalex-snapshot

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

inferredcites →https://doi.org/10.1126/science.aai8690openalex-snapshot

DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification

inferredcites →https://doi.org/10.1371/journal.pbio.1000294openalex-snapshot

Rare Variants Create Synthetic Genome-Wide Associations

inferredcites →https://doi.org/10.1371/journal.pbio.1000579openalex-snapshot

Synthetic Associations Created by Rare Variants Do Not Explain Most GWAS Results

inferredcites →https://doi.org/10.1371/journal.pgen.1000083openalex-snapshot

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

inferredcites →https://doi.org/10.1371/journal.pgen.1000592openalex-snapshot

Evolutionary Processes Acting on Candidate cis-Regulatory Regions in Humans Inferred from Patterns of Polymorphism and Divergence

inferredcites →https://doi.org/10.1371/journal.pgen.1001157openalex-snapshot

Balancing Selection Maintains a Form of ERAP2 that Undergoes Nonsense-Mediated Decay and Affects Antigen Presentation

inferredcites →https://doi.org/10.1371/journal.pgen.1001317openalex-snapshot

Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals

inferredcites →https://doi.org/10.1371/journal.pgen.1002144openalex-snapshot

Rare and Common Regulatory Variation in Population-Scale Sequenced Human Genomes

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.1004379openalex-snapshot

The Impact of Population Demography and Selection on the Genetic Architecture of Complex Traits

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s00439-019-02040-6openalex-snapshot

Evolutionary perspectives on polygenic selection, missing heritability, and GWAS

inferred← citeshttps://doi.org/10.1038/s41588-021-00997-7openalex-snapshot

Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data

inferred← citeshttps://doi.org/10.1101/199927openalex-snapshot

Many rare genetic variants have unrecognized large-effect disruptions to exon recognition

inferred← citeshttps://doi.org/10.1101/345801openalex-snapshot

Measurement of selective constraint on human gene expression

inferred← citeshttps://doi.org/10.1126/science.aay0256openalex-snapshot

Genetic regulatory variation in populations informs transcriptome analysis in rare disease

inferred← citeshttps://doi.org/10.1534/genetics.117.300489openalex-snapshot

Detecting Polygenic Adaptation in Admixture Graphs

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