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

https://doi.org/10.1101/199927

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What this work says

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

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BEDTools: The Swiss‐Army Tool for Genome Feature Analysis

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The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities

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CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions

inferredcites →https://doi.org/10.1016/j.cell.2015.09.054openalex-snapshot

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

inferredcites →https://doi.org/10.1038/gim.2013.176openalex-snapshot

In silico tools for splicing defect prediction: a survey from the viewpoint of end users

inferredcites →https://doi.org/10.1038/nature09158openalex-snapshot

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

inferredcites →https://doi.org/10.1038/nature13127openalex-snapshot

Guidelines for investigating causality of sequence variants in human disease

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/nature15521openalex-snapshot

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

inferredcites →https://doi.org/10.1038/nature19057openalex-snapshot

Analysis of protein-coding genetic variation in 60,706 humans

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/nature25461openalex-snapshot

Enhancer redundancy provides phenotypic robustness in mammalian development

inferredcites →https://doi.org/10.1038/nbt.3468openalex-snapshot

High-throughput mapping of regulatory DNA

inferredcites →https://doi.org/10.1038/ncomms11558openalex-snapshot

The complete local genotype–phenotype landscape for the alternative splicing of a human exon

inferredcites →https://doi.org/10.1038/ncomms15824openalex-snapshot

Genetic diagnosis of Mendelian disorders via RNA sequencing

inferredcites →https://doi.org/10.1038/ng.2892openalex-snapshot

A general framework for estimating the relative pathogenicity of human genetic variants

inferredcites →https://doi.org/10.1038/ng.3196openalex-snapshot

A method for calculating probabilities of fitness consequences for point mutations across the human genome

inferredcites →https://doi.org/10.1038/ng.3220openalex-snapshot

Identification of common genetic variants controlling transcript isoform variation in human whole blood

inferredcites →https://doi.org/10.1038/ng.3810openalex-snapshot

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

inferredcites →https://doi.org/10.1038/ng.3837openalex-snapshot

Pathogenic variants that alter protein code often disrupt splicing

inferredcites →https://doi.org/10.1038/ng.3840openalex-snapshot

Population- and individual-specific regulatory variation in Sardinia

inferredcites →https://doi.org/10.1038/nn.3801openalex-snapshot

Genetic variability in the regulation of gene expression in ten regions of the human brain

inferredcites →https://doi.org/10.1038/nprot.2016.135openalex-snapshot

The power of multiplexed functional analysis of genetic variants

inferredcites →https://doi.org/10.1038/nrg3031openalex-snapshot

Exome sequencing as a tool for Mendelian disease gene discovery

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

Rare and common variants: twenty arguments

inferredcites →https://doi.org/10.1042/cs20160211openalex-snapshot

RNA splicing in human disease and in the clinic

inferredcites →https://doi.org/10.1073/pnas.0136770100openalex-snapshot

Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans

inferredcites →https://doi.org/10.1089/1066527041410418openalex-snapshot

Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals

inferredcites →https://doi.org/10.1093/bioinformatics/btu703openalex-snapshot

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

inferredcites →https://doi.org/10.1093/bioinformatics/btv009openalex-snapshot

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

inferredcites →https://doi.org/10.1093/database/baw093openalex-snapshot

The Ensembl gene annotation system

inferredcites →https://doi.org/10.1093/nar/gkq163openalex-snapshot

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

inferredcites →https://doi.org/10.1093/nar/gku1082openalex-snapshot

A platform for rapid prototyping of synthetic gene networks in mammalian cells

inferredcites →https://doi.org/10.1093/nar/gkx323openalex-snapshot

kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences

inferredcites →https://doi.org/10.1101/014126openalex-snapshot

Alternative splicing QTLs in European and African populations using Altrans, a novel method for splice junction quantification

inferredcites →https://doi.org/10.1101/219238openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gr.097857.109openalex-snapshot

Detection of nonneutral substitution rates on mammalian phylogenies

inferredcites →https://doi.org/10.1101/gr.119628.110openalex-snapshot

Quantitative evaluation of all hexamers as exonic splicing elements

inferredcites →https://doi.org/10.1101/gr.135350.111openalex-snapshot

GENCODE: The reference human genome annotation for The ENCODE Project

inferredcites →https://doi.org/10.1101/gr.197152.115openalex-snapshot

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening

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/10.1101/gr.3715005openalex-snapshot

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

inferredcites →https://doi.org/10.1126/science.1156409openalex-snapshot

Genetic Mapping in Human Disease

inferredcites →https://doi.org/10.1126/science.1160631openalex-snapshot

Shadow Enhancers as a Source of Evolutionary Novelty

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.1217876openalex-snapshot

An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

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.1254806openalex-snapshot

The human splicing code reveals new insights into the genetic determinants of disease

inferredcites →https://doi.org/10.1126/science.1262110openalex-snapshot

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

inferredcites →https://doi.org/10.1126/science.aad9417openalex-snapshot

RNA splicing is a primary link between genetic variation and disease

inferredcites →https://doi.org/10.1126/science.aaf7613openalex-snapshot

High-resolution interrogation of functional elements in the noncoding genome

inferredcites →https://doi.org/10.1126/scitranslmed.aal5209openalex-snapshot

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

inferredcites →https://doi.org/10.1186/s13059-016-0974-4openalex-snapshot

The Ensembl Variant Effect Predictor

inferredcites →https://doi.org/10.1186/s13059-017-1212-4openalex-snapshot

The impact of rare and low-frequency genetic variants in common disease

inferredcites →https://doi.org/10.1186/s13059-018-1437-xopenalex-snapshot

Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency

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

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

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.2018.10.027openalex-snapshot

The Genetic Landscape of Diamond-Blackfan Anemia

inferred← citeshttps://doi.org/10.1101/365890openalex-snapshot

The Genetic Landscape of Diamond-Blackfan Anemia

inferred← citeshttps://doi.org/10.1101/gr.226621.117openalex-snapshot

ABCA4midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease

inferred← citeshttps://doi.org/10.1186/s13059-018-1437-xopenalex-snapshot

Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency

inferred← citeshttps://doi.org/10.1186/s13059-019-1653-zopenalex-snapshot

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing

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