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Transcript expression-aware annotation improves rare variant discovery and interpretation

https://doi.org/10.1101/554444
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What this work says

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

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Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2
inferredcites →https://doi.org/10.1002/humu.23610openalex-snapshot
Copy number variant discrepancy resolution using the ClinGen dosage sensitivity map results in updated clinical interpretations in ClinVar
inferredcites →https://doi.org/10.1007/s00424-009-0753-0openalex-snapshot
CaV1.2 channelopathies: from arrhythmias to autism, bipolar disorder, and immunodeficiency
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A Mutation in a Skin-Specific Isoform of SMARCAD1 Causes Autosomal-Dominant Adermatoglyphia
inferredcites →https://doi.org/10.1016/j.biocel.2017.07.013openalex-snapshot
The role of alternative splicing coupled to nonsense-mediated mRNA decay in human disease
inferredcites →https://doi.org/10.1016/j.cell.2004.09.011openalex-snapshot
CaV1.2 Calcium Channel Dysfunction Causes a Multisystem Disorder Including Arrhythmia and Autism
inferredcites →https://doi.org/10.1016/j.cub.2008.04.074openalex-snapshot
Natural Selection on Genes that Underlie Human Disease Susceptibility
inferredcites →https://doi.org/10.1016/j.tibs.2016.08.008openalex-snapshot
Alternative Splicing May Not Be the Key to Proteome Complexity
inferredcites →https://doi.org/10.1016/j.tibs.2017.04.001openalex-snapshot
The Relationship between Alternative Splicing and Proteomic Complexity
inferredcites →https://doi.org/10.1016/s0140-6736(12)61480-9openalex-snapshot
Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/emm.2013.32openalex-snapshot
Pitt–Hopkins Syndrome: intellectual disability due to loss of TCF4-regulated gene transcription
inferredcites →https://doi.org/10.1038/gim.2012.112openalex-snapshot
An informatics approach to analyzing the incidentalome
inferredcites →https://doi.org/10.1038/nature13127openalex-snapshot
Guidelines for investigating causality of sequence variants in human disease
inferredcites →https://doi.org/10.1038/nature19057openalex-snapshot
Analysis of protein-coding genetic variation in 60,706 humans
inferredcites →https://doi.org/10.1038/nature21062openalex-snapshot
Prevalence and architecture of de novo mutations in developmental disorders
inferredcites →https://doi.org/10.1038/nature24277openalex-snapshot
Genetic effects on gene expression across human tissues
inferredcites →https://doi.org/10.1038/nbt.3519openalex-snapshot
Near-optimal probabilistic RNA-seq quantification
inferredcites →https://doi.org/10.1038/ncomms10370openalex-snapshot
Arrhythmogenesis in Timothy Syndrome is associated with defects in Ca2+-dependent inactivation
inferredcites →https://doi.org/10.1038/ng.3970openalex-snapshot
Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands
inferredcites →https://doi.org/10.1038/nmeth.4197openalex-snapshot
Salmon provides fast and bias-aware quantification of transcript expression
inferredcites →https://doi.org/10.1038/nn.4352openalex-snapshot
Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability
inferredcites →https://doi.org/10.1038/nrg3455openalex-snapshot
Sequencing studies in human genetics: design and interpretation
inferredcites →https://doi.org/10.1038/s41467-017-01261-5openalex-snapshot
Functional mapping and annotation of genetic associations with FUMA
inferredcites →https://doi.org/10.1038/s41586-020-2267-zopenalex-snapshot
Evaluating drug targets through human loss-of-function genetic variation
inferredcites →https://doi.org/10.1056/nejmoa1206524openalex-snapshot
Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability
inferredcites →https://doi.org/10.1073/pnas.0502506102openalex-snapshot
Severe arrhythmia disorder caused by cardiac L-type calcium channel mutations
inferredcites →https://doi.org/10.1093/bib/bbs017openalex-snapshot
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
inferredcites →https://doi.org/10.1093/bioinformatics/btr209openalex-snapshot
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
inferredcites →https://doi.org/10.1093/bioinformatics/bts196openalex-snapshot
RNA-SeQC: RNA-seq metrics for quality control and process optimization
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/biomet/31.3-4.313openalex-snapshot
HOMOGENEITY OF RESULTS IN TESTING SAMPLES FROM POISSON SERIES
inferredcites →https://doi.org/10.1093/nar/27.1.29openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/gkq1018openalex-snapshot
Reactome: a database of reactions, pathways and biological processes
inferredcites →https://doi.org/10.1093/nar/gkx1153openalex-snapshot
ClinVar: improving access to variant interpretations and supporting evidence
inferredcites →https://doi.org/10.1093/nar/gky955openalex-snapshot
GENCODE reference annotation for the human and mouse genomes
inferredcites →https://doi.org/10.1101/277707openalex-snapshot
ASD and ADHD have a similar burden of rare protein-truncating variants
inferredcites →https://doi.org/10.1101/531210openalex-snapshot
The mutational constraint spectrum quantified from variation in 141,456 humans
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.229102openalex-snapshot
The Human Genome Browser at UCSC
inferredcites →https://doi.org/10.1126/science.1215040openalex-snapshot
A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
inferredcites →https://doi.org/10.1126/scitranslmed.3010134openalex-snapshot
Integrated allelic, transcriptional, and phenomic dissection of the cardiac effects of titin truncations in health and disease
inferredcites →https://doi.org/10.1136/jmedgenet-2012-101313openalex-snapshot
TBC1D24 truncating mutation resulting in severe neurodegeneration
inferredcites →https://doi.org/10.1186/1471-2105-12-290openalex-snapshot
Bias detection and correction in RNA-Sequencing data
inferredcites →https://doi.org/10.1186/1471-2105-12-323openalex-snapshot
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
inferredcites →https://doi.org/10.1186/s13059-016-0940-1openalex-snapshot
A benchmark for RNA-seq quantification pipelines
inferredcites →https://doi.org/10.1186/s13059-016-0974-4openalex-snapshot
The Ensembl Variant Effect Predictor
inferredcites →https://doi.org/10.1371/journal.pgen.1004772openalex-snapshot
De Novo Mutations in Moderate or Severe Intellectual Disability
inferredcites →https://doi.org/10.3389/fnana.2016.00086openalex-snapshot
HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s00439-022-02509-xopenalex-snapshot
Targeting de novo loss-of-function variants in constrained disease genes improves diagnostic rates in the 100,000 Genomes Project
inferred← citeshttps://doi.org/10.1007/s11825-019-0241-7openalex-snapshot
Molecular diagnostics of Mendelian disorders via combined DNA and RNA sequencing
inferred← citeshttps://doi.org/10.1016/j.ejmg.2022.104531openalex-snapshot
Defining causal variants in rare epilepsies: an essential team effort between biomedical scientists, geneticists and epileptologists
inferred← citeshttps://doi.org/10.1016/j.tig.2020.08.009openalex-snapshot
Where Are the Disease-Associated eQTLs?
inferred← citeshttps://doi.org/10.1038/s41467-020-14284-2openalex-snapshot
Human and mouse essentiality screens as a resource for disease gene discovery
inferred← citeshttps://doi.org/10.1038/s41467-021-23556-4openalex-snapshot
Determinants of penetrance and variable expressivity in monogenic metabolic conditions across 77,184 exomes
inferred← citeshttps://doi.org/10.1038/s41591-020-0893-5openalex-snapshot
The effect of LRRK2 loss-of-function variants in humans
inferred← citeshttps://doi.org/10.1038/s41598-020-58179-0openalex-snapshot
Depicting the genetic architecture of pediatric cancers through an integrative gene network approach
inferred← citeshttps://doi.org/10.1038/s41598-021-95321-yopenalex-snapshot
“Guilt by association” is not competitive with genetic association for identifying autism risk genes
inferred← citeshttps://doi.org/10.1093/bfgp/elaa009openalex-snapshot
Challenges in the diagnosis and discovery of rare genetic disorders using contemporary sequencing technologies
inferred← citeshttps://doi.org/10.1093/neuonc/noz108openalex-snapshot
Germline genetic landscape of pediatric central nervous system tumors
inferred← citeshttps://doi.org/10.1101/2020.02.15.936351openalex-snapshot
Promoter CpG density predicts downstream gene loss-of-function intolerance
inferred← citeshttps://doi.org/10.1101/2020.11.26.394676openalex-snapshot
Can machine learning aid in identifying disease genes? The case of autism spectrum disorder
inferred← citeshttps://doi.org/10.1101/2023.01.31.23285025openalex-snapshot
A panel-agnostic strategy ‘HiPPo’ improves diagnostic efficiency in the UK Genome Medicine Service
inferred← citeshttps://doi.org/10.1101/531210openalex-snapshot
The mutational constraint spectrum quantified from variation in 141,456 humans
inferred← citeshttps://doi.org/10.21542/gcsp.2020.13openalex-snapshot
The role of genomics and genetics in pulmonary arterial hypertension
inferred← citeshttps://doi.org/10.3390/healthcare11243179openalex-snapshot
A Panel-Agnostic Strategy ‘HiPPo’ Improves Diagnostic Efficiency in the UK Genomic Medicine Service
inferred← citeshttps://doi.org/10.70675/c9668778z4218z4692z908fz449455de3a1eopenalex-snapshot
Integration de multiples approches omiques pour ameliorer la prise en charge des patients atteints de cancer pediatrique
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