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SVFX: a machine-learning framework to quantify the pathogenicity of structural variants

https://doi.org/10.1101/739474
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What this work says

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

inferredcites →https://doi.org/10.1016/j.cell.2018.02.060openalex-snapshot
Comprehensive Characterization of Cancer Driver Genes and Mutations
inferredcites →https://doi.org/10.1016/j.semcdb.2009.10.007openalex-snapshot
Histone methyltransferases in cancer
inferredcites →https://doi.org/10.1016/s0006-291x(02)03069-3openalex-snapshot
Homozygous deletions and point mutations of the Rit1/Bcl11b gene in γ-ray induced mouse thymic lymphomas
inferredcites →https://doi.org/10.1038/bjc.1998.71openalex-snapshot
The ubiquitin-proteasome pathway in cancer
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
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/nature14248openalex-snapshot
Integrative analysis of 111 reference human epigenomes
inferredcites →https://doi.org/10.1038/nature15394openalex-snapshot
An integrated map of structural variation in 2,504 human genomes
inferredcites →https://doi.org/10.1038/ncomms8256openalex-snapshot
Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms
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.3722openalex-snapshot
Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking
inferredcites →https://doi.org/10.1038/nrg3373openalex-snapshot
Phenotypic impact of genomic structural variation: insights from and for human disease
inferredcites →https://doi.org/10.1038/s41467-018-08148-zopenalex-snapshot
Multi-platform discovery of haplotype-resolved structural variation in human genomes
inferredcites →https://doi.org/10.1038/s41576-018-0007-0openalex-snapshot
Structural variation in the 3D genome
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/10.1073/pnas.1808631116openalex-snapshot
Chromatin features constrain structural variation across evolutionary timescales
inferredcites →https://doi.org/10.1074/jbc.m110.203307openalex-snapshot
Histone Methyltransferase SETD3 Regulates Muscle Differentiation
inferredcites →https://doi.org/10.1074/jbc.m117.778001openalex-snapshot
Cell cycle-dependent degradation of the methyltransferase SETD3 attenuates cell proliferation and liver tumorigenesis
inferredcites →https://doi.org/10.1093/bioinformatics/btr357openalex-snapshot
CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer
inferredcites →https://doi.org/10.1093/bioinformatics/btw789openalex-snapshot
SVScore: an impact prediction tool for structural variation
inferredcites →https://doi.org/10.1093/nar/gkw927openalex-snapshot
Localized structural frustration for evaluating the impact of sequence variants
inferredcites →https://doi.org/10.1093/nar/gkz103openalex-snapshot
Chromatin organization modulates the origin of heritable structural variations in human genome
inferredcites →https://doi.org/10.1101/162784openalex-snapshot
Pan-cancer analysis of whole genomes
inferredcites →https://doi.org/10.1101/181339openalex-snapshot
Patterns of structural variation in human cancer
inferredcites →https://doi.org/10.1101/187609openalex-snapshot
Selective and mechanistic sources of recurrent rearrangements across the cancer genome
inferredcites →https://doi.org/10.1101/193144openalex-snapshot
Multi-platform discovery of haplotype-resolved structural variation in human genomes
inferredcites →https://doi.org/10.1101/508515openalex-snapshot
Mapping and characterization of structural variation in 17,795 deeply sequenced human genomes
inferredcites →https://doi.org/10.1101/578674openalex-snapshot
An open resource of structural variation for medical and population genetics
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.135350.111openalex-snapshot
GENCODE: The reference human genome annotation for The ENCODE Project
inferredcites →https://doi.org/10.1101/gr.221028.117openalex-snapshot
SvABA: genome-wide detection of structural variants and indels by local assembly
inferredcites →https://doi.org/10.1126/science.aan2261openalex-snapshot
Paternally inherited cis-regulatory structural variants are associated with autism
inferredcites →https://doi.org/10.1186/preaccept-1739683221127290openalex-snapshot
FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer
inferredcites →https://doi.org/10.1186/s13059-018-1519-9openalex-snapshot
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions
inferredcites →https://doi.org/10.1371/journal.pgen.1002692openalex-snapshot
Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome
inferredcites →https://doi.org/10.3324/haematol.2012.066977openalex-snapshot
The role of a newly identified SET domain-containing protein, SETD3, in oncogenesis
inferredcites →https://doi.org/10.3390/jcm5020026openalex-snapshot
Homeostatic Signaling by Cell–Cell Junctions and Its Dysregulation during Cancer Progression
inferredcites →https://doi.org/10.4049/jimmunol.1602054openalex-snapshot
Early B Cell Progenitors Deficient for GON4L Fail To Differentiate Due to a Block in Mitotic Cell Division

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.2021.12.007openalex-snapshot
StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants
inferred← citeshttps://doi.org/10.1016/j.cell.2020.01.032openalex-snapshot
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences
inferred← citeshttps://doi.org/10.1101/2021.07.10.451798openalex-snapshot
CADD-SV – a framework to score the effects of structural variants in health and disease
inferred← citeshttps://doi.org/10.1111/jgh.15500openalex-snapshot
Noninvasive early diagnosis of intestinal diseases based on artificial intelligence in genomics and microbiome
inferred← citeshttps://doi.org/10.1186/s13059-022-02631-zopenalex-snapshot
TADA—a machine learning tool for functional annotation-based prioritisation of pathogenic CNVs
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