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Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans

https://doi.org/10.1101/714477
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What this work says

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

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Craniofacial abnormalities and developmental delay in two families with overlapping 22q12.1 microdeletions involving the MN1 gene
inferredcites →https://doi.org/10.1002/cphg.59openalex-snapshot
PLINK: Key Functions for Data Analysis
inferredcites →https://doi.org/10.1002/em.21943openalex-snapshot
Structural variation mutagenesis of the human genome: Impact on disease and evolution
inferredcites →https://doi.org/10.1007/978-1-4939-0512-6_3openalex-snapshot
edgeR for Differential RNA-seq and ChIP-seq Analysis: An Application to Stem Cell Biology
inferredcites →https://doi.org/10.1016/b978-0-12-802395-2.00027-4openalex-snapshot
Trinucleotide repeat disorders
inferredcites →https://doi.org/10.1016/j.cell.2012.02.039openalex-snapshot
CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics
inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
inferredcites →https://doi.org/10.1016/j.cell.2015.07.024openalex-snapshot
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
inferredcites →https://doi.org/10.1016/j.cell.2018.08.005openalex-snapshot
Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries
inferredcites →https://doi.org/10.1016/j.neuron.2013.02.022openalex-snapshot
The Unstable Repeats—Three Evolving Faces of Neurological Disease
inferredcites →https://doi.org/10.1016/j.stem.2016.11.005openalex-snapshot
Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity
inferredcites →https://doi.org/10.1016/j.stem.2017.03.009openalex-snapshot
Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells
inferredcites →https://doi.org/10.1016/j.stem.2017.03.017openalex-snapshot
Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated Loci
inferredcites →https://doi.org/10.1016/j.stemcr.2017.03.012openalex-snapshot
iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types
inferredcites →https://doi.org/10.1038/nature05977openalex-snapshot
Expandable DNA repeats and human disease
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/nature19057openalex-snapshot
Analysis of protein-coding genetic variation in 60,706 humans
inferredcites →https://doi.org/10.1038/nature22403openalex-snapshot
Common genetic variation drives molecular heterogeneity in human iPSCs
inferredcites →https://doi.org/10.1038/nature24267openalex-snapshot
The impact of rare variation on gene expression across tissues
inferredcites →https://doi.org/10.1038/ng.3200openalex-snapshot
Large multiallelic copy number variations in humans
inferredcites →https://doi.org/10.1038/ng.3461openalex-snapshot
Abundant contribution of short tandem repeats to gene expression variation in humans
inferredcites →https://doi.org/10.1038/ng.3638openalex-snapshot
Patterns of genic intolerance of rare copy number variation in 59,898 human exomes
inferredcites →https://doi.org/10.1038/ng.3834openalex-snapshot
The impact of structural variation on human gene expression
inferredcites →https://doi.org/10.1038/nmeth.3505openalex-snapshot
SpeedSeq: ultra-fast personal genome analysis and interpretation
inferredcites →https://doi.org/10.1038/nmeth.4267openalex-snapshot
Genome-wide profiling of heritable and de novo STR variations
inferredcites →https://doi.org/10.1038/nrg3461openalex-snapshot
Pleiotropy in complex traits: challenges and strategies
inferredcites →https://doi.org/10.1038/s41467-019-08940-5openalex-snapshot
Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression
inferredcites →https://doi.org/10.1073/pnas.1530509100openalex-snapshot
Statistical significance for genomewide studies
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btv722openalex-snapshot
Fast and efficient QTL mapper for thousands of molecular phenotypes
inferredcites →https://doi.org/10.1093/hmg/ddv033openalex-snapshot
Mosaic structural variation in children with developmental disorders
inferredcites →https://doi.org/10.1093/nar/gkt1196openalex-snapshot
Ensembl 2014
inferredcites →https://doi.org/10.1093/nar/gkt857openalex-snapshot
Higher-order chromatin domains link eQTLs with the expression of far-away genes
inferredcites →https://doi.org/10.1093/nar/gkw928openalex-snapshot
The human-induced pluripotent stem cell initiative—data resources for cellular genetics
inferredcites →https://doi.org/10.1093/nar/gkw971openalex-snapshot
The ExAC browser: displaying reference data information from over 60 000 exomes
inferredcites →https://doi.org/10.1101/003905openalex-snapshot
LIMIX: genetic analysis of multiple traits
inferredcites →https://doi.org/10.1101/713198openalex-snapshot
Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.122614.111openalex-snapshot
Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions
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.185272.114openalex-snapshot
The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
inferredcites →https://doi.org/10.1101/gr.218032.116openalex-snapshot
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
inferredcites →https://doi.org/10.1101/gr.224436.117openalex-snapshot
Impact of regulatory variation across human iPSCs and differentiated cells
inferredcites →https://doi.org/10.1126/science.aan2261openalex-snapshot
Paternally inherited cis-regulatory structural variants are associated with autism
inferredcites →https://doi.org/10.1136/jmedgenet-2014-102582openalex-snapshot
De novo and rare inherited mutations implicate the transcriptional coregulator TCF20/SPBP in autism spectrum disorder
inferredcites →https://doi.org/10.1186/gb-2014-15-6-r84openalex-snapshot
LUMPY: a probabilistic framework for structural variant discovery
inferredcites →https://doi.org/10.1371/journal.pone.0049475openalex-snapshot
Characteristics and Predictive Value of Blood Transcriptome Signature in Males with Autism Spectrum Disorders
inferredcites →https://doi.org/10.7554/elife.34110openalex-snapshot
A novel source of arterial valve cells linked to bicuspid aortic valve without raphe in mice
inferredcites →https://doi.org/10.7554/elife.35788openalex-snapshot
A promoter interaction map for cardiovascular disease genetics

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41588-021-00800-7openalex-snapshot
Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics
inferred← citeshttps://doi.org/10.1101/713198openalex-snapshot
Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats
inferred← citeshttps://doi.org/10.7554/elife.48476openalex-snapshot
Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease
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