Functional annotation of rare structural variation in the human brain.

Nature Communications
Lide HanDouglas Ruderfer

Abstract

Structural variants (SVs) contribute to many disorders, yet, functionally annotating them remains a major challenge. Here, we integrate SVs with RNA-sequencing from human post-mortem brains to quantify their dosage and regulatory effects. We show that genic and regulatory SVs exist at significantly lower frequencies than intergenic SVs. Functional impact of copy number variants (CNVs) stems from both the proportion of genic and regulatory content altered and loss-of-function intolerance of the gene. We train a linear model to predict expression effects of rare CNVs and use it to annotate regulatory disruption of CNVs from 14,891 independent genome-sequenced individuals. Pathogenic deletions implicated in neurodevelopmental disorders show significantly more extreme regulatory disruption scores and if rank ordered would be prioritized higher than using frequency or length alone. This work shows the deleteriousness of regulatory SVs, particularly those altering CTCF sites and provides a simple approach for functionally annotating the regulatory consequences of CNVs.

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Citations

Sep 26, 2020·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Eva D'haene, Sarah Vergult
Oct 7, 2020·International Journal of Molecular Sciences·Ashley HallKimberley J Billingsley
May 22, 2021·Nucleic Acids Research·Francisco RequenaAntonio Rausell

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Methods Mentioned

BETA
exome-sequencing
RNAseq
PCR
RNA-seq
ChIP-seq

Software Mentioned

Manta
PsychENCODE
Plink
bioconductor
CNVnator
Roadmap Epigenomics
Fragment analyzer
Picard
DELLY
GenomeSTRiP

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