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A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability
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A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability
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Journal Article
A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability
2024
Overview
GC-rich tandem repeat expansions (TREs) are often associated with DNA methylation, gene silencing and folate-sensitive fragile sites, and underlie several congenital and late-onset disorders. Through a combination of DNA-methylation profiling and tandem repeat genotyping, we identified 24 methylated TREs and investigated their effects on human traits using phenome-wide association studies in 168,641 individuals from the UK Biobank, identifying 156 significant TRE–trait associations involving 17 different TREs. Of these, a GCC expansion in the promoter of
AFF3
was associated with a 2.4-fold reduced probability of completing secondary education, an effect size comparable to several recurrent pathogenic microdeletions. In a cohort of 6,371 probands with neurodevelopmental problems of suspected genetic etiology, we observed a significant enrichment of
AFF3
expansions compared with controls. With a population prevalence that is at least fivefold higher than the TRE that causes fragile X syndrome,
AFF3
expansions represent a major cause of neurodevelopmental delay.
Phenome-wide analysis in the UK Biobank identifies GC-rich tandem repeat expansions associated with a range of traits, including a GCC expansion in
AFF3
contributing to intellectual disability.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
/ 45/23
/ 45/43
/ 45/61
/ 45/91
/ Animal Genetics and Genomics
/ Ataxia
/ Biobanks
/ Biomedical and Life Sciences
/ DNA
/ DNA Repeat Expansion - genetics
/ Female
/ Genome-Wide Association Study
/ Genomes
/ Humans
/ Intellectual Disability - genetics
/ Male
/ Mutation
