Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA.

Creator(s)

Cristian Groza
Bing Ge
Warren A. Cheung, Children's Mercy HospitalFollow
Tomi Pastinen, Children's Mercy HospitalFollow
Guillaume Bourque

Document Type

Article

Publication Date

4-14-2025

Identifier

DOI: 10.1101/gr.279240.124

Abstract

Structural variants (SVs) are omnipresent in human DNA, yet their genotype and methylation statuses are rarely characterized due to previous limitations in genome assembly and detection of modified nucleotides. Also, the extent to which SVs act as methylation quantitative trait loci (SV-mQTLs) is largely unknown. Here, we generated a pangenome graph summarizing SVs in 782 de novo assemblies obtained from Genomic Answers for Kids, capturing 14.6 million CpG dinucleotides that are absent from the CHM13v2 reference (SV-CpGs), thus expanding their number by 43.6%. Using 435 methylomes, we genotyped 4.06 million SV-CpGs, of which 3.93 million (96.8%) are methylated at least once. Nonrepeat sequences contribute 1.59 × 10⁶ novel SV-CpGs, followed by centromeric satellites (6.57 × 10⁵), simple repeats (5.40 × 10⁵), Alu elements (5.07 × 10⁵), satellites (2.17 × 10⁵), LINE-1s (1.83 × 10⁵), and SVA (SINE-VNTR-Alu) elements (1.50 × 10⁵). Centromeric satellites, simple repeats, and SVAs are overrepresented in SV-CpGs versus reference CpGs. Similarly, methylation levels in SV-CpGs are more variable than in reference CpGs. To explore if SVs are potentially causal for functional variation, we measured SV-mQTLs. This revealed over 230,464 methylation bins where the methylation is associated with common SVs within 100 kbp. Finally, we identified 65,659 methylation bins (28.5%) where the leading QTL variant is an SV. In conclusion, we demonstrate that graph pangenomes provide full SV structures, the associated methylation variation, and reveal tens of thousands of SV-mQTLs, underscoring the importance of assembly based analyses of human traits.

Journal Title

Genome research

Volume

35

Issue

4

First Page

644

Last Page

652

MeSH Keywords

Humans; Quantitative Trait Loci; DNA Methylation; CpG Islands; Genome, Human; Epigenome; Genomic Structural Variation

PubMed ID

40113263

Keywords

Humans; Quantitative Trait Loci; DNA Methylation; CpG Islands; Genome, Human; Epigenome; Genomic Structural Variation

Recommended Citation

Groza C, Ge B, Cheung WA, Pastinen T, Bourque G. Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA. Genome Res. 2025;35(4):644-652. Published 2025 Apr 14. doi:10.1101/gr.279240.124