Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs
MetadataShow full item record
AbstractVariable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. In this work, we solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We develop software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We use this to discover VNTRs with length stratified by continental population, and expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease. © 2021, The Author(s).
Rights/Terms© 2021. The Author(s).
Keywordrepeat-pangenome graph (RPGG)
variable-number tandem repeats
Identifier to cite or link to this itemhttp://hdl.handle.net/10713/16279
- Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression.
- Authors: Garg P, Martin-Trujillo A, Rodriguez OL, Gies SJ, Hadelia E, Jadhav B, Jain M, Paten B, Sharp AJ
- Issue date: 2021 May 6
- Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences.
- Authors: Eslami Rasekh M, Hernández Y, Drinan SD, Fuxman Bass JI, Benson G
- Issue date: 2021 May 7
- Genome-wide prediction of human VNTRs.
- Authors: Näslund K, Saetre P, von Salomé J, Bergström TF, Jareborg N, Jazin E
- Issue date: 2005 Jan
- Extreme enrichment of VNTR-associated polymorphicity in human subtelomeres: genes with most VNTRs are predominantly expressed in the brain.
- Authors: Linthorst J, Meert W, Hestand MS, Korlach J, Vermeesch JR, Reinders MJT, Holstege H
- Issue date: 2020 Nov 2
- Targeted genotyping of variable number tandem repeats with adVNTR.
- Authors: Bakhtiari M, Shleizer-Burko S, Gymrek M, Bansal V, Bafna V
- Issue date: 2018 Nov