Phasing DNA Methylation

Vahid Akbari; Steven J M Jones

doi:10.1007/978-1-0716-2819-5_14

Phasing DNA Methylation

Methods Mol Biol. 2023:2590:219-235. doi: 10.1007/978-1-0716-2819-5_14.

Authors

Vahid Akbari^{1

2}, Steven J M Jones^{3

4}

Affiliations

¹ Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
² Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
³ Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada. sjones@bcgsc.ca.
⁴ Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. sjones@bcgsc.ca.

PMID: 36335502
DOI: 10.1007/978-1-0716-2819-5_14

Abstract

Haplotyping enables the study of allele-specific events. Heterozygous variants, primarily single nucleotide variants (SNVs), enable the assignment of the paternal and maternal origin of the chromosomes and are widely employed to phase sequencing reads to their haplotype of origin. Certain long-read technologies enable the detection of both the DNA sequence and DNA modifications. These long reads and their inherent methylation information are suitable for genome-wide haplotyping and allele-specific DNA methylation analysis. Here, we describe the workflow to phase reads and DNA methylation using nanopore sequencing.

Keywords: Allele-specific methylation; DNA methylation; Haplotyping; Long read; Phasing.

MeSH terms

Alleles
DNA Methylation*
Genome, Human
Haplotypes / genetics
High-Throughput Nucleotide Sequencing*
Humans
Sequence Analysis, DNA