Determining Complete Chromosomal Haplotypes by mLinker

Sumit Sinha; Cheng-Zhong Zhang

doi:10.1007/978-1-0716-2819-5_10

Determining Complete Chromosomal Haplotypes by mLinker

Methods Mol Biol. 2023:2590:149-159. doi: 10.1007/978-1-0716-2819-5_10.

Authors

Sumit Sinha^{1

2}, Cheng-Zhong Zhang^{3

4

5}

Affiliations

¹ Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA. ssinha@g.harvard.edu.
² School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA. ssinha@g.harvard.edu.
³ Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA. cheng-zhong_zhang@dfci.harvard.edu.
⁴ Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. cheng-zhong_zhang@dfci.harvard.edu.
⁵ Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. cheng-zhong_zhang@dfci.harvard.edu.

PMID: 36335498
DOI: 10.1007/978-1-0716-2819-5_10

Abstract

Haplotype ("haploid genotype") phase is the combination of genotypes at sites of genetic variation along a chromosome [1]. We previously demonstrated that the complete chromosomal haplotype of diploid human genomes can be determined using molecular linkage from Hi-C sequencing and linked-reads sequencing [2]. In this chapter, we present a step-by-step guide to perform this analysis using mLinker, a software package for haplotype inference.

Keywords: Haplotype phasing; Hi-C sequencing; Long-read sequencing.

MeSH terms

Algorithms*
Chromosomes
Genome, Human*
Genotype
Haplotypes / genetics
Humans
Polymorphism, Single Nucleotide
Sequence Analysis, DNA