Whole-genome sequencing and mutational analysis of human cord-blood derived stem and progenitor cells

Axel Rosendahl Huber; Anaïs J C N van Leeuwen; Flavia Peci; Jurrian K de Kanter; Eline J M Bertrums; Ruben van Boxtel

doi:10.1016/j.xpro.2022.101361

Whole-genome sequencing and mutational analysis of human cord-blood derived stem and progenitor cells

STAR Protoc. 2022 May 6;3(2):101361. doi: 10.1016/j.xpro.2022.101361. eCollection 2022 Jun 17.

Authors

Axel Rosendahl Huber¹, Anaïs J C N van Leeuwen¹, Flavia Peci¹, Jurrian K de Kanter¹, Eline J M Bertrums^{1

2}, Ruben van Boxtel¹

Affiliations

¹ Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands.
² Department of Pediatric Oncology, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands.

Abstract

Mutational signatures have been identified in cancer genomes, providing information about the causes of cancer and treatment vulnerabilities. This protocol describes an assay to determine the genotoxic mechanisms underlying these signatures using cord-blood derived hematopoietic stem and progenitor cells (CB-HSPCs). CB-HSPCs have a low mutation background, enabling sensitive detection of mutations. First, CB-HSPCs are exposed in vitro, sorted, and clonally expanded. This expansion enables whole-genome sequencing to detect the mutation load and respective patterns induced during genotoxic exposure. For complete details on the use and execution of this protocol, please refer to de Kanter et al. (2021).

Keywords: Bioinformatics; Cancer; Cell isolation; Flow Cytometry/Mass Cytometry; Genomics; Molecular Biology; Sequence analysis; Sequencing; Single Cell; Stem Cells.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Damage
Fetal Blood*
Genome
Hematopoietic Stem Cells*
Humans
Whole Genome Sequencing