Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation

Cell Stem Cell. 2022 Mar 3;29(3):472-486.e7. doi: 10.1016/j.stem.2022.01.011. Epub 2022 Feb 16.

Abstract

Despite their widespread use in research, there has not yet been a systematic genomic analysis of human embryonic stem cell (hESC) lines at a single-nucleotide resolution. We therefore performed whole-genome sequencing (WGS) of 143 hESC lines and annotated their single-nucleotide and structural genetic variants. We found that while a substantial fraction of hESC lines contained large deleterious structural variants, finer-scale structural and single-nucleotide variants (SNVs) that are ascertainable only through WGS analyses were present in hESC genomes and human blood-derived genomes at similar frequencies. Moreover, WGS allowed us to identify SNVs associated with cancer and other diseases that could alter cellular phenotypes and compromise the safety of hESC-derived cellular products transplanted into humans. As a resource to enable reproducible hESC research and safer translation, we provide a user-friendly WGS data portal and a data-driven scheme for cell line maintenance and selection.

Keywords: embryonic stem cell; genetic variant; genomics; pluripotent; rational selection; resource; whole-genome sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genetic Variation
  • Genome, Human / genetics
  • Human Embryonic Stem Cells*
  • Humans
  • Nucleotides
  • Whole Genome Sequencing

Substances

  • Nucleotides