Abstract

Background Cultured porcine cell lines are powerful tools for functional genomics and in vitro phenotypic testing of candidate causal variants. However, to be utilised for genomic or variant interrogation assays, the genome sequence and structure of cultured cell lines must be realised. In this work, we called variants and used read coverage in combination with within-sample allele frequency to detect potential aneuploidy in two immortalised porcine kidney epithelial (PK15) cell lines and in a pig embryonic fbroblast line. Results We compared two PK15 cultured cells samples: a new American Type Culture Collection (ATCC) sample and one that has been utilised and passaged within the laboratory for an extended period (>10 years). Read coverage and within-sample allele frequencies showed that several chromosomes are fully or partially aneuploid in both PK15 lines, including potential trisomy of chromosome 4 and tetrasomy of chromosome 17. The older PK15 line showed evidence of additional structural variation and potentially clonal variation. By comparison, the pig embryonic fbroblast line was free from the gross aneuploidies seen in the PK15s. Conclusions Our results show that the PK15 cell lines examined have aneuploidies and complex structural variants in their genomes. We propose that screening for aneuploidy should be considered for cell lines, and discuss implications for livestock genomics.

Keywords

Pig; Cell lines; PK15; Aneuploidy

Published in

BMC Genomics
2024, Volume: 25, article number: 49

SLU Authors

• Johnsson, Martin

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Genetics and Breeding
Animal and Dairy Science


Publication identifier

DOI: https://doi.org/10.1186/s12864-023-09931-z

Permanent link to this page (URI)

https://res.slu.se/id/publ/128839