Engineering large-scale chromosomal deletions by CRISPR-Cas9

Thomas F Eleveld, Chaimaa Bakali, Paul P Eijk, Phylicia Stathi, Lianne E Vriend, Pino J Poddighe, Bauke Ylstra

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)


Large-scale chromosomal deletions are a prevalent and defining feature of cancer. A high degree of tumor-type and subtype specific recurrencies suggest a selective oncogenic advantage. However, due to their large size it has been difficult to pinpoint the oncogenic drivers that confer this advantage. Suitable functional genomics approaches to study the oncogenic driving capacity of large-scale deletions are limited. Here, we present an effective technique to engineer large-scale deletions by CRISPR-Cas9 and create isogenic cell line models. We simultaneously induce double-strand breaks (DSBs) at two ends of a chromosomal arm and select the cells that have lost the intermittent region. Using this technique, we induced large-scale deletions on chromosome 11q (65 Mb) and chromosome 6q (53 Mb) in neuroblastoma cell lines. A high frequency of successful deletions (up to 30% of selected clones) and increased colony forming capacity in the 11q deleted lines suggest an oncogenic advantage of these deletions. Such isogenic models enable further research on the role of large-scale deletions in tumor development and growth, and their possible therapeutic potential.

Original languageEnglish
Pages (from-to)12007-12016
Number of pages10
JournalNucleic acids research
Issue number21
Publication statusPublished - 2 Dec 2021
Externally publishedYes


  • CRISPR-Cas Systems
  • Cell Line, Tumor
  • Chromosome Aberrations
  • Chromosome Deletion
  • DNA/metabolism
  • Humans
  • Neuroblastoma/genetics


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