Engineering large chromosomal deletions by CRISPR-Cas9

Study ID Alternative Stable ID Type
EGAS00001005134 Other

Study Description

Arm-level 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 arm-level deletions are limited. Here we present an effective technique to engineer arm-level 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 arm-level deletions on chromosome 11q (65 MB) and chromosome 6q (53 MB) in neuroblastoma cell lines. Such isogenic models enable further research on the role of arm-level deletions in tumor development and growth, and their possible therapeutic potential.

Study Datasets 1 dataset.

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Dataset ID Description Technology Samples
Shallow WGS of neuroblastoma cell lines with large-scale deletions induced through CRISPR-Cas9 and matching controls. Deletion of 11q was induced in the cell line SKNSH and loss of 6q was induced in the cell line NMB.
Illumina HiSeq 2000 13

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