Optical genome mapping identifies clinically relevant genomic rearrangements in prostate cancer biopsy sample

Yeeun Shim, Jongsoo Lee, Jieun Seo, Cheol Keun Park, Saeam Shin, Hyunho Han, Seung Tae Lee, Jong Rak Choi, Byung Ha Chung, Young Deuk Choi

Research output: Contribution to journalArticlepeer-review


Background: Prostate cancer (PCa) is characterized by complex genomic rearrangements such as the ETS oncogene family fusions, yet the clinical relevance is not well established. While paneled genetic tests of DNA repair genes are recommended in advanced PCa, conventional genomic or cytogenetic tools are not ideal for genome-wide screening of structural variations (SVs) such as balanced translocation due to cost and/or resolution issues. Methods: In this study, we tested the feasibility of whole-genome optical genomic mapping (OGM), a newly developed platform for genome-wide SV analysis to detect complex genomic rearrangements in consecutive unselected PCa samples from MRI/US-fusion targeted biopsy. Results: We tested ten samples, and nine (90%) passed quality check. Average mapping rate and coverage depth were 58.1 ± 23.7% and 157.3 ± 97.7×, respectively (mean ± SD). OGM detected copy number alterations such as chr6q13 loss and chr8q12-24 gain. Two adjacent tumor samples were distinguished by inter/intra-chromosomal translocations, revealing that they’re from the same ancestor. Furthermore, OGM detected large deletion of chr13q13.1 accompanied by inter-chromosomal translocation t(13;20)(q13.1;p13) occurring within BRCA2 gene, suggesting complete loss of function. Conclusion: In conclusion, clinically relevant genomic SVs were successfully detected in PCa samples by OGM. We suggest that OGM can complement panel sequencing of DNA repair genes BRCA1/2 or ATM in high-risk PCa.

Original languageEnglish
Article number306
JournalCancer Cell International
Issue number1
Publication statusPublished - 2022 Dec

Bibliographical note

Funding Information:
This study was supported by research grants from Gangnam Severance Hospital Prostate Cancer Center Research Committee (DI00560) and National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2022R1A2C3005586).

Publisher Copyright:
© 2022, The Author(s).

All Science Journal Classification (ASJC) codes

  • Oncology
  • Genetics
  • Cancer Research


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