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

Authors
 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 
Citation
 CANCER CELL INTERNATIONAL, Vol.22(1) : 306, 2022-10 
Journal Title
CANCER CELL INTERNATIONAL
Issue Date
2022-10
Keywords
BRCA2 ; Genomic rearrangement ; Optical genome mapping ; Prostate cancer ; Structural variation
Abstract
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.
Files in This Item:
T202204643.pdf Download
DOI
10.1186/s12935-022-02728-2
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Urology (비뇨의학교실) > 1. Journal Papers
Yonsei Authors
Park, Cheol Keun(박철근) ORCID logo https://orcid.org/0000-0001-7689-0386
Shin, Saeam(신새암) ORCID logo https://orcid.org/0000-0003-1501-3923
Lee, Seung-Tae(이승태) ORCID logo https://orcid.org/0000-0003-1047-1415
Lee, Jong Soo(이종수) ORCID logo https://orcid.org/0000-0002-9984-1138
Chung, Byung Ha(정병하) ORCID logo https://orcid.org/0000-0001-9817-3660
Choi, Young Deuk(최영득) ORCID logo https://orcid.org/0000-0002-8545-5797
Choi, Jong Rak(최종락) ORCID logo https://orcid.org/0000-0002-0608-2989
Han, Hyun Ho(한현호) ORCID logo https://orcid.org/0000-0002-6268-0860
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/192168
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