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

被引:9
|
作者
Shim, Yeeun [1 ]
Lee, Jongsoo [2 ]
Seo, Jieun [3 ]
Park, Cheol Keun [4 ,5 ]
Shin, Saeam [6 ]
Han, Hyunho [2 ]
Lee, Seung-Tae [6 ,7 ]
Choi, Jong Rak [6 ,7 ]
Ha Chung, Byung [2 ]
Choi, Young Deuk [2 ]
机构
[1] Yonsei Univ, Grad Sch Med Sci, Dept Lab Med, Brain Korea 21 Project,Coll Med, Seoul, South Korea
[2] Yonsei Univ, Urol Sci Inst, Dept Urol, Coll Med, Seoul, South Korea
[3] Washington Univ, Dept Genet, Sch Med, St Louis, MO 63110 USA
[4] Yonsei Univ, Dept Pathol, Coll Med, Seoul, South Korea
[5] Seegene Med Fdn, Pathol Ctr, Seoul, South Korea
[6] Yonsei Univ, Dept Lab Med, Coll Med, Seoul, South Korea
[7] Dxome Seongnam Daero 331 Beon Gil, Seongnam Si, Gyeonggi Do, South Korea
基金
新加坡国家研究基金会;
关键词
Prostate cancer; Optical genome mapping; Structural variation; Genomic rearrangement; BRCA2; BRCA2;
D O I
10.1186/s12935-022-02728-2
中图分类号
R73 [肿瘤学];
学科分类号
100214 ;
摘要
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 +/- 97.7x, 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.
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页数:8
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