The Impact of Liquid Biopsy in Advanced Ovarian Cancer Care
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Design and Patient Characteristics
2.2. Genomic DNA and cfDNA Isolation
2.3. Sequencing
2.4. Bioinformatic Analysis for Mutation Detection and Evaluation
2.5. Primer and Probe Design for ddPCR
- dHsaMDV2010105 for the TP53R175H mutation;
- dHsaMDV2010127 for the TP53R248Q mutation;
- dHsaMDV2510542 for the TP53G245D mutation;
- dHsaMDS99673883 for the BRCA1 E272*(stop) mutation;
- dHsaMDS544377207 for the TP53c.994C-1G mutation.
2.6. Droplet Digital PCR (ddPCR)
2.7. Statistical Analysis
3. Results
3.1. Overview
3.2. ctDNA Mutations and the Clinical Outcome
- (A)
- First patient with complete records. (Patient with clear disease progression on treatment)
- (B)
- Second patient with complete records. (Patient with clear disease progression on treatment)
- (C)
- Third patient with complete records. (Patient with stable disease monitoring)
- (D)
- Fourth patient with complete records. (Patient with evidence of relapse only in cfDNA, indicating changes in tumour cell subpopulations)
3.3. Correlations between Individualised ctDNA Mutations and Serum Biomarkers
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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PATIENT | Age | Sample Time Points | Study Length (Days) | Neo-adyuvance | FIGO | PCI | R Surgery | Relapse | Origin | Exitus | Mutation(s) Identified by NGS | Mutation-Specific ctDNA Detected by dPCR (Líquid Biopsy) | Verified in Tumor by dPCR (Tumor Tissue) | Further NGS-Identified Pathogenic Mutations | Further NGS-Identified Mutations Classified as VUS (Variant of Uncertain Significance) |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 61 | 5 | 538 | YES | IIIC | 30 | R1 | YES | Bulgarian | YES | TP53 C135Sfs*35 | ||||
2 | 42 | 5 | 391 | YES | IVA | 18 | R1 | YES | Spanish | YES | BRCA2 G2793V | ||||
3 | 61 | 6 | 882 | NO | IIIC2 | 2 | R0 | NO | Spanish | NO | |||||
4 | 72 | 5 | 401 | YES | IVB | 11 | YES | YES | TP53 P27L | ||||||
5 | 70 | 4 | 400 | YES | IIIA2 | 7 | R0 | YES | Spanish | NO | TP53 R175H | + | + | BRCA1 T688* | |
6 | 80 | 4 | 384 | YES | IIB | 23 | R0 | YES | Spanish | NO | |||||
7 | 70 | 3 | 301 | NO | IVB | 9 | R1 | NO | Spanish | NO | TP53 R175H BRCA1 E1210R | + | + | ||
8 | 60 | 6 | 997 | NO | IVB | 18 | R0 | YES | Spanish | NO | TP53 p.? | + | + | ||
9 | 63 | 4 | 357 | YES | IIIC | 12 | YES | YES | TP53 A86Hfs*37 BRCA2 K3326* | ||||||
10 | 53 | 9 | 933 | YES | IIIA2 | 16 | R0 | NO | Moroccan | NO | TP53 G245D | o | + | BRCA1 G1770V | |
11 | 51 | 7 | 812 | YES | IIIC | 21 | R0 | YES | Romanian | NO | BRCA1 E272* TP53 R248Q | + + | + + | ||
12 | 75 | 7 | 835 | YES | NA | 35 | R0 | YES | Spanish | NO | |||||
13 | 75 | 4 | 356 | NO | IIIC | 13 | R0 | YES | Spanish | NO | TP53 c.911_919+7delCTAAGCGAGGTAAGCA | ||||
14 | 51 | 4 | 532 | YES | IIIA | 22 | R0 | NO | Chinese | NO | TP53 Y220C | + | + | BRCA2 S611Yfs*5 | BRCA1 K654R |
15 | 53 | 4 | 365 | NO | IC | 10 | R0 | NO | Spanish | NO | BRCA1 Y655* C994* | ||||
16 | 74 | 7 | 314 | NO | IIIA | 17 | R0 | NO | Spanish | NO | TP53 R249S | + | + | TP53 R254S | |
17 | 64 | 5 | 288 | NO | IIIB | 7 | R0 | NO | Spanish | NO | |||||
18 | 59 | 5 | 300 | NO | IIIc | 12 | R0 | NO | Spanish | NO | TP53 C275F | ||||
19 | 63 | 5 | 280 | YES | IVa | 19 | R1 | YES | Spanish | NO | BRCA2c.8332-1G>A = p.? | BRCA2 G2270R E2832K S2984L BRCA1 E438K S186F | |||
20 | 72 | 4 | 360 | NO | IVa | 15 | R1 | NO | Spanish | NO | BRCA1 S1428* | ||||
21 | 70 | 5 | 420 | YES | IIIc | 20 | R0 | NO | Romanian | NO | TP53 Y236* | BRCA2 D1441N BRCA1 P1010S | |||
22 | 68 | 5 | 400 | YES | IIIc | 18 | R0 | YES | Moroccan | NO | TP53 H193R | BRCA2 A2851L |
Cycling Step | Temperature (°C) | Time (s) | Number of Cycles |
---|---|---|---|
Enzyme activation | 95 | 600 | 1 |
Denaturation | 94 | 30 | 40 |
Annealing/extension | 50–60 * (optimum) | 60 ** | 40 |
Enzyme deactivation | 98 | 600 | 1 |
Hold | 4 | Infinite | 1 |
Patient | Correlation between: | ||||
cfDNA-TP53 (R175H)ctDNA | cfDNA-CA125 | TP53 (R175H) ctDNA-CA125 | |||
5 | 0.53 (p = 0.09) | 0.88 (p < 0.001) | 0.73 (p = 0.011) | ||
Patient | Correlation between: | ||||
cfDNA-TP53 R248Q (c.743 G>A) ctDNA | cfDNA- BRCA1 E272* (c.814 G>T) ctDNA | cfDNA-CA125 | TP53 R248Q (c.743 G>A) ctDNA-CA125 | BRCA1 E272* (c.814 G>T) ctDNA-CA125 | |
11 | 0.58 (p = 0.001) | 0.59 (p = 0.001) | 0.87 (p < 0.01) | 0.43 (p = 0.02) | 0.52 (p = 0.005) |
Patient | Correlation between | ||||
cfDNA-TP53 G245 ctDNA | cfDNA-CA125 | TP53 G245 ctDNA-CA125 | |||
10 | 0.93 (p < 0.001) | 0.68 (p < 0.001) | 0.66 (p < 0.001) | ||
Patient | Correlation between | ||||
cfDNA-TP53 (c.994C-1G) ctDNA | cfDNA-CA125 | TP53 (c.994C-1G) ctDNA-CA125 | |||
8 | 0.59 (p = 0.05) | 0.61 (p = 0.04) | 0.71 (p = 0.01) |
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Llueca, A.; Canete-Mota, S.; Jaureguí, A.; Barneo, M.; Ibañez, M.V.; Neef, A.; Ochoa, E.; Tomas-Perez, S.; Mari-Alexandre, J.; Gilabert-Estelles, J.; et al. The Impact of Liquid Biopsy in Advanced Ovarian Cancer Care. Diagnostics 2024, 14, 1868. https://doi.org/10.3390/diagnostics14171868
Llueca A, Canete-Mota S, Jaureguí A, Barneo M, Ibañez MV, Neef A, Ochoa E, Tomas-Perez S, Mari-Alexandre J, Gilabert-Estelles J, et al. The Impact of Liquid Biopsy in Advanced Ovarian Cancer Care. Diagnostics. 2024; 14(17):1868. https://doi.org/10.3390/diagnostics14171868
Chicago/Turabian StyleLlueca, Antoni, Sarai Canete-Mota, Anna Jaureguí, Manuela Barneo, Maria Victoria Ibañez, Alexander Neef, Enrique Ochoa, Sarai Tomas-Perez, Josep Mari-Alexandre, Juan Gilabert-Estelles, and et al. 2024. "The Impact of Liquid Biopsy in Advanced Ovarian Cancer Care" Diagnostics 14, no. 17: 1868. https://doi.org/10.3390/diagnostics14171868
APA StyleLlueca, A., Canete-Mota, S., Jaureguí, A., Barneo, M., Ibañez, M. V., Neef, A., Ochoa, E., Tomas-Perez, S., Mari-Alexandre, J., Gilabert-Estelles, J., Serra, A., Climent, M. T., Bellido, C., Ruiz, N., Segarra-Vidal, B., & Llueca, M. (2024). The Impact of Liquid Biopsy in Advanced Ovarian Cancer Care. Diagnostics, 14(17), 1868. https://doi.org/10.3390/diagnostics14171868