Revolutionizing Detection of Minimal Residual Disease in Breast Cancer Using Patient-Derived Gene Signature
Round 1
Reviewer 1 Report
Comments and Suggestions for Authors
Revolutionizing Detection of Minimal Residual Disease in Breast Cancer Using Patient-Derived Gene Signature
Suggestion: major
- Please provide details of the company/commercial repository from where the samples were purchased.
- Please provide the following information in the form of a table – number of patient samples acquired commercially, no. of males, females, their ages, what treatments were these patients on at the time the sample was collected from them. You have provided some of these details for section 2.6, but please provide these for all the sample and no just those that were used for the proof-of-concept clinical study.
- Biomarker 1-11 in Figure 1 – what are these? These remain undefined in the manuscript. Please provide details of the same. Table 1 has 7 biomarkers, but it doesn’t say which one is which.
- Discussion - If I understand correctly, you used blood samples and tissues that was commercially available. That doesn’t make the method non-invasive. Please correct this sentence.
- Please reflect on your study and outline the limitations of your work and how this may be extended into future perspectives.
Author Response
Reviewer #1
Suggestion: major
1. Please provide details of the company/commercial repository from where the samples were purchased.
Reply: The authors have added the purchase information in section 2.1. as highlighted in GREEN (page 3).
2. Please provide the following information in the form of a table – number of patient samples acquired commercially, no. of males, females, their ages, what treatments were these patients on at the time the sample was collected from them. You have provided some of these details for section 2.6, but please provide these for all the sample and no just those that were used for the proof-of-concept clinical study.
Reply: The samples used for biomarker discovery have been reported previously. The authors have included the following 4 publications in references.
- Yeh C, Lin S-T, Lai H-C. A transformative technology linking patient’s mRNA expression profile to anticancer drug efficacy. Onco 2024; 4(3):143-162. https://doi.org/10.3390/onco4030012
- Lin S-T, Lai H-C, Yeh C. Single-tube two-pronged approach using both cell-free DNA and RNA for multimodal biomarker tests at the time of biopsy. Precision Medical Sciences. 2023; 12(4): 233-241. doi:10.1002/prm2.12115
- Yeh C. Circulating cell-free transcriptomics in cancer. J Lung Pulm Respir Res. 2023;10(2):27-29. DOI: 10.15406/jlprr.2023.10.00297
- Lin, Shu-Ti and Chun Hung Yip. Harnessing the Power of CpG Methylation Biomarkers for Early Cancer Detection. J Mol Genet Med 16 (2022): 537.
3. Biomarker 1-11 in Figure 1 – what are these? These remain undefined in the manuscript. Please provide details of the same. Table 1 has 7 biomarkers, but it doesn’t say which one is which.
Reply: The biomarker composition information are strictly confidential and proprietary, the authors cannot disclose.
4. Discussion - If I understand correctly, you used blood samples and tissues that was commercially available. That doesn’t make the method non-invasive. Please correct this sentence.
Reply: The authors applied matched tissue and blood samples as a part of validation studies to demonstrate that the selected OncoMRD BREAST biomarkers behave concordantly in tissue and blood, therefore they can be used faithfully to serve as the surrogate markers for tumor tissues. Most importantly, our OncoMRD BREAST assay is blood-based and tumor-agnostic, capable of longitudinally monitoring treatment efficacy, prognosis and recurrence risk.
5. Please reflect on your study and outline the limitations of your work and how this may be extended into future perspectives.
Reply: The authors have corresponding content to address the reviewer’s comment in the last paragragh of section 5 as highlighted in GREEN (page 20).
Reviewer 2 Report
Comments and Suggestions for Authors
- Add mention of quantitive measure of performance e.g. improved sensitivity of OncoMRD BREAST by X% compared to ctDNA in abstract.
- Include a paragraph comparing cfmRNA to other liquid biopsy analyte (e.g. CTCs, exosomes). 3. Explain how OncoMRD BREAST deals with a problem of tumor activity in a better way than the DNA-based assays.
- Include a table that compares MRD technologies (ctDNA, cfmRNA, CTCs) on the basis of sensitivity, cost and clinical utility.
- Explore the limitations of tumor-informed approaches compared to the tumor-agnostic ones.
- Defend on the power.
- Provide a sensitivity/specificity comparison with ctDNA analysis (e.g. ROC).
- Include a table with major findings (e.g. concordance rates with PET/CT).
- Provide a discussion of false positive reasons.
- OncoMRD BREAST comparisons to business assays
- Better label figures and statistical reporting.
Author Response
Reviewer #2
1. Add mention of quantitive measure of performance e.g. improved sensitivity of OncoMRD BREAST by X% compared to ctDNA in abstract.
Reply: The current study focused on biomarker development, validation and proof-of-concept of the OncoMRD BREAST assay. Comparison with standard-of-care and other ctDNA MRD tests will be our next endeavor which would need a larger prospective clinical study to establish test sensitivity and specificity.
2. Include a paragraph comparing cfmRNA to other liquid biopsy analyte (e.g. CTCs, exosomes).
Reply: The authors have compared different liquid biopsy MRD biomarkers in the first 3 paragraghs of section 4 as highlighted in BLUE (page 16).
3. Explain how OncoMRD BREAST deals with a problem of tumor activity in a better way than the DNA-based assays.
Reply: The authors have elaborated the potential of OncoMRD BREAST as a measurement of tumor activities in section 4 as highlighted in BLUE (page 19).
4. Include a table that compares MRD technologies (ctDNA, cfmRNA, CTCs) on the basis of sensitivity, cost and clinical utility.
Reply: The authors have completed and added a table as Table 3 in page 17.
5. Explore the limitations of tumor-informed approaches compared to the tumor-agnostic ones. Defend on the power.
Reply: The authors have added the content to explore limitations of tumor-informed and tumor-agnostic MRD approaches in section 4 as highlighted in BLUE (page 17).
6. Provide a sensitivity/specificity comparison with ctDNA analysis (e.g. ROC).
Reply: The current study focused on biomarker development, validation and proof-of-concept of the OncoMRD BREAST assay. Comparison with standard-of-care and other ctDNA MRD tests will be our next endeavor which would need a larger prospective clinical study to establish test sensitivity and specificity.
7. Include a table with major findings (e.g. concordance rates with PET/CT).
Reply: Due to the radiation exposure complications, generally, for surveillance after treatment, intervals of 3-6 months between PET/CT scans are common. Therefore, the data points of PET/CT in this study are small and not enough for statistical analysis. Nevertheless, the authors have added a paragraph to state our major findings of concordance in the section 3.7 at page 14.
8. Provide a discussion of false positive reasons.
Reply: The authors have added a discussion of false positivity in page 18 as highlighted in BLUE.
9. OncoMRD BREAST comparisons to business assays
Reply: The current study focused on biomarker development, validation and proof-of-concept of the OncoMRD BREAST assay. It is not the intention of this study to compare it with other commercial MRD testing. The authors believe that OncoMRD BREAST still needs a larger prospective clinical study before a head-to-head comparison with major ctDNA-based MRD tests.
10. Better label figures and statistical reporting.
Reply: The authors agreed and completed the request.
Round 2
Reviewer 1 Report
Comments and Suggestions for Authors
The authors have justified the queries raised.
I would still urge the authors to prepare he table - to make it easier for their readers to see the information rather than refer to the 4 cited papers again and again. This would also enhance the strength of the manuscript.
Author Response
The authors respected the point of view from the reviewer #1. However, the authors believe that it is the rule of thumb for any publication to reduce redundancy, to avoid re-publishing already published data! That is the reason we cited references.
We believe this is the right and best way that people publish new findings and cite previous published data as references. Most importantly, this is the current gold-standard SOP that everyone is following. Actually, this is how "Scientific Impact Factor" is generated!
Reviewer 2 Report
Comments and Suggestions for Authors
I have no more comments
Author Response
The authors are grateful that the reviewer #2 has accepted our revised manuscript.
