Cell-Free DNA Methylation as Blood-Based Biomarkers for Pancreatic Adenocarcinoma—A Literature Update
Round 1
Reviewer 1 Report
Dear Authors,
This is a good review exploring potential biomarkers for pancreatic carcinoma based on cell free DNA methylation. I have some comments:
- It will be interesting to explain more in deep the relevance of the genes identified, their functions, and based on that, how they could contribute to the prognosis and diagnosis of the pancreatic carcinoma.
- In the prognosis section, you referred to your own articles, please, refer to them in third person, as it is more appropriate. Also, please, review the first paragraphs of this section, there is an incomplete sentence.
Thank you very much.
Author Response
Dear Editor.
Thank you for the useful comments.
Rebuttal letter - Reviewer 1
-It will be interesting to explain more in deep the relevance of the genes identified, their functions, and based on that, how they could contribute to the prognosis and diagnosis of the pancreatic carcinoma.
Answer: I agree with the reviewer, the function of all the genes analyzed is a very interesting aspect. However, I believe it will be to comprehensive to do a description of the gene function e.c. in this present article, as so many different genes are mentioned in the review. The function of the individual genes and the contribution to diagnosis and prognosis is often decribes very well in the original studies referred to.
-In the prognosis section, you referred to your own articles, please, refer to them in third person, as it is more appropriate.
Answer:
Correction has been made, please see;
Line 177-179- Subsequently, an external validation study of the diagnostic gene panel has been initiated, and in addition the additive effect of CA-19-9 was analyzed.
Line 211-212- Nevertheless, so far, the results from the validation study of the diagnostic gene panel developed by our group,...
Line 235-237- Similar to other studies, a study by our group demonstrated that hypermethylated cell-free DNA is detectable in all stages of PDAC[25], [35], [38]. Furthermore, the study discovered that...
Line 247- Another study by our group demonstrated that the number of....
Line 254-256- Cell-free DNA hypermethylation of seven individual genes ALX4, BNC1, HIC1 , SEPT9v2, SST, TFPI2, and TAC1 has been associated with distant metastasis in a study by our group[25].
Line 265-266- To enable differentiation of PDAC patients according to cancer stage two prediction models were developed by our group[25].
Line 275-276- Furthermore, the association between cell-free DNA hypermethylation and survival of PDAC patients was investigated by our group[38].
Line 285-286- Based on hypermethylated cell-free DNA prediction models for survival of patients with PDAC were developed[38],
Line 299-300- An external validation of the prognostic biomarker studies by our group has just been initiated.
-please, review the first paragraphs of this section, there is an incomplete sentence.
Answer: The incomplete sentence (line 233) was ment as a subheading for the following section. It has now been corrected.
Kind regards
Stine Dam Henriksen
Reviewer 2 Report
The authors have assembled a fairly comprehensive review of liquid biopsy for early detection or prognosis of PDAC. This is a very active area of research and this broad overview is timely.
The paper is acceptable but would be made stronger by the following:
-A table could be used to summarize the section on liquid biopsy for early detection; this could include a column of each studies limitations or a description of the level of maturity according to a recognized framework for biomarker development (Pepe JNCI, 2001)
-What technical advances are needed to make liquid biopsy a reality? There are many recent innovations in this field that have improved analytical sensitivity or resulted in greater standardization of sample collection/processing.
-The conclusions paragraph is very limited. Could a bullet-point summary of recommended future directions for the field be added?
Author Response
Dear Editor
Thank you for the useful comments.
Rebuttal letter - Reviewer 2.
-A table could be used to summarize the section on liquid biopsy for early detection; this could include a column of each studies limitations or a description of the level of maturity according to a recognized framework for biomarker development (Pepe JNCI, 2001)
-Answer:
A table (Table 1) has been added. It summarizes the diagnostic studies including strenghs, limitations and level of maturity.
The following section has been added from line 212-229: According to the five phase structure of biomarker development described by Pepe et al.[38] studies on DNA methylation as diagnostic biomarkers for PDAC only reach phase 2 (see Table 1). Currently, no diagnostic biomarker for PDAC based on cell-free DNA methylation has reach phase 3, which involves a retrospective longitudinal study of clinical specimens collected from cancer patients before their clinical diagnosis. In addition, no phase 4 studies (prospective studies) or phase 5 studies, which estimate the reduction of cancer mortality afforded by the biomarker, do exist. In general, further research is needed. Well-designed validation studies...
-What technical advances are needed to make liquid biopsy a reality? There are many recent innovations in this field that have improved analytical sensitivity or resulted in greater standardization of sample collection/processing.
Answer: The reviewer it correct, the whole subject concerning the analytical and technical aspect of liquid biopsies and the advances and progress in the field is interesting and an important aspect. However, I do feel it is outside the scope of this present review.
-The conclusions paragraph is very limited. Could a bullet-point summary of recommended future directions for the field be added?
Answer:
A bullet-point summary has been added as Fig. 1
Kind regards
Stine Dam Henriksen
