Review for 10.1186/s12876-022-02573-7 (2022)

Reviewer’s report
Title: 
Tissue Microarrey: A potential cost-effective approach for mismatch
repair testing in colorectal cancer
Version: 
0 
Date: 
31 Mar 2022
Reviewer's report:
Thank you very much for this work. 
This is an interesting study and very timely
as the role of MMR IHC continues to expand, including reflexive staining for
colorectal and other tumours.
There are several issues with the study which would need to be addressed before
the work is suitable for publication.
The work starts with a bias in selection - as the TMA was guaranteed to have
reasonable IHC staining. 
Only cases with IHC staining were selected for the
TMA. 
This, in part, explains the higher sensitivity 
/ specificity of this work
compared to previous work. 
The need for larger and multiple cores is addressed in the discussion. 
The need
for normal tissue is questionable and should be addressed, including the impact
of not having the normal cores on the interpretation of the tumour MMR IHC
should be discussed.
The exclusion of PMS2 staining from over-fixation is questionable. 
In the study
337 cores were excluded because they showed lack of PMS2 nuclear staining.
I'm assuming that this lack of nuclear staining was in tumour and normal tissue.
There is variability in the staining quality in large tissue sections and this
exclusion speaks to the overall use of TMAs to assess MMR IHC in colorectal
cancer. 
More explanation around this exclusion and its impact is needed,
including some reference to the explanation that this is due to over fixation.
While the image analysis of the sections is interesting, the results are
disappointing with a lower sensitivity than hoped. 
Given the ability of deep
learning to identify dMMR / MSI tumours based on H&E, it would be hoped
that an algorithm could detect abnormal MMR-IHC with a higher degree of
accuracy.
The workflow is hard to visualize in practice. 
There is evidence to suggest that
MMR IHC should be done on biopsy samples. 
While the work flow may suit
identification of potential CRC associated with Lynch Syndrome, MMR status is
also used to determine treatment. 
The delays involved in the creation of a TMA,
accruing sufficient cases and then having the results reviewed (centrally),
reported and incorporated back with the original case may not occur in a timely
manner. 
Further logistic reviews and economic analysis would be required
before being able to consider the proposed workflow.
Minor Points -
In the materials and methods section, the reference to the research ethics could
be shortened. 
The line "Institutional ethical approval was granted for the
performance of this study" was repeated with different sites / IDs.
There are many spelling mistakes and typographic issues which need to be
addressed. 
The section - TMA accuracy measurements of IHC for MMR proteins
is missing a key word - "If at least of these proteins does not show nuclear
staining of tumor cells, the test is considered pathologic and the tumor potentially
dMMR." 
The spelling mistakes are especially evident in the discussion section.
In the 1st 2 paragraphs of page 13 alone there are at least 6 spelling mistakes
("evalute", "heterogenity", :decreaase", "suggeste", "comparisson", "fasion"). 
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Is the study design appropriate to answer the research question (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
Yes
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
Yes
Are the images in this manuscript (including electrophoretic gels and blots) free
from apparent manipulation?
Yes