Review for 10.1186/1471-230X-12-181 (2012)

Reviewer's report
Title:Correlation of the Presence and Extent of Loss of Heterozygosity
Mutations with Histological Classifications of Barrett's Esophagus
Version: 1Date:12 October 2012
Reviewer: Anna van Nistelrooij
Reviewer's report:
The authors explore the mutational profiling of Barrett’s Esophagus biopsy
specimens as a means to add supplementary information to the histological
classification. They use Loss of Heterozygosity (LOH) as a tool to establish the
genetic instability in different lesions found in the progression of normal
epithelium to high grade dysplasia. LOH can be a good indicator for genetic
instability, and the idea of establishing the rate of genetic instability in different
lesions in the malignant transformation of Barrett’s Esophagus can perhaps give
more insides in the development of the esophageal adenocarcinoma.
Minor essential revisions:
1.
Page 6, line 134 -140: It is not clear to me how many targets there were obtained
from one patient. The authors included 271 patients in the study and state that
3-8 targets were taken from a given slide, but in total only 568 targets were
obtained. The authors should better define how many targets exactly were taken
from each patient.
2.
The authors use the definition “loss of heterozigosity mutations”. This is
confusing because they are analyzing LOH. The authors should consider leaving
out the word mutations. In my view they are mixing up LOH and mutations. I
suggest that the authors use LOH in stead of LOH mutations.
Major compulsory revisions:
3.
Figure 1: not informative. The authors should show a high magnification of a
histological slide to show the targets that they had isolated and give an
assessment of the percentage of affected cells isolated. This amount is important
if you want to interpret your results of LOH. The percentage should be
established after the isolating of the cells was performed and not during LOH
analysis.
4.
Page 8, line 177: How did the authors establish high and low clonality from a
LOH analysis? Is it correct that they use a lower limit of <50%. But it is not clear
to me how they established the percentage of affected cells (as mentioned
before). They give the impression that they obtained 100% of affected cells,
which I find hard to believe. It should be informative if the authors show a
histological slide with the dissected parts of metaplasia, LGD, HDG and the
associated LOH analysis and comment whether they classify it as low or high
clonality. They are defining high and low clonality as a certain "percentage of the
DNA mutated" but it should be more correct if they use "percentage of cells
showing LOH". Once more the authors are looking, in my view, to LOH and not to
mutations.
Discretionary revisions:
5.
Did the authors obtained normal squamous epithelium or columnar epithelium
from each patient? To better interpret the results of the LOH analysis it is routine
to perform LOH at a paired normal-tumor sample obtained from the same tissue
block. The normal epithelium of each sample as a reference should be better in
stead of taking an average of a group of normal samples.
If more targets were taken from one patient is should be correct to analyze all
these targets together and compare it with the normal epithelium of the same
patient. This is also important because of the quality of the DNA can differ
between patients and can influence your results.
If DNA of normal epithelium or columnar epithelium is available, the authors
should consider using the normal epithelium of the same tissue block as a
reference in their analysis. If this is not possible then they should mention this as
a limitation of their study.
6.
Table 3: Showing percentages is more informative than making the numbers
bold.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests