Cheng et al present a copy number/mutation analysis of a 100 oesohpageal tumours based on 3 sequencing approaches. This is an interesting paper; however I think the authors could have made a better use of the data.

Major Compulsory revisions:

1.- It is my understanding (please correct me if I'm wrong, as I'm no oncologist) that stage III tumours should have been first stage I tumours. Is that right? On the other hand, not all stage I tumours should progress to stage III. If that is the case, then the analysis should have taken this into account, and many interesting questions have not been answered, like are there any alterations that can predict if an early tumour will progress towards stage III? What I'm trying to ask is if treating these two groups as independent entities is the best approach for the analysis.
2.- The identification of FAM84B seems a bit weak. Why did the authors used only 14 tumours to identify common regions of alteration? Is it because it's easier to call copy number on whole genome than on whole exome? Still, I think it'd pay to use all the samples, and methods for copy number in exomes work relatively well. To me, Figure 2a doesn't stand out as big piece of evidence.

Minor Essential revisions:
1.- The description of the pipeline used is important in a paper like this. At some point in the text the authors mention Firehose but in the paper they mention an in-house pipeline.
2.- All the methods used should be properly referenced, not only named.

Level of interest An article of importance in its field
Quality of written English Acceptable
Statistical review Yes, and I have assessed the statistics in my report.
Declaration of competing interests I declare that I have no competing interests.

Authors' response to reviews: (http://www.gigasciencejournal.com/imedia/1682852505161404_comment.pdf)

The reviewed version of the manuscript can be seen here:
http://www.gigasciencejournal.com/imedia/5235196031442538_manuscript.pdf
All revised versions are also available:
Draft - http://www.gigasciencejournal.com/imedia/5235196031442538_manuscript.pdf

The authors have improved the manuscript and have answered my questions. I understand that they need more data to answer some of them.
Level of interest An article whose findings are important to those with closely related research interests
Quality of written English Acceptable
Statistical review Yes, and I have assessed the statistics in my report.
Declaration of competing interests I declare that I have no competing interests.

The reviewed version of the manuscript can be seen here:
http://www.gigasciencejournal.com/imedia/1408580998161405_manuscript.pdf
All revised versions are also available:
First revision - http://www.gigasciencejournal.com/imedia/1408580998161405_manuscript.pdf