Reviewer ’s report  
 
Title:  Spectrum of genomic variations in Indian patients with progressive familial intrahepatic 
cholestasis  
 
Version: 1 Date: 06 Jun 2018 
 
Reviewer:  Jean Louis  Delaunay  
 
Reviewer’s report:  
 
The authors responded well to the remarks or comments point by point. Although clearly noted 
in the authors' response as well as in the text, the corrected manuscript presents major problem 
concerning  two tables which must be absolutely corrected to make the final version. in the 
BMGE -D-1800168R1 version, there was an unfortunate exchange between the documents, the 
authors took the extra table 1 instead of supplemental  table 2 to create the table1, if we resume 
well in the order:  
 
 
Table 1 Clinical Features of Patients in Which Pathogenic Or Liable Pathogenic Genomic 
Variations were Identified (supplemented with extrahepatic and liver biopsy data added)  
  
 
Table 2: 'Pathogenic' or 'Likely pathogenic' ge nomic variations identified in Indian patients with 
PFIC syndrome  
 
 
Table 3: 'Benign' or 'likely benign' non -synonymous genomic variations identified in Indian 
patients with PFIC syndrome  
 
 
Figure 1: Family tree for 9 patients in whom major variations in AT P8B1  
 
 
Supplemental Table1 Clinical and laboratory features of patients included in the study (n = 25)  
 
 
Supplementary Table 2: Results of prediction of effect, using various bioinformatic tools, of 
various 'pathogenic' or 'likely pathogenic' non -synonymous genomic variations.  
 
 
Supplementary Table 3: Results of prediction of effect, using various bioinformat ic tools, various 
'neutral' non -synonymous genomic variations.  
 
 
Supplementary Table 4: Synonymous genomic variations identified in Indian patients with PFIC 
syndrome.  
 
Once the authors have made a corrective version with these changes, the manuscript wil l be 
acceptable for publication  
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistics in the manuscript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality of written English  
Please indicate the quality of language in the manuscr ipt: 
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, fees, funding, or salary from an 
organisation that may in any way gain or lose financially from the publication of this 
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose 
financially fro m the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the 
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organization that 
holds or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial competing interests in relation to this paper?  
 
If you can answer no to all of the above, write  'I declare that I have no competing interests' 
below. If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests  
 
I agree to the open peer review policy of the journal. I understand that my name will be included 
on my rep ort to the authors and, if the manuscript is accepted for publication, my named report 
including any attachments I upload will be posted on the website along with the authors' 
responses. I agree for my report to be made available under an Open Access Creat ive Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do not wish to be included in my named report can be included as confidential comments  
to the editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
Reviewer ’s report  
 
Title:  Spectrum of genomic variations in Indian patients with progressive familial intrahepatic 
cholestasis  
 
Version: 1 Date: 06 Jun 2018 
 
Reviewer:  Jean Louis  Delaunay  
 
Reviewer’s report:  
 
The authors responded well to the remarks or comments point by point. Although clearly noted 
in the authors' response as well as in the text, the corrected manuscript presents major problem 
concerning  two tables which must be absolutely corrected to make the final version. in the 
BMGE -D-1800168R1 version, there was an unfortunate exchange between the documents, the 
authors took the extra table 1 instead of supplemental  table 2 to create the table1, if we resume 
well in the order:  
 
 
Table 1 Clinical Features of Patients in Which Pathogenic Or Liable Pathogenic Genomic 
Variations were Identified (supplemented with extrahepatic and liver biopsy data added)  
  
 
Table 2: 'Pathogenic' or 'Likely pathogenic' ge nomic variations identified in Indian patients with 
PFIC syndrome  
 
 
Table 3: 'Benign' or 'likely benign' non -synonymous genomic variations identified in Indian 
patients with PFIC syndrome  
 
 
Figure 1: Family tree for 9 patients in whom major variations in AT P8B1  
 
 
Supplemental Table1 Clinical and laboratory features of patients included in the study (n = 25)  
 
 
Supplementary Table 2: Results of prediction of effect, using various bioinformatic tools, of 
various 'pathogenic' or 'likely pathogenic' non -synonymous genomic variations.  
 
 
Supplementary Table 3: Results of prediction of effect, using various bioinformat ic tools, various 
'neutral' non -synonymous genomic variations.  
 
 
Supplementary Table 4: Synonymous genomic variations identified in Indian patients with PFIC 
syndrome.  
 
Once the authors have made a corrective version with these changes, the manuscript wil l be 
acceptable for publication  
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistics in the manuscript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality of written English  
Please indicate the quality of language in the manuscr ipt: 
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, fees, funding, or salary from an 
organisation that may in any way gain or lose financially from the publication of this 
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose 
financially fro m the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the 
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organization that 
holds or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial competing interests in relation to this paper?  
 
If you can answer no to all of the above, write  'I declare that I have no competing interests' 
below. If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests  
 
I agree to the open peer review policy of the journal. I understand that my name will be included 
on my rep ort to the authors and, if the manuscript is accepted for publication, my named report 
including any attachments I upload will be posted on the website along with the authors' 
responses. I agree for my report to be made available under an Open Access Creat ive Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do not wish to be included in my named report can be included as confidential comments  
to the editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
Please review this paper.
user
Reviewer ’s report  
 
Title:  Spectrum of genomic variations in Indian patients with progressive familial intrahepatic 
cholestasis  
 
Version: 1 Date: 06 Jun 2018 
 
Reviewer:  Jean Louis  Delaunay  
 
Reviewer’s report:  
 
The authors responded well to the remarks or comments point by point. Although clearly noted 
in the authors' response as well as in the text, the corrected manuscript presents major problem 
concerning  two tables which must be absolutely corrected to make the final version. in the 
BMGE -D-1800168R1 version, there was an unfortunate exchange between the documents, the 
authors took the extra table 1 instead of supplemental  table 2 to create the table1, if we resume 
well in the order:  
 
 
Table 1 Clinical Features of Patients in Which Pathogenic Or Liable Pathogenic Genomic 
Variations were Identified (supplemented with extrahepatic and liver biopsy data added)  
  
 
Table 2: 'Pathogenic' or 'Likely pathogenic' ge nomic variations identified in Indian patients with 
PFIC syndrome  
 
 
Table 3: 'Benign' or 'likely benign' non -synonymous genomic variations identified in Indian 
patients with PFIC syndrome  
 
 
Figure 1: Family tree for 9 patients in whom major variations in AT P8B1  
 
 
Supplemental Table1 Clinical and laboratory features of patients included in the study (n = 25)  
 
 
Supplementary Table 2: Results of prediction of effect, using various bioinformatic tools, of 
various 'pathogenic' or 'likely pathogenic' non -synonymous genomic variations.  
 
 
Supplementary Table 3: Results of prediction of effect, using various bioinformat ic tools, various 
'neutral' non -synonymous genomic variations.  
 
 
Supplementary Table 4: Synonymous genomic variations identified in Indian patients with PFIC 
syndrome.  
 
Once the authors have made a corrective version with these changes, the manuscript wil l be 
acceptable for publication  
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistics in the manuscript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality of written English  
Please indicate the quality of language in the manuscr ipt: 
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, fees, funding, or salary from an 
organisation that may in any way gain or lose financially from the publication of this 
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose 
financially fro m the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the 
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organization that 
holds or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial competing interests in relation to this paper?  
 
If you can answer no to all of the above, write  'I declare that I have no competing interests' 
below. If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests  
 
I agree to the open peer review policy of the journal. I understand that my name will be included 
on my rep ort to the authors and, if the manuscript is accepted for publication, my named report 
including any attachments I upload will be posted on the website along with the authors' 
responses. I agree for my report to be made available under an Open Access Creat ive Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do not wish to be included in my named report can be included as confidential comments  
to the editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
assistant