Reviewer ’s report  
 
Title:  Spectrum of genomic variations in Indian patients with progressive familial intrahepatic 
cholestasis  
 
Version: 0 Date: 16 Apr 2018 
 
Reviewer:  Jonas  Rosendahl  
 
Reviewer’s report:  
 
Summ ary: 
 
The authors investigated variants in ATP8B1, ABCB11 or ABCB4 genes associated with a PFIC 
phenotype in 25 Indian children. In total 9 genetic variants were found, three were novel, 7 were 
pathogenic according to in -silco analysis, two were of unknown significance. In 16 patients no 
variants were detected (in the coding region).  
 
 
Major:  
 
Would it be possible to investigate more controls for the identified variants? If not can the 
authors give some arguments that this is not needed?  
 
As one of the patients  with a novel mutation has been presented before in another publication it 
might be more straightforward to exclude this patient from this study and just cite it in the 
discussion?  
 
 
Minor:  
 
Within the manuscript mutation nomenclature might be adapted according to current guidelines 
(hgvs mutnomen) so that all variants are displayed uniformly.  
 
Did you confirm each of the identified variants by an independent PCR and sequencing 
procedure?  
 
Some minor corrections of the written English might be performed, e.g. in the sentence: "It 
should be possible to work around some of these limitations in future, by using whole exome or 
whole genome sequencing."  
 
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.  
 
None.  
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: 0 Date: 16 Apr 2018 
 
Reviewer:  Jonas  Rosendahl  
 
Reviewer’s report:  
 
Summ ary: 
 
The authors investigated variants in ATP8B1, ABCB11 or ABCB4 genes associated with a PFIC 
phenotype in 25 Indian children. In total 9 genetic variants were found, three were novel, 7 were 
pathogenic according to in -silco analysis, two were of unknown significance. In 16 patients no 
variants were detected (in the coding region).  
 
 
Major:  
 
Would it be possible to investigate more controls for the identified variants? If not can the 
authors give some arguments that this is not needed?  
 
As one of the patients  with a novel mutation has been presented before in another publication it 
might be more straightforward to exclude this patient from this study and just cite it in the 
discussion?  
 
 
Minor:  
 
Within the manuscript mutation nomenclature might be adapted according to current guidelines 
(hgvs mutnomen) so that all variants are displayed uniformly.  
 
Did you confirm each of the identified variants by an independent PCR and sequencing 
procedure?  
 
Some minor corrections of the written English might be performed, e.g. in the sentence: "It 
should be possible to work around some of these limitations in future, by using whole exome or 
whole genome sequencing."  
 
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.  
 
None.  
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: 0 Date: 16 Apr 2018 
 
Reviewer:  Jonas  Rosendahl  
 
Reviewer’s report:  
 
Summ ary: 
 
The authors investigated variants in ATP8B1, ABCB11 or ABCB4 genes associated with a PFIC 
phenotype in 25 Indian children. In total 9 genetic variants were found, three were novel, 7 were 
pathogenic according to in -silco analysis, two were of unknown significance. In 16 patients no 
variants were detected (in the coding region).  
 
 
Major:  
 
Would it be possible to investigate more controls for the identified variants? If not can the 
authors give some arguments that this is not needed?  
 
As one of the patients  with a novel mutation has been presented before in another publication it 
might be more straightforward to exclude this patient from this study and just cite it in the 
discussion?  
 
 
Minor:  
 
Within the manuscript mutation nomenclature might be adapted according to current guidelines 
(hgvs mutnomen) so that all variants are displayed uniformly.  
 
Did you confirm each of the identified variants by an independent PCR and sequencing 
procedure?  
 
Some minor corrections of the written English might be performed, e.g. in the sentence: "It 
should be possible to work around some of these limitations in future, by using whole exome or 
whole genome sequencing."  
 
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.  
 
None.  
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