Polygenic risk score for acute rejection based on donor-recipient non-HLA genotype mismatch

Rui Cao; David P. Schladt; Casey Dorr; Arthur J. Matas; William S. Oetting; Pamala A. Jacobson; Ajay Israni; Jinbo Chen; Weihua Guan

doi:10.1371/journal.pone.0303446

Peer Review History

Original SubmissionSeptember 11, 2023
4 Dec 2023 Decision Letter - Pierre Bobé, Editor PONE-D-23-29389Polygenic Risk Score for Acute Rejection Based on Donor-Recipient non-HLA Genotype MismatchPLOS ONE Dear Dr. Guan, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. ============================== We consider that the manuscript lacks precision in various aspects, and the data presented need to be completed and strengthened. We invite you to submit a revised version of the manuscript that addresses all the points raised during the review process (see below Reviewer's comments). ============================== Please submit your revised manuscript by Jan 18 2024 11:59PM. 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Currently, your Funding Statement reads as follows: “This study was supported in part by NIH/NIAID grants 5U19-AI070119 and 5U01-AI058013. The grants were awarded to David P. Schladt, Casey Dorr, Arthur J. Matas, William S. Oetting, Pamala A. Jacobson, Ajay Israni, Weihua Guan” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Partly Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: No Reviewer #2: No ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: In this manuscript, Cao et al reported associations between donor-recipient polygenic risk and acute rejection in two donor-recipient pairs of European ancestry. They first carried out a GWAS for time to AR, selected SNPs of interest to generate a PRS (within and/or outside the HLA region) and applied it to an external donor-recipient cohort. They reported significant associations between the non-HLA PRS with acute rejection in both cohorts. I have several concerns about this study. 1. In the introduction, the authors state that several genome-wide studies have reported associations between D-R genetic mismatches and graft outcomes. In particular, the study from Zhang et al reported associations between D-R pIBD and graft outcomes. The authors of this manuscript propose to study an IBS PRS, without adding much novelty to the current literature. 2. The IBS PRS was constructed using arbitrary p value and r2 threshold. It might be useful to create different PRSs using several pruning parameters. The top 10 SNPs included in the PRS that are shown in table 2 have a MAF of less than 10%, and only 4 SNPs reached the genome-wide significance. Given the relatively low number of DR pairs, there is a concern that this study is not statistically powered, and the associations might be spurious. In addition, since this is a genome-wide association study, the authors should add lambda calculation, heritability estimates, as well as the Manhattan plot of the genome-wide significant signals for a quality check. The Authors might consider imputing genotype data to allow for higher SNP coverage and power. 3. Despite several studies showing that HLA mismatch is a strong predictor of AR, the Authors found no significant association. This may represent a concern regarding the validity of the PRS. The Authors should expand a discussion on this finding. Reviewer #2: The manuscript describes an interesting approach to transplantation matching, PRS based on non-HLA genetics of recipients and donors of kidney tx. It is well written and results are sound. I have two major points. The first one is, I'd assume, easy to correct: only some of the papers published on genomics of kidney transplantation have been cited. It would be fair (and correct scientific conduct) to make a more comprehensive list, missing appears at least Reindl-Schwaighofer et al 2019, Markkinen et al 2022, and Sun et al 2023. I do agree they are not on PRS but are important steps in the field. The second one is something that I see too often: there is no access to or descriptions of data analysis details at all. For example, the github portal, or similar, would be a good way to show the code and how analyses were conducted. We usually do not accept laboratory reports without sufficient descriptions of methods (not always very detsiled, agreed!), in the same way reports heavily based on data analysis should show how the data analyses were done. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0303446.r001
Revision 1
2 Feb 2024 Author Response Reviewer #1: In this manuscript, Cao et al reported associations between donor-recipient polygenic risk and acute rejection in two donor-recipient pairs of European ancestry. They first carried out a GWAS for time to AR, selected SNPs of interest to generate a PRS (within and/or outside the HLA region) and applied it to an external donor-recipient cohort. They reported significant associations between the non-HLA PRS with acute rejection in both cohorts. I have several concerns about this study. 1. In the introduction, the authors state that several genome-wide studies have reported associations between D-R genetic mismatches and graft outcomes. In particular, the study from Zhang et al reported associations between D-R pIBD and graft outcomes. The authors of this manuscript propose to study an IBS PRS, without adding much novelty to the current literature. Authors’ reply: The authors appreciate the feedback and hope to clarify. Unlike previous studies, our study is the first one identifying a set of SNPs from the whole genome whose matching can predict AR risk. Specifically, Zhang et al. leveraged an unsupervised approach to study AR in a single cohort, with their main focus on the proportion of IBD which represents donor-recipient relatedness. In contrast, our study involved two independent cohorts and leveraged a supervised approach based on clumping and thresholding PRS. We successfully identified and validated a subset of SNPs from the whole genome whose IBS matching are potentially associated with the AR risk to create the polygenic risk score. The PRS SNPs are worth further study to investigate their roles in AR occurrence. To make the novelty of our study clearer, we added a sentence at the last of Introduction section, addressing the novelty of our study compared to previous ones. 2. The IBS PRS was constructed using arbitrary p value and r2 threshold. It might be useful to create different PRSs using several pruning parameters. The top 10 SNPs included in the PRS that are shown in table 2 have a MAF of less than 10%, and only 4 SNPs reached the genome-wide significance. Given the relatively low number of DR pairs, there is a concern that this study is not statistically powered, and the associations might be spurious. In addition, since this is a genome-wide association study, the authors should add lambda calculation, heritability estimates, as well as the Manhattan plot of the genome-wide significant signals for a quality check. The Authors might consider imputing genotype data to allow for higher SNP coverage and power. Authors’ reply: The authors sincerely appreciate the valuable feedback. We agree with the concern of the power of our study given the high dimensionality of GWAS data. We take the PRS approach in hope to include SNPs that have moderate effect sizes and cannot be detected using the stringent GWAS p-value cutoff. For the GWAS part, we updated our analysis by adding an additional SNP QC: mean IBS mismatch score > 0.05 to avoid extreme values in the GWAS results, similar to the GWAS filtering of low MAF SNPs. Additionally, the number of 2-digit HLA mismatches was also adjusted in the GWAS model. The GWAS results including lambda calculation, heritability estimates, and a Manhattan plot were added to the main text. We observed little inflation of the test statistics with a genomic control lambda of 1.05. We agree that the imputed genotype may improve the statistical power. In fact, we used the imputed genotype data and applied an imputation info > 0.8 filter to QC the SNPs. To avoid confusion, we now added more detailed imputation information in the Method section. 3. Despite several studies showing that HLA mismatch is a strong predictor of AR, the Authors found no significant association. This may represent a concern regarding the validity of the PRS. The Authors should expand a discussion on this finding. Authors’ reply: Thank you for the feedback provided. We acknowledge the HLA mismatching is highly related to AR. We hypothesize that the nonsignificant association between HLA mismatch and AR is likely due to: 1). the donors and recipients in our cohorts are already HLA-matched since that is part of donor selection in the clinic, and 2). we adjusted the 2-digit HLA matching in our GWAS model. In our updated GWAS result, there is only one HLA SNP rs9380207 that can potentially be included in the PRS. The P-value of the HLA SNP was 1.73×10^(-4) and did not pass the genome-wide significance. We excluded this SNP to create a non-HLA PRS specifically. We have clarified our method and the reason for excluding the non-HLA SNP in the Results section. Reviewer #2: The manuscript describes an interesting approach to transplantation matching, PRS based on non-HLA genetics of recipients and donors of kidney tx. It is well written and results are sound. I have two major points. 1. The first one is, I'd assume, easy to correct: only some of the papers published on genomics of kidney transplantation have been cited. It would be fair (and correct scientific conduct) to make a more comprehensive list, missing appears at least Reindl-Schwaighofer et al 2019, Markkinen et al 2022, and Sun et al 2023. I do agree they are not on PRS but are important steps in the field. Authors’ reply: The authors appreciate the comment and the mentioned reference. We acknowledge the significance of their discoveries on non-HLA matching and renal post-transplant outcomes and added them into citation list of this paper. 2. The second one is something that I see too often: there is no access to or descriptions of data analysis details at all. For example, the github portal, or similar, would be a good way to show the code and how analyses were conducted. We usually do not accept laboratory reports without sufficient descriptions of methods (not always very detailed, agreed!), in the same way reports heavily based on data analysis should show how the data analyses were done. Authors’ reply: The authors thank and agree with the comment. We have uploaded all the codes involved in this study to a github folder https://github.com/RuiCao34/PRS_Kidney_AR. Unfortunately, due to a consent limitation, the phenotype and genotype data in the DeKAF Genomics cohort are not publicly available. Data from the GEN-03 cohort are available through dbGaP. We also annotated the code to ensure its reproducibility. Attachments Attachment Submitted filename: ResponseToReviewers_Jan312024.docx https://doi.org/10.1371/journal.pone.0303446.r002
25 Apr 2024 Decision Letter - Pierre Bobé, Editor Polygenic Risk Score for Acute Rejection Based on Donor-Recipient non-HLA Genotype Mismatch PONE-D-23-29389R1 Dear Dr. Guan, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Prof. Pierre Bobé Academic Editor PLOS ONE Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #2: Thank you for the amendments you have done to the revised version of the manuscript, the manuscript now is fine to me. ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #2: Yes: Partanen, Jukka ******** https://doi.org/10.1371/journal.pone.0303446.r003
Formally Accepted
20 May 2024 Acceptance Letter - Pierre Bobé, Editor PONE-D-23-29389R1 PLOS ONE Dear Dr. Guan, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Prof Pierre Bobé Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0303446.r004

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