A systematic review of statistical methodology used to evaluate progression of chronic kidney disease using electronic healthcare records

Faye Cleary; David Prieto-Merino; Dorothea Nitsch

doi:10.1371/journal.pone.0264167

Peer Review History

Original SubmissionFebruary 12, 2021
11 May 2021 Decision Letter - Stanislaw Stepkowski, Editor Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. PONE-D-21-03779 A systematic review of statistical methodology used to evaluate progression of chronic kidney disease using electronic healthcare records PLOS ONE Dear Dr. Cleary, 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. The authord need to address reviewers' comments. Reviewer # 1: The systematic analysis by Faye Cleary et al. is useful in terms of identifying the opportunities coming from increasing availability of electronic health records, as well as pointing to common mistakes and challenges associated with their intrinsic nature. In this regard, the authors did a good job summarizing the methodology across the 65 included studies. It would be nice to note that retrospective studies using traditional paper records will suffer from the same problems as those using electronic health records: incomplete records, variation in logging practices, addressing AKI when modeling CKD progression, loss to follow-up and competing risks. I don't have other concerns about this work. Reviewer # 2: A well written systematic review with proper design, presentation of result, and discussion. I have few comments: -The search needs to be updated beyond 7th May 2020. Multiple studies were published after this date. -Clarify the study methodology: Sample size (before and after exclusions for reasons of data completeness); -The authors stated that “It is likely that if research is missing from review, then data quality issues in missing studies are likely to be of a similar quality or worse quality than studies reviewed”. Only studies reported in English language were included in this review. Therefore, it is unfair to label studies in non-English language as inferior in quality. -What is the outcome for Cox proportional hazards regression? I assume time to event !! Please submit your revised manuscript by Jun 25 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Stanislaw Stepkowski Academic Editor PLOS ONE Additional Editor Comments: The authord need to address reviewers' comments. Reviewer # 1: The systematic analysis by Faye Cleary et al. is useful in terms of identifying the opportunities coming from increasing availability of electronic health records, as well as pointing to common mistakes and challenges associated with their intrinsic nature. In this regard, the authors did a good job summarizing the methodology across the 65 included studies. It would be nice to note that retrospective studies using traditional paper records will suffer from the same problems as those using electronic health records: incomplete records, variation in logging practices, addressing AKI when modeling CKD progression, loss to follow-up and competing risks. I don't have other concerns about this work. Reviewer # 2: A well written systematic review with proper design, presentation of result, and discussion. I have few comments: -The search needs to be updated beyond 7th May 2020. Multiple studies were published after this date. -Clarify the study methodology: Sample size (before and after exclusions for reasons of data completeness); -The authors stated that “It is likely that if research is missing from review, then data quality issues in missing studies are likely to be of a similar quality or worse quality than studies reviewed”. Only studies reported in English language were included in this review. Therefore, it is unfair to label studies in non-English language as inferior in quality. -What is the outcome for Cox proportional hazards regression? I assume time to event !! Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. 3. Please remove your figures from within your manuscript file, leaving only the individual TIFF/EPS image files, uploaded separately. These will be automatically included in the reviewers’ PDF. [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: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes 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: Yes Reviewer #2: Yes ****** 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: The systematic analysis by Faye Cleary et al. is useful in terms of identifying the opportunities coming from increasing availability of electronic health records, as well as pointing to common mistakes and challenges associated with their intrinsic nature. In this regard, the authors did a good job summarizing the methodology across the 65 included studies. It would be nice to note that retrospective studies using traditional paper records will suffer from the same problems as those using electronic health records: incomplete records, variation in logging practices, addressing AKI when modeling CKD progression, loss to follow-up and competing risks. I don't have other concerns about this work. Reviewer #2: A well written systematic review with proper design, presentation of result, and discussion. I have few comments: -The search needs to be updated beyond 7th May 2020. Multiple studies were published after this date. -Clarify the study methodology: Sample size (before and after exclusions for reasons of data completeness); -The authors stated that “It is likely that if research is missing from review, then data quality issues in missing studies are likely to be of a similar quality or worse quality than studies reviewed”. Only studies reported in English language were included in this review. Therefore, it is unfair to label studies in non-English language as inferior in quality. -What is the outcome for Cox proportional hazards regression? I assume time to event !! ****** 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: Yes: Dulat Bekbolsynov Reviewer #2: Yes:** Sadik A. Khuder [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.0264167.r001
Revision 1
26 Oct 2021 Author Response I respond to specific reviewer comments individually below. I break this down point by point for reviewer 2 using the word 'RESPONSE' for each individual point separately. Comments reviewer #1: The systematic analysis by Faye Cleary et al. is useful in terms of identifying the opportunities coming from increasing availability of electronic health records, as well as pointing to common mistakes and challenges associated with their intrinsic nature. In this regard, the authors did a good job summarizing the methodology across the 65 included studies. It would be nice to note that retrospective studies using traditional paper records will suffer from the same problems as those using electronic health records: incomplete records, variation in logging practices, addressing AKI when modeling CKD progression, loss to follow-up and competing risks. I don't have other concerns about this work. RESPONSE: We are pleased that the reviewer sees the value and quality of our work. In response to reviewer suggestions, we have updated text in the discussion to note that traditional paper records will suffer from the same problems as those using electronic healthcare records. Comments Reviewer #2: A well written systematic review with proper design, presentation of result, and discussion. RESPONSE: We are pleased that the reviewer believes we have conducted a well-designed and presented review of the literature. -The search needs to be updated beyond 7th May 2020. Multiple studies were published after this date. RESPONSE: We have updated the search dates to include studies available in the 4 databases covered by the review as of August 2021, allowing us to capture more recently published studies. -Clarify the study methodology: Sample size (before and after exclusions for reasons of data completeness); RESPONSE: We have clarified in the methods text that data completeness inclusion criteria refer to the specific study inclusion criteria applied prior to main analyses being performed that aimed to restrict analyses to only those patients with sufficient data completeness to be deemed suitable for analysis, with such criteria expected to vary between studies. The explanation of the calculation for “percent of target population analysed” also shows readers how we used sample size data before and after data completeness inclusion criteria were applied to uncover the extent to which patients were excluded from analysis purely due to failure to meet a study’s data completeness requirements. -The authors stated that “It is likely that if research is missing from review, then data quality issues in missing studies are likely to be of a similar quality or worse quality than studies reviewed”. Only studies reported in English language were included in this review. Therefore, it is unfair to label studies in non-English language as inferior in quality. RESPONSE: Our comment that “With peer-reviewed literature expected to go through certain research quality checks, it is likely that if research is missing from review, then data quality issues in missing studies are likely to be of a similar quality or worse quality than studies reviewed” was intended to convey that studies missing from review due to not being peer-reviewed are likely to be of similar or worse quality as/than those peer-reviewed, due to the quality checks that peer-reviewed studies go through. It was not intended to say anything about studies published in non-English languages. We have clarified in the methods text that we anticipate that studies published in both English and non-English languages are likely to be of similar quality. -What is the outcome for Cox proportional hazards regression? I assume time to event !! RESPONSE: I’m not 100% sure where exactly in the manuscript the reviewer is referring to in this comment, but I imagine it may be results Tables 2 and 4. I would like to clarify what is reported and what is not. Due to the anticipated variation in how researchers define progression of kidney disease over time and the challenges this may pose in clinical interpretability of findings of research studies, a key aim of our review was to summarise how researchers measured changes in renal function over time. We also reported methods for analysis (which include as the reviewer states Cox proportional hazards regression models with such models using as outcome time to some event). In our reporting of study methodology (Table 2), we summarise “Measure of change in renal function over time”. As an example, an event of a 30% decline in eGFR between measures would be reported as “Raw percent change in eGFR between measures” (as this captures how changes over time were measured) and we do not specifically state whether this was analysed as time to event or as a binary outcome but we do report the method of analysis (“Statistical model used”), for example Cox proportional hazards regression. Table 4 further clarifies precise measures of changes in renal function over time for each individual study (e.g. percent loss in eGFR between measures >30%) alongside the methods used (e.g. Cox PH regression). Although we do not specifically state what the outcome is (e.g. time to percent loss in eGFR between measures >30%), this is inferred. We have added a comment to Table 4 to clarify this. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0264167.r002
7 Feb 2022 Decision Letter - Mabel Aoun, Editor A systematic review of statistical methodology used to evaluate progression of chronic kidney disease using electronic healthcare records PONE-D-21-03779R1 Dear Dr. Cleary, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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, Mabel Aoun, MD, MPH Academic Editor PLOS ONE Additional Editor Comments (optional): 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 #1: 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 #1: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 #1: 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 #1: 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 #1: (No Response) ****** 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 #1: Yes:** Dulat Bekbolsynov https://doi.org/10.1371/journal.pone.0264167.r003
Formally Accepted
9 Feb 2022 Acceptance Letter - Mabel Aoun, Editor PONE-D-21-03779R1 A systematic review of statistical methodology used to evaluate progression of chronic kidney disease using electronic healthcare records Dear Dr. Cleary: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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 Dr. Mabel Aoun Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0264167.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .