Publication bias in trials registered in the Australian New Zealand Clinical Trials Registry: Is it a problem? A cross-sectional study

Marian Showell; Sam Buckman; Slavica Berber; Nada Ata Allah; Ben Patterson; Samantha Cole; Cynthia Farquhar; Vanessa Jordan

doi:10.1371/journal.pone.0279926

Peer Review History

Original SubmissionAugust 30, 2022
11 Nov 2022 Decision Letter - Nabeel Al-Yateem, Editor PONE-D-22-24255Publication bias in trials registered in the Australian New Zealand Clinical Trials Registry: Is it a problem? A cross-sectional studyPLOS ONE Dear Dr. Showell, 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. Please submit your revised manuscript by Dec 26 2022 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: https://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, Nabeel Al-Yateem, PhD Academic Editor PLOS ONE Journal Requirements: 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. 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We will update your Data Availability statement to reflect the information you provide in your cover letter. 3. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 4. 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. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: An important piece of work on the dissemination status of registered trials at the ANZCTR. The methodology is sound and the report clear and easy to follow. I have only the following minor suggestions: 1. Introduction: lines 69-70: " We know that the quicker trial results are disseminated, the more clinically relevant these results become (16, 17)" - the authors may wish to clarify what is meant by the term "clinically relevant" when used in this context - are the results more likely to be incorporated in clinical decision making or practice guideline, lead to practice change, or the authors meant something else? 2. Introduction, lines 102-103: the authors may wish to explain here specifically why these three particular years (2007, 2009 and 2011) were selected for this study. 3. Data collection, lines 124-125: "We calculated the time to publication in years and months, from the date of anticipated first enrolment, found in the data of the ANZCTR download, to the publication date found in the paper." - what about retrospectively registered trial? Which date was taken as the first point of measurement? 4. Data collection, lines 142-143: "Any trials that did not describe their RCT design type (parallel, cross over, or factorial) and trials coded as other were considered as one group, 'Other.'" - should they instead be labelled as "unclear" as there was a lack of required information? 5. Search Strategy to identify the publication of trials - it will be very helpful for future researchers who wish to do similar work if a generic methodology or algorithm in tracing publication used in this study, if available, be made available either in the main text or in the appendix. This will set a standard for others to follow and possibly update as required. The rest of the manuscript is well-written and comprehensively reported. ****** 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: Nai Ming Lai ******** [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.0279926.r001
Revision 1
16 Nov 2022 Author Response Reply to the comments from the Journal Editor Comment 1: “Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming Response: I have followed the guidance provided regarding PLOS ONE’s style requirements and made changes as necessary. Comment 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”. Response: I have uploaded our underlying data det as a Supporting Information file S2 (excel spreadsheet) to PLOS ONE Comment 3: “We note that you have stated that you will provide repository information for your data at acceptance” Response: I have now decided to upload the data to PLOS ONE so the repository information is no longer required. I have described these changes in the cover letter. Comment 4: “Please review your reference list to ensure that it is complete and correct” Response: I have reviewed the reference list and no changes were made. Reply to the comments from the reviewers Reviewer one Introduction Comment 1: “lines 69-70: " We know that the quicker trial results are disseminated, the more clinically relevant these results become (16, 17)" - the authors may wish to clarify what is meant by the term "clinically relevant" when used in this context - are the results more likely to be incorporated in clinical decision making or practice guideline, lead to practice change, or the authors meant something else?” Response: I have reworded this sentence to clearly explain what we meant by “clinically relevant” Comment 2: “lines 102-103: the authors may wish to explain here specifically why these three particular years (2007, 2009 and 2011) were selected for this study.” Response: I have added an explanation for the selected years. Data collection Comment 3: lines 124-125: "We calculated the time to publication in years and months, from the date of anticipated first enrolment, found in the data of the ANZCTR download, to the publication date found in the paper." - what about retrospectively registered trial? Which date was taken as the first point of measurement? Response: Both prospectively and retrospectively registered trials provided a date of first participant enrolment which was taken as the first point of measurement. Comment 4: “lines 142-143: "Any trials that did not describe their RCT design type (parallel, cross over, or factorial) and trials coded as other were considered as one group, 'Other.'" - should they instead be labelled as "unclear" as there was a lack of required information?” Response: I have now changed this category from “Other” to “Unclear” Comment 5: Search Strategy to identify the publication of trials - it will be very helpful for future researchers who wish to do similar work if a generic methodology or algorithm in tracing publication used in this study, if available, be made available either in the main text or in the appendix. This will set a standard for others to follow and possibly update as required. Response: Thank-you for this suggestion. I have now created a pdf of the search algorithm and uploaded it to PLOS ONE as a supplementary file (S1_Appendix). Comment 6: “PLOS authors have the option to publish the peer review history of their article. If published, this will include your full peer review and any attached files.” Response: Yes Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0279926.r002
12 Dec 2022 Decision Letter - Nabeel Al-Yateem, Editor PONE-D-22-24255R1Publication bias in trials registered in the Australian New Zealand Clinical Trials Registry: Is it a problem? A cross-sectional studyPLOS ONE Dear Dr. Showell, 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. Please submit your revised manuscript by Jan 26 2023 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: https://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, Nabeel Al-Yateem, PhD Academic Editor PLOS ONE 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. [Note: HTML markup is below. Please do not edit.] 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: Thank you for attending to the comments. There remains one point that I would like clarification. In my comment no 2: “lines 102-103: the authors may wish to explain here specifically why these three particular years (2007, 2009 and 2011) were selected for this study.” As far as I can see, the author justified the selection of the years by stating that they wished to allow at least 10 years to assess publication status. That is fine, my point was why picked 2007, 2009 and 2011, i.e. and not including years like 2008 and 2010. I don't seem to have seen any explanation on this. Apologies if I have missed something obvious. All the best. ****** 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: Nai Ming Lai ******** [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.0279926.r003
Revision 2
15 Dec 2022 Author Response Thank you for clarifying your comment regarding the need for a clearer explanation of why we chose to study the years 2007, 2009 and 2011. We have added this explanation to the methods section. You will see that 2007 is chosen as the year when trial registration become mandatory and the ANZCTR became a recognised registry by the WHO, the year 2011 allowed for at least ten years to publication and we chose to use 2009 as the mid point as we were unable to cope in practical terms with five years of data from the years 2007, 2008, 2009, 2010 and 2011. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0279926.r004
19 Dec 2022 Decision Letter - Nabeel Al-Yateem, Editor Publication bias in trials registered in the Australian New Zealand Clinical Trials Registry: Is it a problem? A cross-sectional study PONE-D-22-24255R2 Dear Dr. Showell, 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, Nabeel Al-Yateem, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0279926.r005
Formally Accepted
22 Dec 2022 Acceptance Letter - Nabeel Al-Yateem, Editor PONE-D-22-24255R2 Publication bias in trials registered in the Australian New Zealand Clinical Trials Registry: Is it a problem? A cross-sectional study Dear Dr. Showell: 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. Nabeel Al-Yateem Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0279926.r006

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