Classification performance of administrative coding data for detection of invasive fungal infection in paediatric cancer patients

Jake C. Valentine; Leon J. Worth; Karin M. Verspoor; Lisa Hall; Daniel K. Yeoh; Karin A. Thursky; Julia E. Clark; Gabrielle M. Haeusler

doi:10.1371/journal.pone.0238889

Peer Review History

Original SubmissionJune 3, 2020
24 Jul 2020 Decision Letter - Ales Vicha, Editor PONE-D-20-16766 Classification performance of administrative coding data for detection of invasive fungal infection in paediatric cancer patients PLOS ONE Dear Dr. Valentine, 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 Sep 07 2020 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 We look forward to receiving your revised manuscript. Kind regards, Ales Vicha, M.D., 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.We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. In your revised cover letter, please address the following prompts: a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially identifying or sensitive patient information) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. Please see http://www.bmj.com/content/340/bmj.c181.long for guidelines on how to de-identify and prepare clinical data for publication. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. We will update your Data Availability statement on your behalf to reflect the information you provide. 3.Thank you for stating the following in the Competing Interests section: [G.M.H. and J.E.C. report investigator-initiated grant funding from Gilead Sciences. K.M.V. reports grant funding from the National Health and Medical Research Council. All other authors declare no conflicts of interest relevant to this article.]. Please confirm that this does not alter your adherence to all PLOS ONE policies on sharing data and materials, by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests). If there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared. Please include your updated Competing Interests statement in your cover letter; we will change the online submission form on your behalf. Please know it is PLOS ONE policy for corresponding authors to declare, on behalf of all authors, all potential competing interests for the purposes of transparency. PLOS defines a competing interest as anything that interferes with, or could reasonably be perceived as interfering with, the full and objective presentation, peer review, editorial decision-making, or publication of research or non-research articles submitted to one of the journals. Competing interests can be financial or non-financial, professional, or personal. Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests Additional Editor Comments (if provided): The text of the manuscript is well written, but it needs minor adjustments. It is necessary to adjust the text according to the comments of reviewers. [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: This is a very interesting manuscript and it is well written and study well conducted. My only question is if the authors have tried to analyze the PPV by stratifying the number of codes assigned. In other words: is there any difference in sensitivity of the diagnostic code if the patient received 1 only code vs 2 or more? In the manuscript the authors stated >=1 but it would be interesting to see if any difference. Reviewer #2: The authors evaluated the classification performance of ICD-10-AM codes for detecting IFI using a gold-standard dataset of confirmed IFIs in paediatric cancer patients at a quaternary referral centre. But there were some limitations and unclear descriptions that they need to revise. Minor 1. Page 8, line 180, “ICD-10-AM codes: C00.x - C76.x, C80.x, C81.x [0/1] - C88.x [0/1], C90.x [0/1] - C96.x [0/1], and D46” In table 3, some of code were seemed to not be included above descriptions. Please check it. 2. Table 2 the number described in parenthesis ( ) Please describe the number that described in parenthesis ( ). “Male 55” meant percentage of male? Please describe the meaning of other numbers, too. 3. Although the results of EORTC/MSG were described in Table 3, no description exist in the text. Please add the results of EORTC/MSG in the results section. 4. Were there the case with two or more infection of fungi? If the two or more infection of fungi exist, how did the authors manage these cases? ****** 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: Yes:** Toshihiko Mayumi [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.0238889.r001
Revision 1
1 Aug 2020 Author Response Dr. Ales Vicha, M.D., Ph.D. Academic Editor, PLOS ONE 1st August 2020 Dear Dr. Vicha, R.E.: Article ID: PONE-D-20-16766 Please find attached revisions to the attached manuscript, entitled ‘Classification performance of administrative coding data for detection of invasive fungal infection in paediatric cancer patients’. All reviewer comments have been considered, with modifications made to the manuscript. Please find enclosed both a clean version as well as the copy containing the tracked changes to the manuscript. Please note that there are ethical restrictions concerning public provision of these data due to the sensitive nature of medical information contained in these datasets. As previously stipulated in our Data Availability Statement, data sharing is restricted to the researchers, clinical staff and the individual patient’s healthcare provider participating in the project analysis. The ethics approval (HREC/59636/RCHM-2019) maintains that public data provision is contingent on authorisation from the Principal Investigator and associated ethics applications to the Royal Children’s Hospital Human Research Ethics Committee for researchers who meet the criteria for access to confidential data. Contact details for the relevant ethics committee to which data requests may be sent is rch.ethics@rch.org.au. Updated Financial Disclosure Statement: J.C.V. was supported by an Australian Government Research Training Program Scholarship (grant number: 290465) awarded by the University of Melbourne (URL: https://www.education.gov.au/research-training-program) and a Cardinal Health Infection Control Scholarship awarded by the Australasian College for Infection Prevention and Control (URL: https://www.cardinalhealth.com/en.html). The TERIFIC study was supported by an Investigator Initiated Grant (grant number: IN-AU-131-1314) from Gilead Sciences, Inc. (https://www.gilead.com/). The funders had no role in study design, data collection and analysis, decision to publish, preparation or review of the manuscript. Updated Competing Interest Statement: I have read the journal’s policy and the authors of this manuscript have the following competing interests: G.M.H. and J.E.C. report investigator-initiated grant funding from Gilead Sciences, Inc. K.M.V. reports grant funding from the National Health and Medical Research Council. All other authors declare no conflicts of interest relevant to this article. This does not alter our adherence to PLOS ONE policies on sharing data and materials. Please also note that the authors have updated the visual aesthetics to Figure 1. All content in Figure 1 is identical to the original submission. Figure 1 has been uploaded to PACE and satisfies PACE requirements. We look forward to hearing from you regarding publication of this manuscript. Yours sincerely, Mr. Jake C. Valentine, BBiomedSc(Hons) (corresponding author) T: (03) 8559 7036 \| F: (03) 8559 7999 \| E: jvalentine@student.unimelb.edu.au or Jake.Valentine@petermac.org A: 305 Grattan Street, Melbourne, Victoria, Australia 3000 Response to reviewers: PONE-D-20-16766 Reviewer 1 Comment 1 This is a very interesting manuscript and it is well written and study well conducted. My only question is if the authors have tried to analyze the PPV by stratifying the number of codes assigned. In other words: is there any difference in sensitivity of the diagnostic code if the patient received 1 only code vs 2 or more? In the manuscript the authors stated >=1 but it would be interesting to see if any difference. Response: The authors thank the reviewer for their comment and agree that determining any variation in sensitivity and PPV of the coding data according to the number of assigned codes in the r-TERIFIC gold-standard dataset is highly relevant to the current study. Mathematically, the sensitivity decreases for r-TERIFIC patients in receipt of ≥2 codes within each combination of IFI codes, as the number of true positive cases naturally diminishes (namely, the set of invasive aspergillosis patients with 3 codes is a subset of patients with 2 codes, which is a subset of patients with 1 code etc). Please see page 18 (lines 392-397) and page 23 (lines 485-492) for the results and discussion on this point. Notwithstanding, the authors acknowledge that variation in the classification performance of specific codes within each combination of IFI codes is likely, given our current methodology evaluates the performance of a composite set of codes stratified by IFI type (according to composite coding definitions in Table S3). Thus, we have expanded our analysis to also evaluate any variation in the sensitivity, PPV and F1 scores for each specific code within each IFI code combination, first as a single set of codes, then as increasing sets of codes (Table 4, methodology discussed on pages 9 and 10, lines 227-239). See Table 4 and page 18 (lines 382-390) for results). This analysis will give an indication as to the individual sets of IFI codes yielding the highest sensitivity, PPV and F1 estimates in development of a coding algorithm for case detection of IFI in this population. Reviewer 2 Comment 1 The authors evaluated the classification performance of ICD-10-AM codes for detecting IFI using a gold-standard dataset of confirmed IFIs in paediatric cancer patients at a quaternary referral centre. But there were some limitations and unclear descriptions that they need to revise. Page 8, line 180, “ICD-10-AM codes: C00.x - C76.x, C80.x, C81.x [0/1] - C88.x [0/1], C90.x [0/1] - C96.x [0/1], and D46” In table 3, some of code were seemed to not be included above descriptions. Please check it. Response: The authors thank the reviewer for their comment. The authors have revisited the ICD-10-AM coding definitions for the malignancy subgroups reported in Table 3 and can confirm that all coding rules for each cancer type are correctly specified and included as stipulated in Table S3 (Supporting Information). The IFI coding performance in any patient in receipt of a Principal Diagnosis code (Australian Coding Standards 0001) listed on page 8, lines 185-186, were included in the ‘All cancers’ column of the analysis in Table 3. Given a significant majority of our cohort were diagnosed with acute lymphoblastic leukaemia, acute myeloid leukaemia and neuroblastoma (as indicated in Table 2), we conducted a subgroup analysis of IFI coding performance in these discrete subpopulations in order to discern any variation in IFI coding sensitivity based on underlying malignancy. Comment 2 Table 2 the number described in parenthesis ( ) Please describe the number that described in parenthesis ( ). “Male 55” meant percentage of male? Please describe the meaning of other numbers, too. Response: Numbers in the parenthesis denote percentages as indicated in the Table column heading. To avoid confusion regarding statistics in squared brackets, the population size (i.e. N=1,671) has been moved from the Table column heading to the Table title. Therefore, numbers in squared brackets represent the descriptive statistics indicated in the respective Table rows. See Table 2, page 14. Comment 3 Although the results of EORTC/MSG were described in Table 3, no description exist in the text. Please add the results of EORTC/MSG in the results section. Response: The authors thank the reviewer for their comment. The sensitivity, PPV and F1 scores of the IFI codes in the studied population after stratifying by EORTC/MSG classification have now been inserted in the Results Section (page 15, lines 364-368). Comment 4 Were there the case with two or more infection of fungi? If the two or more infection of fungi exist, how did the authors manage these cases? Response: Regarding use of ≥2 discrete IFI codes assigned to the same patient: we have indicated in the Methods Section that duplicate IFI codes denoting the same IFI in the same hospitalisation, as well as those reported at the time of admission in subsequent hospitalisations, were considered the same IFI and were counted only once per patient. Multiple discrete IFI codes appearing in the same hospitalisation per patient were counted as separate IFI episodes (page 8, lines 193-196). Regarding cases with ≥2 discrete gold-standard IFI diagnoses: patients with ≥2 mutually exclusive gold-standard IFI diagnoses in the r-TERIFIC dataset were counted as individual gold-standard cases (for example, one patient with invasive aspergillosis and invasive candidiasis was counted as one case of invasive aspergillosis and one case of invasive candidiasis accordingly). This occurred in only 1 instance. This clarification has now been inserted in the Methods Section (page 8, lines 196-200). https://doi.org/10.1371/journal.pone.0238889.r002
26 Aug 2020 Decision Letter - Ales Vicha, Editor Classification performance of administrative coding data for detection of invasive fungal infection in paediatric cancer patients PONE-D-20-16766R1 Dear Dr. Valentine, 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, Ales Vicha, M.D., PhD 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 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 #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes 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 #1: Yes 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 #1: Yes 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 #1: Thank you for the clarifications. The comments were addressed properly, this reviewer does not have additional edits. Reviewer #2: The authors evaluated the classification performance of ICD-10-AM codes for detecting IFI using a gold-standard dataset of confirmed IFIs in paediatric cancer patients at a quaternary referral centre. After the revisions according to the reviewers, the quality of the paper had improved. ****** 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: No Reviewer #2: Yes:** Toshihiko Mayumi, M.D. & Ph.D. https://doi.org/10.1371/journal.pone.0238889.r003
Formally Accepted
31 Aug 2020 Acceptance Letter - Ales Vicha, Editor PONE-D-20-16766R1 Classification performance of administrative coding data for detection of invasive fungal infection in paediatric cancer patients Dear Dr. Valentine: 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. Ales Vicha Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0238889.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 .