Using referral rates for genetic testing to determine the incidence of a rare disease: The minimal incidence of congenital hyperinsulinism in the UK is 1 in 28,389

Daphne Yau; Thomas W. Laver; Antonia Dastamani; Senthil Senniappan; Jayne A. L. Houghton; Guftar Shaikh; Tim Cheetham; Talat Mushtaq; Ritika R. Kapoor; Tabitha Randell; Sian Ellard; Pratik Shah; Indraneel Banerjee; Sarah E. Flanagan

doi:10.1371/journal.pone.0228417

Peer Review History

Original SubmissionSeptember 22, 2019
18 Nov 2019 Decision Letter - Klaus Brusgaard, Editor PONE-D-19-26690 Using referral rates for genetic testing to determine the incidence of a rare disease: the minimal incidence of congenital hyperinsulinism in the UK is 1 in 28,389 PLOS ONE Dear Dr. Daphne Yau, 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 authors present a interesting study but some areas needs attention. Please, respond to th questions raised by reviewer 1. Indeed, the questions around the use of C-peptide as a diagnostic criteria is relevant and presentation of the actual measurements including p-insulin and p-glucose would be of great value. ============================== We would appreciate receiving your revised manuscript by Jan 02 2020 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. 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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: 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 an interesting study of clinical importance, however with some epidemiological flaws. 1. In the methods, it is not clear how the clinical data were obtained. Did you have access to hospital file data or were the data based on questionnaires in the genetic testing request form? Genetic testing usually takes place prior to surgery. How did you obtain the surgery data? How did you know what age the patients had when determining persistence > 6 or 12 months? 2. Methods: An “or” diagnostic criteria of elevated C-peptide is doubtful, as the prolonged half-life of C-peptide compared to insulin implies that p-C-peptide does not reflect rapid changes in p-glucose. Indeed, the two references mentioned (Stanley, Banerjee) did not use elevated C-peptide as a diagnostic criteria. However, the inclusion criteria were sound (>6 mo CHI or surgery). However, it is very unlikely that an infant with an erroneous diagnosis of CHI based on C-peptide would be subjected to pancreatectomy or would still require therapy after 6 mo. The diagnostic problem on C-peptide should be mentioned in Limitations. 3. In Results, the only included patients had CHI persisting > 6 months’ age. Did no patient undergo pancreatic surgery <6 months’ age? And if they did, did you miss to detect them? 4. Why are the p-glucose, p-insulin and C-peptide data not presented? Is the study based on genetic testing requests only without actual data on the diagnosis? If the diagnoses were not actually validated it would be fair to state. 5. A patient inclusion flow chart is missing. The 104 patients lost to follow-up should be presented in a Results flow chart Figure 1. Why was it not possible in a country like the UK to perform a follow-up on these children? 6. An incidence calculation is always an estimate of the true, unknown incidence. Although many publications on incidences do not deal with details, a report on incidence only definitely should. For epidemiologists, a 95% confidence interval would be a demand. Your sampling is large enough to give a narrower C.I. than most others in the field. If you compute 95% C.I.s on the other incidences reported from other countries, one would better understand whether differences are significant or due to small samples. 7. Moreover, your data set is large enough to dive a little into time trends and geographical distribution. Did the incidence increase with time? This would suggest more referrals rather than a true increase. Were some geographic areas underrepresented? If yes, why? 8. In Discussion, the calculation is presented as a minimal incidence, as probably, or almost, all UK patients had genetic testing done in Exeter. Is it possible that some persistent CHI patients did not undergo genetic testing at all, perhaps especially in the beginning of the period studied? Reviewer #2: This is a well designed and conducted epidemiological study that is presented in a clearly and concisely. The methods and interpretation of data are appropriate. The limitations noted are comprehensive and reasonable. While this is not a landmark study, it does add valuable incidence information that will be useful for planning and operationalizing treatment of a condition that affects a very small population. ****** 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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0228417.r001
Revision 1
26 Dec 2019 Author Response The authors present a interesting study but some areas needs attention. Please, respond to th questions raised by reviewer 1. Indeed, the questions around the use of C-peptide as a diagnostic criteria is relevant and presentation of the actual measurements including p-insulin and p-glucose would be of great value. Thank you for your reply regarding our manuscript, “Using referral rates for genetic testing to determine the incidence of a rare disease: the minimal incidence of congenital hyperinsulinism in the UK is 1 in 28,389”. We have addressed the points raised during the review process and enclose a point-by-point response as well as revised manuscript. We hope these changes are found to be satisfactory. Reviewer #1: This is an interesting study of clinical importance, however with some epidemiological flaws. 1. In the methods, it is not clear how the clinical data were obtained. Did you have access to hospital file data or were the data based on questionnaires in the genetic testing request form? Genetic testing usually takes place prior to surgery. How did you obtain the surgery data? How did you know what age the patients had when determining persistence > 6 or 12 months? We thank the Reviewer for their positive and constructive comments. The clinical data were obtained from the genetic testing request form, which encompassed details regarding hyperinsulinism treatment including surgery. If the outcome was unknown, the requesting clinician was contacted to provide data regarding persistence at 6 and 12 months of age, and treatment including surgery. We have revised the manuscript to reflect this. 2. Methods: An “or” diagnostic criteria of elevated C-peptide is doubtful, as the prolonged half-life of C-peptide compared to insulin implies that p-C-peptide does not reflect rapid changes in p-glucose. Indeed, the two references mentioned (Stanley, Banerjee) did not use elevated C-peptide as a diagnostic criteria. However, the inclusion criteria were sound (>6 mo CHI or surgery). However, it is very unlikely that an infant with an erroneous diagnosis of CHI based on C-peptide would be subjected to pancreatectomy or would still require therapy after 6 mo. The diagnostic problem on C-peptide should be mentioned in Limitations. We acknowledge the Reviewer’s point regarding the use of C-peptide in diagnosing hyperinsulinism. We used C-peptide as an additional biomarker in the context of recurrent, severe hypoglycaemia and high glucose infusion rates consistent with hyperinsulinism causing hypoglycaemia while recognizing the importance of insulin as a prime diagnostic marker. We have revised the manuscript to reflect the Reviewer’s comments. 3. In Results, the only included patients had CHI persisting > 6 months’ age. Did no patient undergo pancreatic surgery <6 months’ age? And if they did, did you miss to detect them? We thank the Reviewer for clarifying this. The patients undergoing surgery were included in N=278 patients. We apologise for not having made this clearer and have amended the manuscript to indicate the number of patients undergoing pancreatic surgery. 4. Why are the p-glucose, p-insulin and C-peptide data not presented? Is the study based on genetic testing requests only without actual data on the diagnosis? If the diagnoses were not actually validated it would be fair to state. The genetic testing request form included data on glucose, insulin and c-peptide to confirm evidence of CHI prior to genetic testing. We have now included these values in the results of the manuscript. 5. A patient inclusion flow chart is missing. The 104 patients lost to follow-up should be presented in a Results flow chart Figure 1. Why was it not possible in a country like the UK to perform a follow-up on these children? A patient inclusion flow chart was provided as a supplemental figure. We have now provided this as figure 1 and the incidence data as figure 2. For the 104 patients lost to follow up, we had contacted the referring physicians to obtain outcome data, but either the patient was no longer in the physician’s care or were lost to their follow up, or we did not receive a reply despite several attempts. 6. An incidence calculation is always an estimate of the true, unknown incidence. Although many publications on incidences do not deal with details, a report on incidence only definitely should. For epidemiologists, a 95% confidence interval would be a demand. Your sampling is large enough to give a narrower C.I. than most others in the field. If you compute 95% C.I.s on the other incidences reported from other countries, one would better understand whether differences are significant or due to small samples. We have now calculated 95% confidence intervals for our data set as well as for the incidences reported from other countries. These are included these in figure 2 and the data used for calculation in supporting table S1. However, we were unable to calculate 95% CI for the incidences for Ireland and Japan. The former is based on unpublished data and the latter is published in Japanese. Overall, the estimates from the outbred populations are overlapping or nearly overlapping, in the case of the Czech Republic estimate. It therefore appears the differences are due to small sample sizes in the other populations versus a significant differences between the populations. We have revised our discussion to reflect this analysis. 7. Moreover, your data set is large enough to dive a little into time trends and geographical distribution. Did the incidence increase with time? This would suggest more referrals rather than a true increase. Were some geographic areas underrepresented? If yes, why? As the reviewer has suggested, we have examined the incidence over time (S2 table). Although the annual incidence fluctuated year by year, a sustained increase was not observed over the time period studied. We have not examined the incidence by geography as we do not have data on the location of birth, only location of treatment. It would not be accurate to include data on treatment location given that there are two tertiary referral centres to which patients are referred from all over the UK. 8. In Discussion, the calculation is presented as a minimal incidence, as probably, or almost, all UK patients had genetic testing done in Exeter. Is it possible that some persistent CHI patients did not undergo genetic testing at all, perhaps especially in the beginning of the period studied? We anticipate most if not all patients undergoing genetic testing for CHI in the UK would have been referred to Exeter. However, it is possible, as the reviewer states, that some patients with CHI may not have undergone testing at all, particularly if the hypoglycaemia could be managed with diazoxide. Reviewer #2: This is a well designed and conducted epidemiological study that is presented in a clearly and concisely. The methods and interpretation of data are appropriate. The limitations noted are comprehensive and reasonable. While this is not a landmark study, it does add valuable incidence information that will be useful for planning and operationalizing treatment of a condition that affects a very small population. We kindly thank the Reviewer for their positive comments regarding our study. Attachments Attachment Submitted filename: Yau Response to Reviewers_final.docx https://doi.org/10.1371/journal.pone.0228417.r002
15 Jan 2020 Decision Letter - Klaus Brusgaard, Editor Using referral rates for genetic testing to determine the incidence of a rare disease: the minimal incidence of congenital hyperinsulinism in the UK is 1 in 28,389 PONE-D-19-26690R1 Dear Dr. Daphne Yau, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. 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With kind regards, Klaus Brusgaard 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: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: (No Response) ****** 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: (No Response) ****** 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: (No Response) ****** 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: The authors have responded well to the questions raised. A few typos remains: Line 109: "This data" should be "These data" Line 114: "incidence 1 in 51,247" should be "incidence was 1 in 51,247" Line 144: "under detection" should be "underdetection" Line 180: "incidence data is" should be "incidence data are" Reviewer #2: (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: Henrik Thybo Christesen Reviewer #2: Yes: Trevor Richter https://doi.org/10.1371/journal.pone.0228417.r003
Formally Accepted
21 Jan 2020 Acceptance Letter - Klaus Brusgaard, Editor PONE-D-19-26690R1 Using referral rates for genetic testing to determine the incidence of a rare disease: the minimal incidence of congenital hyperinsulinism in the UK is 1 in 28,389 Dear Dr. Yau: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Klaus Brusgaard Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0228417.r004

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