Peer Review History
| Original SubmissionApril 5, 2021 |
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PONE-D-21-11145 Implications of OPRM1 and CYP2B6 variants on treatment outcomes in methadone-maintained patients in Ontario: Exploring sex differences PLOS ONE Dear Dr. Samaan, 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.
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We will update your Data Availability statement on your behalf to reflect the information you provide. [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: Partly Reviewer #3: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: I Don't Know Reviewer #3: 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 Reviewer #3: No ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: 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 authors performed a genetic association study of methadone maintenance treatment (MMT) of opioid use disorder among ~1100 persons of European origin (~65% male) who had urine drug screen (UDS) data and methadone plasma levels available over a 3-15 month period, across a consortium of MMT clinics in Canada. They did array genotyping which yielded ~5 million SNPs after imputation. Despite this wealth of genetic data, they report on 3 OPRM1 and 2 CYP2B6 SNPs. There were 3 phenotypes: methadone plasma levels, any lapse to illicit opioid use (a single + UDS) and relapse (a single + UDS after at least 3 months of – UDS results). Logistic regression and linear regression analyses were implemented. Sex-specific results are reported. There were no statistically significant results. The following comments are relevant: 1. The authors must be clear about whether they analyzed (or plan to analyze) the methadone dose and other phenotypes using other SNPs, or whether they restricted analysis to only those 5 SNPs reported here. This has implications for multiple hypothesis testing. 2. The authors should consider analysis of relapse as a continuous variable, using % UDS +, instead of defining relapse as a single + UDS. 3. ~10-15% of the sample had missing data, but is it not possible to obtain the methadone dose or weight from the EHR? 4. The authors should report the numbers of patients in each of the categories for the two binary phenotypes in Table 2. 5. The authors might consider the use of generalized estimating equations in analysis of these data. Reviewer #2: Comments to the Authors: This manuscript employs a relatively large population of European MMT patients to examine the pharmacogenetic effects of variants in OPRM1 and CYP2B6 on MMT outcome measures. The authors further explore the effect of sex on these outcome measures (which the authors state has not been done in previous studies in the literature). While enthusiastic about the data set, the reviewer has reservations about the lack of information in the description of the study, the statistical methods and about the outcome measures used. Specifically, the outcome measures used by these authors are not consistent with those used in some previous literature, and, thus, cannot be used as a test of replication of previous findings (which is a stated objective of this manuscript). The reviewer believes that although the data analysis was likely done correctly, the manuscript could be improved before publication. Major issues: The authors state that sex-based analyses have not been done or have been overlooked by past studies. The reviewer finds the literature contains at least one study (Crist et al, 2018a) on OPRM1 genotypes and MMT efficacy to have used sex as a covariate in their statistical analyses. Although the Crist et al, 2018a study had fewer participants on MMT, sex was considered in their analysis, and the authors found no effect of sex on the measured outcome. The authors state that the objective of the present study is to “replicate findings from the literature within a larger sample of European descent”. However, the defined outcome measures in the current study are not equivalent to those used in previous studies in the literature. The authors should reference those studies in the literature in which their outcome definitions have been used. For example, these authors employ binary data, rather than percent positive UTS over time by rs10485058 genotype (Crist et al, 2018a), as their outcome measure for “continued opioid use”. In addition, the authors use initial methadone dose at intake, rather than maximum methadone dose (Crist et al, 2018b; ref 28 - Smith et al, 2017), as their outcome measure (but, see question below about methadone dose at time of GENOA enrollment). How long was each participant on MMT before enrollment in GENOA? The average time on MMT in the GENOA study was 3.7 years (Table 2), but the standard deviation is quite large. Did participants in the current study need to be on MMT for a minimum defined time to be included? If so, what was that minimum time requirement? The authors state that “primary sources of information used” were “data collected at baseline (enrollment in the study), 3 months prior to study enrollment, and up to 12 months follow up”. So, does the current manuscript encompass only data from a 15 months period that includes 3 months before enrollment into GENOA and 12 months of follow-up of participants after GENOA enrollment? Was UTS data available before enrollment of participants in the GENOA study, specifically at 3 months prior to enrollment? Were all participants enrolled in GENOA on a stable (maximal) dose of methadone at the time of enrollment, or were some participants enrolled before or during methadone titration up to a stable dose? The authors should indicate how often UTS were done throughout the MMT period. Were they weekly or monthly? How were missed UTS appointments handled? Were they treated as missing or as positive? The definitions of “continued opioid use” and “relapse” do not seem rigorous enough because some level of continued opioid use is anticipated in real world settings of MMT, especially at the start of treatment. The reviewer suggests an analysis using percent positive UTS over time by genotype to determine MMT efficacy (see Crist et al, 2018a) especially at the start of MMT. Similarly, depending on the time on MMT of patients in the current study, the definition of relapse could be defined as more than 1 positive UTS after 3 months of clean UTS because some “breakthrough use” is to be expected as the clinician titrates the methadone dose to an effective level. The maximum dose of methadone is a better indication of therapeutic dose than the initial dose of methadone at intake (but, see question above about stable dose of methadone at time of GENOA enrollment). This is especially true for pharmacokinetic metabolic gene analysis, such as CYP2B6. Regarding the discussion of SNP rs3745274 (*9 variant of CYP2B6), it is the R-enantiomer of methadone that is the therapeutic enantiomer and binds 50 times more strongly to the MOR (encoded by OPRM1), not the S-enantiomer. Because the authors did not determine the effect of rs3745274 on the R:S-enantiomer ratio, it is speculative to suggest that “[its] effect on continued opioid use in MMT patients could be explained as a decrease in the CYP2B6 gene activity, which could increase plasma methadone concentrations and subside the need for additional opioid intake.” The S-enantiomer is metabolized by CYP2B6, but the *9 variant is predicted to be benign by SIFT and PolyPhen, and was found not to significantly alter mean plasma methadone or the methadone:EDDP ratio (Figure 1 in reference 21 – Ahmad et al, 2017). Also, in Ahmad et al, the significant finding for rs3745274 is likely due to a skewing of the minor allele frequencies in different directions among the controls and methadone groups (overall predicted MAF=27%, controls=22%, methadone=31%) due to sampling error in small group sizes. (The reviewer also points out that the Ahmad et al study considered sex in their statistical analysis). Previous literature (ref 20 – Levran et al, 2013) indicates that it is the CYP2B6*6 haplotype (combined rs2279343 *4 with rs3745274 *9 genotypes) that led to differences in methadone dose requirements. The authors provide an image of the LD structure for CYP2B6 in their study population, but do not give the actual D’ and r2 values. From the image, it appears that although LD is high between *4 and *9 SNPs, it is not perfect. As such, to attempt to replicate previous findings in the literature, the authors should re-run the statistical analysis using the haplotype of these two SNPs, as was done in Levran et al, 2013. What statistics program did the authors use to impute the missing covariate data? How many imputations did the authors run? If missing data imputations were run in R, the authors should state the package they used – for instance, did they use ‘norm’? Could the authors have instead used the 'keep-pheno-on-missing-cov' option for covariates in PLINK 1.07? Did the authors test models other than the ‘Genotypic’ (ADD) model? Other genetic models were used in previous literature (see Crist et al, 2018a). For covariates that were not significant in the full model, the authors should re-run the statistics without them in the model to determine whether the significance of the outcome measures change. Minor issues: Some of the references are incorrect. For example, reference 32 in the manuscript is supposed to reference R (page 11, line 208) but is listed in the references as Cahn et al, 2011, J. Wildl Manage 75(8):1753-66. Was this supposed to be reference 33 for R as listed in the references section? The authors should state which analyzed SNPs were directly genotyped (on the chip) and which were imputed. The authors should clarify what the reference condition was for each statistical analysis. For instance, was the reference condition defined as an individual ‘having the minor allele and being positive for the particular outcome measure’, or was it ‘having the minor allele and not being positive for the outcome measure’? References mentioned (but not referenced in the manuscript): Crist RC, Doyle GA, Nelson EC, Degenhardt L, Martin NG, Montgomery GW, Saxon AJ, Ling W, Berrettini WH. A polymorphism in the OPRM1 3'-untranslated region is associated with methadone efficacy in treating opioid dependence. Pharmacogenomics J. 2018a Jan;18(1):173-179. doi: 10.1038/tpj.2016.89. Crist RC, Li J, Doyle GA, Gilbert A, Dechairo BM, Berrettini WH. Pharmacogenetic analysis of opioid dependence treatment dose and dropout rate. Am J Drug Alcohol Abuse. 2018b ;44(4):431-440. doi: 10.1080/00952990.2017.1420795. Reviewer #3: This paper aims to test associations between several OPRM1 and CYP2B6 SNPs on several methadone maintenance treatment outcomes in males and females separately. The strength of the study is the large sample size as well as the high number of females, which is rare in MMT studies. Contradictory findings have been published on these SNPs, mostly in smaller studies, thus a large replicate study is interesting. My main concerns of the manuscript are as follows: - In the abstract and in the results sections (also in the tables), the results are always described in such a way that they first seem to be statistically significant, while they are not. - Most included patients were taking methadone but it seems from table 2 that a few took suboxone. Why they were not excluded as the study is on MMT? - For the outcomes on continued opioid use and relapse, they should be clarified. The frequency of UTS should be indicated to better describe these outcomes. Is the duration of 3 to 15 months for all patients? - For the methadone dose outcome, more information on how long the dose was unchanged before inclusion should be added. Detailed descriptive statistics of the dose should be added (range, normal distribution in the population, …). - The outcome of the methadone dose is questionable as methadone metabolism displays a high interindividual variability and as patients might be in different phase of their MMT (treatment introduction, stabilization or slow tapering of the dose for example). Also, in certain MMT prescribing center, there is a maximal dose not be exceeded but that could remain insufficient for certain patients who therefore continue to use opiates. In general, when discussing the individual SNPs, it will help to include the gene name before the rs number (ex. OPRM1 rs73568641) In the study design and setting section (p.5, line 107): it is not clear which data was collected 3 months prior to study enrollment. In Table 2, the significantly different variables between male and female should be indicated (*). The opioid prescription variable should be clarified. In the discussion (p.16, line 258): no trend was observed for rs73568641 on relapse in female. ********** 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: Wade Berrettini, MD, PhD Reviewer #2: No Reviewer #3: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. |
| Revision 1 |
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PONE-D-21-11145R1Implications of OPRM1 and CYP2B6 variants on treatment outcomes in methadone-maintained patients in Ontario: Exploring sex differencesPLOS ONE Dear Dr. Samaan, 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 address a couple of very minor issues from Reviewer 3. Please ensure that your decision is justified on PLOS ONE’s publication criteria and not, for example, on novelty or perceived impact. Please submit your revised manuscript by Nov 26 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:
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, Huiping Zhang 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 Reviewer #3: (No Response) ********** 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: Partly Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #3: 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 #3: 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 #3: 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) Reviewer #3: Thank you for your response. My comments have been addressed except for the addition of the range (min-max or interquartile) of methadone dose in Table 2. The number of significant digits (for methadone dose but not only) used in table 2 should also be reviewed. And there is an inversion in table 2 in the Continued opioid use frequency. ********** 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: Wade Berrettini Reviewer #3: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. |
| Revision 2 |
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Implications of OPRM1 and CYP2B6 variants on treatment outcomes in methadone-maintained patients in Ontario: Exploring sex differences PONE-D-21-11145R2 Dear Dr. Samaan, 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, Huiping Zhang Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-21-11145R2 Implications of OPRM1 and CYP2B6 variants on treatment outcomes in methadone-maintained patients in Ontario: Exploring sex differences Dear Dr. Samaan: 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. Huiping Zhang Academic Editor PLOS ONE |
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