Genetic insights into number of long-term conditions and their relationship with lifespan

Youngjune Bhak; Bruce Guthrie; Albert Tenesa

doi:10.1371/journal.pone.0340181

Peer Review History

Original SubmissionMarch 3, 2025
21 Jul 2025 Decision Letter - Emmanuel Adewuyi, Editor Dear Dr. Bhak, 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. ============================== ACADEMIC EDITOR: Reviewers have provided feedback and comments for authors to address. In addition to those, authors need to: Ensure the manuscript follows the journal’s style and formatting requirements. Moderate language around causality. For example, instead of using terms like ‘impact,’ consider using ‘association’ where appropriate. Better account for heterogeneity in the LTC burden definition. For example, different conditions may vary in severity and genetic basis, which could affect interpretation. Clarify results presentation and expand the interpretive discussion. For example, include more detail on PRS performance and improve figure legends for clarity. Correct minor typographical and grammatical errors throughout the manuscript. Provide information availability of GWAS summary data from their work. ============================== Please submit your revised manuscript by Sep 04 2025 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. 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, Emmanuel O Adewuyi, BPharm, MPH, 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. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. 3. Please amend either the abstract on the online submission form (via Edit Submission) or the abstract in the manuscript so that they are identical. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. [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? Reviewer #1: Partly Reviewer #2: Partly Reviewer #3: Partly Reviewer #4: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: I Don't Know Reviewer #3: I Don't Know Reviewer #4: I Don't Know ****** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: No Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: Yes ****** Reviewer #1: This study addresses an important and timely question: the genetic underpinnings of long-term condition (LTC) burden and its relationship with lifespan. By leveraging the large-scale UK Biobank resource, the authors provide valuable insights into shared genetic architecture between LTC burden and parental lifespan, with potential implications for understanding biological aging and healthspan. The study is well-conceived, but several aspects of the manuscript require clarification and improvement to ensure transparency, accuracy, and interpretability. I recommend major revision. “At recruitment to the UK Biobank study, average age in the Discovery group was 56.5 (SD 7.9) years vs 61.9 (SD 6.3) years in the Application group, the Discovery group had less males than the Application group (44.9% vs 59.7%)” should be revised to: “At recruitment to the UK Biobank study, average age in the Discovery group was 56.5 (SD 7.9) years vs 61.9 (SD 6.3) years in the Application group, and the Discovery group had fewer males than the Application group (44.9% vs 59.7%).” “Similarly, the average number of LTCs was 1.41 (SD 1.77) lower in the Discovery than the Application group (3.54, SD 2.44)” should be revised to: “Similarly, the average number of LTCs was lower in the Discovery (1.41, SD 1.77) than the Application group (3.54, SD 2.44).” Otherwise, it may be interpreted as “1.41 times lower.” I suggest editing Supplementary Table 2 to include the gene or genomic location of the significantly associated SNPs. If these SNPs are intergenic, that should be explicitly stated. I also suggest including a brief mention of these significant associations in the main Results section. Please clarify or provide evidence supporting the use of parental lifespan as a valid surrogate for lifespan. A brief justification or citation would be appropriate. Consider revising the visual in Panel C. The “little people” icon showing individuals with canes to represent the top 10% PRS group (who actually died younger) could be misleading. I strongly recommend stratifying analyses by sex and reporting findings accordingly. The reporting of findings could be improved. For reference, see: PMID 33692554. In the Discussion, line 32, "LTC" should be used in place of the incorrect term. The Discussion overall is too brief and superficial. I encourage the authors to expand it to better contextualize the findings and acknowledge limitations. Please provide a brief description of the parental lifespan GWAS used in the Methods section to aid readers in understanding the study design. The authors do not explicitly state whether all data underlying their findings have been made available. However, the primary dataset used, the UK Biobank, is accessible to qualified researchers upon application and approval from the UK Biobank. I recommend that the authors clarify this in the manuscript. Additionally, the authors do not mention whether their GWAS summary statistics will be made available. Please include this information. Reviewer #2: The study conducted by the authors are too predictive and ignored the real time conditions such as lifestyle of individuals which largely affect these long term conditions and life expectancy. Though the number of subjects are good enough to predict a strong conclusion but the outcome of study (HLA region, LPA & higher PRS value for shorter life span) is already known and described in different published studies as authors also cited. Reviewer #3: Manuscript Review for PLOS ONE Manuscript ID: PONE-D-25-09280 Title: Genetic insights into number of long-term conditions and their relationship with lifespan. Corresponding author: Youngjune Bhak Ph.D., Albert Tenesa Ph.D. Overall assessment: While this manuscript presents valuable clinical insights, it falls short of meeting the genetic scope expected for a study of this nature. The authors primarily approach the research question from a medical perspective, with limited emphasis on genetic mechanisms, analysis depth, and biological interpretation. Given the study’s aim to investigate genetic associations, the lack of molecular genetic discussion, pathway-based integration, and hypothesis-driven synthesis significantly weakens its contribution to the field. The study fails to articulate how these genetic discoveries could inform future research (e.g., functional studies, multi-omics integration) or clinical applications (e.g., personalized risk stratification, therapeutic targeting). Major Comments 1. Introduction - Background Depth: The introduction should provide a more thorough review of existing literature on genetic factors relevant to the study. Expanding on key genetic mechanisms, prior evidence, and unresolved questions would better contextualize the study’s significance. - Final Paragraph Revision: The concluding paragraph currently summarizes methodological aspects rather than clearly stating the study’s aims, hypothesis, and research questions. 2. Methods - Ethics Statement Placement: To improve logical flow, move the ethics approval statement to the Data Sources subsection, where ethical considerations related to data collection are typically addressed. - Subheading Accuracy: The Study Outcome subheading is misleading, as the content describes long-term condition (LTC) categorizations. Rename this subsection (e.g., LTC Classification and Characterization) to accurately reflect its content. - Group Nomenclature: Clarify the rationale for labeling cohorts as Application Group and Discovery Group. Justify these terms in the context of the study design. 3. Discussion Lack of Integration Between Key Findings The discussion currently presents each result in isolation without synthesizing them into a cohesive narrative. For instance, the GWAS identified HLA as the most significant locus (linked to immunity/inflammation), while the local genetic correlation analysis highlighted LPA as the top candidate. However, the author fails to explore potential biological or mechanistic connections between these findings. A more impactful discussion would: - Hypothesize how inflammation-related pathways (via HLA) might interact with LPA-mediated lipid metabolism to influence the observed phenotype. - Address whether these loci operate independently or synergistically in disease pathogenesis, citing prior evidence (e.g., shared pathways like endothelial dysfunction or oxidative stress). - Propose a research gap: "Given the dual prominence of immune and lipid-related genes, future studies should investigate crosstalk between these pathways in [disease context]." Reviewer #4: Dear authors, The manuscript sheds light on the polygenetic causes that may be related to reduced lifespan in the white ancestry population in the UK by analysis of data from the UK Biobank. It's noteworthy the large number of data included in the study (343868 alive individuals and 34339 dead individuals). Some clarity is needed in the following points: -The term (the long-term condition) is not defined; it includes the risk of diseases that reduce lifespan, the environment and socioeconomic conditions, and the quality of life during the last years before death. - Why the study depends on the genetic correlation with parents’ lifespan rather than the data of the same individuals in the study. - Please specify the studied genetic loci in a table with their importance or correlation with studied LTC. - The categorization of the 32 LTC in the lines (13-31) is not clear. - The results of the studied data do not explain if sex has any correlation with lifespan. - The study does not specify which type/s or gene/s of HLA and LPA are the most frequently associated with aging or reduced lifespan. Best regards, ****** 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: Carolina B. Meloto Reviewer #2: No Reviewer #3: No Reviewer #4: Yes: Luma Hassan Alwan Al Obaidi ******** [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. Attachments Attachment Submitted filename: Manuscript Review for PONE-D-25-09280.docx Attachment Submitted filename: PONE-D25-09280 TO THE EDITOR.pdf https://doi.org/10.1371/journal.pone.0340181.r001
Revision 1
21 Oct 2025 Author Response ACADEMIC EDITOR: We would like to sincerely thank the Academic Editor and reviewers for their thorough evaluation of our manuscript and for providing constructive and insightful comments. We have carefully considered all suggestions and have revised the manuscript accordingly. These revisions have improved the clarity, presentation, and interpretability of our work. Below, we provide a detailed, point-by-point response to each comment, indicating the changes made and where they can be found in the revised manuscript. 1. Ensure the manuscript follows the journal’s style and formatting requirements. � Thank you for your guidance. We have carefully reviewed the PLOS ONE submission guidelines and revised the manuscript accordingly. Tables, figures, references, and line spacing now follow the journal’s style requirements. 2. Moderate language around causality. For example, instead of using terms like ‘impact,’ consider using ‘association’ where appropriate. � We have revised the manuscript to avoid causal language. The term ‘impact’ in the Abstract section has been replaced with ‘association’. 3. Better account for heterogeneity in the LTC burden definition. For example, different conditions may vary in severity and genetic basis, which could affect interpretation. � We have added text in the Discussion sections to acknowledge and account for heterogeneity in LTC burden. Specifically, we note that LTC burden combines conditions with differing severity, chronicity, prevalence, and genetic architecture. This heterogeneity may influence both the genetic signals observed and their interpretation. We have discussed this as a limitation and suggested future analyses stratifying LTCs by severity, mortality risk, or genetic heritability to refine interpretation. 4. Clarify results presentation and expand the interpretive discussion. For example, include more detail on PRS performance and improve figure legends for clarity. � We thank the reviewer for this valuable suggestion. In the Results section, we have now noted the direction and modest magnitude of correlation between PRS for LTC, LTC burden, and age at death. In the Discussion section, we have expanded our interpretation of the PRS findings, emphasising the modest effect sizes observed, and the likely contributions of environmental and lifestyle factors. We have also revised the Figure 1 legend to provide clearer descriptions of each panel, the statistical thresholds used, and the group comparisons shown, so that the figure can be interpreted without referring to the main text. These changes improve the clarity and interpretability of our results without altering the underlying analyses. 5. Correct minor typographical and grammatical errors throughout the manuscript. � We have performed a thorough proofread of the manuscript to correct typographical and grammatical errors, improve sentence clarity, and ensure consistency in terminology (e.g., “UK BioBank” corrected to “UK Biobank,” “less males” changed to “lower proportion of males”). 6. Provide information availability of GWAS summary data from their work. � We have added a Data Availability Statement specifying that the GWAS summary statistics generated in this study will be made publicly available upon the publish. 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 � We have revised the manuscript to meet PLOS ONE formatting guidelines, including file naming, structure, and layout, in accordance with the provided templates. 2. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. � We confirm that all data underlying the findings are now publicly available. The genome-wide association study (GWAS) summary statistics have been deposited in Zenodo under the DOI 10.5281/zenodo.17272288. Data from the UK Biobank are accessible to qualified researchers upon application and approval (https://www.ukbiobank.ac.uk/enable-your-research/apply-for-access). The revised Data Availability statement reflects these updates and complies with PLOS ONE’s open data policy (page 13, lines 10 to 16). 3. Please amend either the abstract on the online submission form (via Edit Submission) or the abstract in the manuscript so that they are identical. � We have reviewed and amended the abstract to ensure that the version in the online submission form is identical to the abstract in the manuscript. Reviewers Reviewer #1: This study addresses an important and timely question: the genetic underpinnings of long-term condition (LTC) burden and its relationship with lifespan. By leveraging the large-scale UK Biobank resource, the authors provide valuable insights into shared genetic architecture between LTC burden and parental lifespan, with potential implications for understanding biological aging and healthspan. The study is well-conceived, but several aspects of the manuscript require clarification and improvement to ensure transparency, accuracy, and interpretability. I recommend major revision. “At recruitment to the UK Biobank study, average age in the Discovery group was 56.5 (SD 7.9) years vs 61.9 (SD 6.3) years in the Application group, the Discovery group had less males than the Application group (44.9% vs 59.7%)” should be revised to: “At recruitment to the UK Biobank study, average age in the Discovery group was 56.5 (SD 7.9) years vs 61.9 (SD 6.3) years in the Application group, and the Discovery group had fewer males than the Application group (44.9% vs 59.7%).” “Similarly, the average number of LTCs was 1.41 (SD 1.77) lower in the Discovery than the Application group (3.54, SD 2.44)” should be revised to: “Similarly, the average number of LTCs was lower in the Discovery (1.41, SD 1.77) than the Application group (3.54, SD 2.44).” Otherwise, it may be interpreted as “1.41 times lower.” � We sincerely thank the reviewer for this helpful suggestion. We have revised the sentences to improve clarity and to avoid any potential ambiguity in interpretation (Page 5, lines 9 to 18). I suggest editing Supplementary Table 2 to include the gene or genomic location of the significantly associated SNPs. If these SNPs are intergenic, that should be explicitly stated. I also suggest including a brief mention of these significant associations in the main Results section. � We thank the reviewer for this helpful suggestion. We have added variant annotations, including gene or genomic location, in Supplementary Table 3. For variants in the HLA region, rs532965, we have explicitly stated the HLA subtype and the variant’s location within the gene. In addition, we have briefly mentioned these significant associations in the main Results section (Page 5, lines 21 to 24). Please clarify or provide evidence supporting the use of parental lifespan as a valid surrogate for lifespan. A brief justification or citation would be appropriate. � We thank the reviewer for raising this important point. We have added a justification in the Methods section, citing previous large-scale GWAS (e.g., Timmers et al. eLife 2019; Joshi et al. Nat Commun 2017) that used parental lifespan as a validated surrogate for individual lifespan (page 9, lines 9 to 13). Consider revising the visual in Panel C. The “little people” icon showing individuals with canes to represent the top 10% PRS group (who actually died younger) could be misleading. � We thank the reviewer for this valuable feedback. To avoid any potential misinterpretation, we have revised Panel C to use a unified icon for all groups. I strongly recommend stratifying analyses by sex and reporting findings accordingly. � We thank the reviewer for this valuable suggestion. We have now performed sex-stratified analyses and incorporated the results into the Results section. Specifically, males in the highest PRSLTC decile had a shorter average lifespan (70.80 years, SD = 7.53) compared with those in the lowest decile (71.92 years, SD = 7.04; p = 2.13E-06), while females showed a weaker and not significant difference (70.62 years, SD = 7.77 vs. 71.28 years, SD = 7.46; p = 0.041). The LTC burden also increased with higher PRSLTC in both sexes. These findings are now described in the Results section (page 7, lines 16 to 21). The reporting of findings could be improved. For reference, see: PMID 33692554. � We thank the reviewer for this helpful suggestion. We have thoroughly revised the manuscript to improve the reporting of findings, taking into account the recommended reference. In the Discussion, line 32, "LTC" should be used in place of the incorrect term. � We thank the reviewer for noticing this error. We have corrected ‘LCT’ to ‘LTC’ in the Discussion. The Discussion overall is too brief and superficial. I encourage the authors to expand it to better contextualize the findings and acknowledge limitations. � We thank the reviewer for this valuable suggestion. We have substantially expanded the Discussion to provide greater context for our findings and to more fully acknowledge the study’s limitations. Please provide a brief description of the parental lifespan GWAS used in the Methods section to aid readers in understanding the study design. � We thank the reviewer for this helpful comment. In the Introduction and Methods section, we have added a brief description of the parental lifespan GWAS, noting that we used summary statistics from large biobank studies (page 5, lines 2 to 3 and page 12, lines 9 to 12). This addition clarifies the data source and addresses the reviewer’s concern. The authors do not explicitly state whether all data underlying their findings have been made available. However, the primary dataset used, the UK Biobank, is accessible to qualified researchers upon application and approval from the UK Biobank. I recommend that the authors clarify this in the manuscript. Additionally, the authors do not mention whether their GWAS summary statistics will be made available. Please include this information. � We thank the reviewer for this helpful suggestion. We have revised the Data Availability section to clarify data access procedures. Specifically, we now state that the data used in this study are part of the UK Biobank resource, which is accessible to qualified researchers upon application and approval. In addition, we have made the GWAS summary statistics generated and analysed in this study publicly available on Zenodo (DOI: 10.5281/zenodo.17272288), which can be accessed without restriction for reuse and further analysis (Page 13, lines 10 to 16). Reviewer #2: The study conducted by the authors are too predictive and ignored the real time conditions such as lifestyle of individuals which largely affect these long term conditions and life expectancy. Though the number of subjects are good enough to predict a strong conclusion but the outcome of study (HLA region, LPA & higher PRS value for shorter life span) is already known and described in different published studies as authors also cited. � We thank the reviewer for these thoughtful comments. We agree that lifestyle and environmental factors play an important role in long-term conditions and lifespan. While these factors were beyond the scope of our genetic analysis, we now acknowledge this limitation more explicitly in the Discussion (From page 8, line 23 to page 9, line 17). We also note that, although associations in the HLA region, LPA, and polygenic risk scores for lifespan have been previously reported, our study extends this literature by focusing on LTC burden as an outcome. We believe this adds value by reinforcing and contextualizing prior findings in a new framework. Reviewer #3: Manuscript Review for PLOS ONE Manuscript ID: PONE-D-25-09280 Title: Genetic insights into number of long-term conditions and their relationship with lifespan. Corresponding author: Youngjune Bhak Ph.D., Albert Tenesa Ph.D. Overall assessment: While this manuscript presents valuable clinical insights, it falls short of meeting the genetic scope expected for a study of this nature. The authors primarily approach the research question from a medical perspective, with limited emphasis on genetic mechanisms, analysis depth, and biological interpretation. Given the study’s aim to investigate genetic associations, the lack of molecular genetic discussion, pathway-based integration, and hypothesis-driven synthesis significantly weakens its contribution to the field. The study fails to articulate how these genetic discoveries could inform future research (e.g., functional studies, multi-omics integration) or clinical applications (e.g., personalized risk stratification, therapeutic targeting). Major Comments 1. Introduction - Background Depth: The introduction should provide a more thorough review of existing literature on genetic factors relevant to the study. Expanding on key genetic mechanisms, prior evidence, and unresolved questions would better contextualize the study’s significance. � We agree and have substantially expanded the Introduction. We now review previous genome-wide studies of longevity, highlighting that genetic loci such as HLA, and LPA have been robustly associated with lifespan in large-scale GWAS. We also discuss biological pathways—immune dysregulation and chronic inflammation (HLA), and lipid metabolism (LPA)—that may plausibly link multimorbidity and reduced lifespan. These additions place our study within the broader context of known genetic contributors to longevity (page 4, lines 10 to 22). - Final Paragraph Revision: The concluding paragraph currently summarizes methodological aspects rather than clearly stating the study’s aims, hypothesis, and research questions. � We thank the reviewer for this constructive comment. We have revised the final paragraph of the Introduction to clearly state the study’s aims and design (From age 4, line 23 to page 5, line 6). Specifically, the revised paragraph now outlines our objectives: (1) to conduct a GWAS of long-term condition (LTC) burden and estimate SNP heritability, (2) to assess both global and local genetic correlations with parental lifespan as a proxy for longevity, and (3) to evaluate the association between a polygenic risk score for LTC burden (PRS_LTC) and both LTC burden and lifespan in an independent group. 2. Methods - Ethics Statement Placement: To improve logical flow, move the ethics approval statement to the Data Sources subsection, where ethical considerations related to data collection are typically addressed. � We thank the reviewer for this suggestion. We have moved the ethics approval statement to the Data Sources subsection in the revised manuscript to improve clarity and logical flow. - Subheading Accuracy: The Study Outcome subheading is misleading, as the content describes long-term condition (LTC) categorizations. Rename this subsection (e.g., LTC Classification and Characterization) to accurately reflect its content. � We appreciate the reviewer’s helpful observation. We have revised the subheading Study Outcome to LTC Classification and Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0340181.r002
26 Nov 2025 Decision Letter - Emmanuel Adewuyi, Editor Dear Dr. Bhak, 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. ============================== ACADEMIC EDITOR: Reviewers have found the study technically sound. A few issues still need to be addressed: 1. Authors need to follow the journal formatting style and guideline, for example, methods before results and discussion. 2. The authors should provide a complete Methods section that can allow the work to be fully reproducible. Additional details may be included in a supplementary section if necessary. 3. The authors should convert numbers from scientific notation using the “E” format to standard mathematical notation (e.g., 1.77E-176 to 1.77 × 10⁻¹⁷⁶). Please submit your revised manuscript by Jan 10 2026 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. 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 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, Emmanuel O Adewuyi, BPharm, MPH, PhD Academic Editor PLOS ONE Journal Requirements: If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. 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 Reviewer #2: All comments have been addressed Reviewer #4: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #2: Yes Reviewer #4: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #2: Yes Reviewer #4: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #2: Yes Reviewer #4: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #2: Yes Reviewer #4: Yes ****** Reviewer #2: The authors have addressed all the concerns of the reviewers and taken measures accordingly in the revised manuscript. I have no further comments. I wish the authors all the best.. Reviewer #4: To the authors, Thank you for carrying out all the comments. The article adds new insight to the genetic correlations of the most important loci with long-term conditions leading to reduced life span. ****** 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 #2: No Reviewer #4: 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 ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. https://doi.org/10.1371/journal.pone.0340181.r003
Revision 2
1 Dec 2025 Author Response ACADEMIC EDITOR: Dear Academic Editor, Thank you very much for your time and for coordinating the review process. We appreciate the constructive feedback provided by the reviewers and have revised the manuscript accordingly. 1. Authors need to follow the journal formatting style and guideline, for example, methods before results and discussion. � We have reorganized the manuscript to comply with the journal formatting guidelines, placing the Methods section before the Results and Discussion. During this revision, we also corrected minor typographical errors and improved clarity where needed. 2. The authors should provide a complete Methods section that can allow the work to be fully reproducible. Additional details may be included in a supplementary section if necessary. � We carefully revisited the Methods section in response to the comment, and we believe that the current level of detail should allow readers to fully reproduce the analysis. 3. The authors should convert numbers from scientific notation using the “E” format to standard mathematical notation (e.g., 1.77E-176 to 1.77 × 10⁻¹⁷⁶). � Numerical values previously presented in scientific “E” notation have been converted to standard mathematical notation throughout the manuscript including figure. The only exception is the reporting in the Methods section, where we retained the original format to reflect the tool’s option. Attachments Attachment Submitted filename: Response to reviewr_2025Dec02.docx https://doi.org/10.1371/journal.pone.0340181.r004
7 Dec 2025 Decision Letter - Emmanuel Adewuyi, Editor Dear Dr. Bhak, 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. ============================== ACADEMIC EDITOR: While the authors have addressed some of my previous comments, the response regarding the Methods section remains insufficient to meet the journal’s standards for full reproducibility, particularly for statistical genetic analyses. Several essential methodological details are still missing. For publication, complete transparency is required. Below, I outline key areas where further clarification and detail are needed (not exhaustive but provided as guidance). 1. LD Score Regression (LDSC) The current description of LDSC is not adequate for replication. Please expand this section to include the following details: LD score reference panel used (e.g., 1000 Genomes Phase 3 European, UK Biobank-specific LD scores, or custom LD scores). Source of LD scores, including links or references. SNP filtering criteria (default LDSC filters vs customised filters). Treatment of regression intercept, including interpretation of the intercept and how potential sample overlap was assessed or mitigated. Any deviations from LDSC default settings, including: handling of high-LD regions (e.g., whether the MHC was removed), use of constrained vs unconstrained intercept, whether genomic control was applied before LDSC. These parameters meaningfully influence heritability and genetic correlation estimates, and therefore must be clearly reported. 2. Local Genetic Correlation Analysis (LAVA) The description of the LAVA analyses remains minimal. To ensure transparency and reproducibility, please provide: The genomic partitioning scheme used: total number of regions, window size, whether the semi-independent LD blocks from Werme et al. (2022) were used or modified. LD reference panel used in LAVA (e.g., 1000 Genomes EUR). Criteria for region inclusion or exclusion, especially for blocks with low SNP density or unstable LD structure. Multiple testing correction approach for determining significant local genetic correlations. The exact version of LAVA, including any non-default settings, arguments, or flags. Local genetic correlation results are highly sensitive to block definitions and LD reference data; thus, full disclosure is required. 3. Need for comprehensive methodological transparency across the manuscript Several additional components of the analysis still lack the detail necessary for reproducibility. The Methods section should allow another researcher to fully reproduce the study without further correspondence. Please ensure that the manuscript reports: Full REGENIE parameters for Step 1 and Step 2. Complete PRSice-2 settings, including all clumping thresholds, p-value thresholds, and LD parameters. Ancestry filtering steps, including thresholds and QC criteria. Software environment, including operating system, R/Python versions, and all package versions. Where possible, full analysis code or command lines provided via Supplementary Materials or a public repository (e.g., GitHub). This is not mandatory for PLOS ONE when standard methods are used, but adequate procedural detail is required. 4. The manuscript would benefit from a more substantive and reflective discussion of its limitations. The current treatment does not adequately address several important constraints inherent in the study design and analytic methods. For example, the reliance on hospital-record-derived phenotypes introduces risks of misclassification, incomplete case capture, and censoring, all of which may affect the accuracy of LTC burden estimates. These issues warrant clearer acknowledgement. Similarly, authors need to mention limitations related to ancestry. Further, the genetic correlation analyses also require more careful framing, as LDSC and LAVA estimate shared genetic signal rather than causality and are sensitive to LD reference panels, block definitions, and SNP density. These interpretive boundaries should be recognised. In addition, the manuscript does not discuss limitations related to genotype QC, imputation quality, or the modest predictive value typically associated with PRS for complex traits. Finally, the discussion presents potential biological implications without balancing them against the environmental and sociodemographic factors that also contribute to LTC burden. ============================== Please submit your revised manuscript by Jan 21 2026 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. 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 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, Emmanuel O Adewuyi, BPharm, MPH, PhD Academic Editor PLOS One Journal Requirements: 1. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. 2. 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.] [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 ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. https://doi.org/10.1371/journal.pone.0340181.r005
Revision 3
8 Dec 2025 Author Response ACADEMIC EDITOR: Thank you very much for your careful review and for highlighting the remaining issues regarding methodological transparency. We appreciate the need for full reproducibility, and we have now revised the Methods section again to include all essential details that were previously missing. We are grateful for your guidance, and we hope that the updated version meets the journal’s standards. While the authors have addressed some of my previous comments, the response regarding the Methods section remains insufficient to meet the journal’s standards for full reproducibility, particularly for statistical genetic analyses. Several essential methodological details are still missing. For publication, complete transparency is required. Below, I outline key areas where further clarification and detail are needed (not exhaustive but provided as guidance). 1. LD Score Regression (LDSC) The current description of LDSC is not adequate for replication. Please expand this section to include the following details: • LD score reference panel used (e.g., 1000 Genomes Phase 3 European, UK Biobank-specific LD scores, or custom LD scores). • Source of LD scores, including links or references. • SNP filtering criteria (default LDSC filters vs customised filters). • Treatment of regression intercept, including interpretation of the intercept and how potential sample overlap was assessed or mitigated. • Any deviations from LDSC default settings, including: o handling of high-LD regions (e.g., whether the MHC was removed), o use of constrained vs unconstrained intercept, o whether genomic control was applied before LDSC. These parameters meaningfully influence heritability and genetic correlation estimates, and therefore must be clearly reported. � Thank you very much for the constructive feedback. We have substantially expanded the LDSC section in the revised manuscript, providing full details on the reference panel, LD score sources, filtering criteria, treatment and interpretation of the regression intercept, and any deviations from default settings. We also clarified whether default or customised options were used in each step. For potential sample overlap, we used HDL, which accounts for overlap internally. 2. Local Genetic Correlation Analysis (LAVA) The description of the LAVA analyses remains minimal. To ensure transparency and reproducibility, please provide: • The genomic partitioning scheme used: o total number of regions, o window size, o whether the semi-independent LD blocks from Werme et al. (2022) were used or modified. • LD reference panel used in LAVA (e.g., 1000 Genomes EUR). • Criteria for region inclusion or exclusion, especially for blocks with low SNP density or unstable LD structure. • Multiple testing correction approach for determining significant local genetic correlations. • The exact version of LAVA, including any non-default settings, arguments, or flags. Local genetic correlation results are highly sensitive to block definitions and LD reference data; thus, full disclosure is required. � Thank you very much for the helpful comments. In the revised manuscript, we have expanded the description of the LAVA analyses to provide clearer methodological transparency. We now specify the genomic partitioning scheme used and its source, except for window sizes as it vary by block and therefore are not uniform which are provided from LAVA. We additionally describe the LD reference panel, all custom options and steps applied during the analysis and clarify where default settings were used. Details on the multiple testing correction approach, as well as the exact LAVA version and parameters, have also been added. 3. Need for comprehensive methodological transparency across the manuscript Several additional components of the analysis still lack the detail necessary for reproducibility. The Methods section should allow another researcher to fully reproduce the study without further correspondence. Please ensure that the manuscript reports: • Full REGENIE parameters for Step 1 and Step 2. • Complete PRSice-2 settings, including all clumping thresholds, p-value thresholds, and LD parameters. • Ancestry filtering steps, including thresholds and QC criteria. • Software environment, including operating system, R/Python versions, and all package versions. • Where possible, full analysis code or command lines provided via Supplementary Materials or a public repository (e.g., GitHub). This is not mandatory for PLOS ONE when standard methods are used, but adequate procedural detail is required. � Thank you very much for the constructive feedback. We have expanded the Methods section to provide clearer methodological transparency across all analyses. The revised manuscript now includes detailed descriptions of the parameters used for each tool, specifying custom settings where applied and noting default options when no customisation was used. We have clarified the ancestry filtering procedure, including reliance on UK Biobank–provided ancestry information, and added the R version used in the analyses. Additional details on software and parameter settings have been incorporated to ensure the workflow is fully reproducible. 4. The manuscript would benefit from a more substantive and reflective discussion of its limitations. The current treatment does not adequately address several important constraints inherent in the study design and analytic methods. For example, the reliance on hospital-record-derived phenotypes introduces risks of misclassification, incomplete case capture, and censoring, all of which may affect the accuracy of LTC burden estimates. These issues warrant clearer acknowledgement. Similarly, authors need to mention limitations related to ancestry. Further, the genetic correlation analyses also require more careful framing, as LDSC and LAVA estimate shared genetic signal rather than causality and are sensitive to LD reference panels, block definitions, and SNP density. These interpretive boundaries should be recognised. In addition, the manuscript does not discuss limitations related to genotype QC, imputation quality, or the modest predictive value typically associated with PRS for complex traits. Finally, the discussion presents potential biological implications without balancing them against the environmental and sociodemographic factors that also contribute to LTC burden. � Thank you sincerely for these thoughtful comments. We have revised the final paragraph of the Discussion to incorporate all of the limitations you highlighted. The updated text now more clearly acknowledges potential phenotype misclassification and incomplete capture associated with hospital-record–based LTC definitions, as well as ancestry-related limitations. We have also added more careful framing of the genetic correlation findings, emphasising that these approaches estimate shared genetic signal rather than causality and are sensitive to LD reference panels, block definitions, and SNP density. In addition, we now discuss limitations related to genotype QC, imputation quality, and the typically modest predictive performance of PRS for complex traits, and we balance the biological interpretation with consideration of relevant environmental and sociodemographic contributors to LTC burden. Attachments Attachment Submitted filename: Response to reviewer_2025Dec08.docx https://doi.org/10.1371/journal.pone.0340181.r006
18 Dec 2025 Decision Letter - Emmanuel Adewuyi, Editor Genetic insights into number of long-term conditions and their relationship with lifespan. PONE-D-25-09280R3 Dear Dr. Bhak, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support . 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, Emmanuel O Adewuyi, BPharm, MPH, PhD Academic Editor PLOS One Additional Editor Comments First, please correct the Bonferroni threshold reported for the LAVA analyses in the Methods section, where the exponent is inconsistent with the stated number of tests and with the threshold used elsewhere in the manuscript. Second, the interpretation of the LDSC intercept should be refined for precision; while an intercept below 1 is consistent with effective genetic correction, it should be described as indicating no evidence of confounding-related inflation rather than interpreted as substantively informative on its own. Reviewers' comments: https://doi.org/10.1371/journal.pone.0340181.r007
Formally Accepted
Acceptance Letter - Emmanuel Adewuyi, Editor PONE-D-25-09280R3 PLOS One Dear Dr. Bhak, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS One. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@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. Emmanuel O Adewuyi Academic Editor PLOS One https://doi.org/10.1371/journal.pone.0340181.r008

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 .