Analysis of low-density lipoprotein receptor gene mutations in a family with familial hypercholesterolemia

Ya-nan Hu; Min Wu; Hong-ping Yu; Qiu-yan Wu; Ying Chen; Jian-Hui Zhang; Dan-dan Ruan; Yan-ping Zhang; Jing Zou; Li Zhang; Xin-fu Lin; Zhu-ting Fang; Li-Sheng Liao; Fan Lin; Hong Li; Jie-Wei Luo

doi:10.1371/journal.pone.0310547

Peer Review History

Original SubmissionApril 6, 2024
5 Jul 2024 Decision Letter - Nejat Mahdieh, Editor PONE-D-24-12858Analysis of low-density lipoprotein receptor gene mutations in a family with familial hypercholesterolemiaPLOS ONE Dear Dr. Luo, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. /> Please submit your revised manuscript by Aug 19 2024 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. 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Please include complete captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [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: Partly Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ******** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The authors reported variants in LDLR gene in a Chinese family with FH. In silico analysis and functional assays were perform. Some major issues need to be addressed. Row 27 (and in whole body of manuscript): LDLR - gene (genes) name should be writen in italics. Row 32: Rather „genotype-phenotype associations“ than „genetic-phenotypic associations“. Rows 49-51: „Conclusions“: Presented information are well known for many years and cannot be presented as conclusions of this study. Please, completely revise the text. Row 69: Rather “caused by pathogenic variations” than “caused by variations”. Row 77: Rather “common population” than “average people”. Row 86: The author is writing about the apolipoprotein APOB, not the gene, so italics cannot be used. Row 93: 1951? Joseph Leonard Goldstein (* 18. April 1940) and Michael Stuart Brown (* 13. April 1941), so at the age of 11 and 10? – reference [17] is from 1974. Row 176: Use italics for LDLR. Row 176: Which “Target genes…”. Row 218: …of PROS1? Why PROS1? This is the reason: PMID: 34496879? In my opinion, you overwrote (copy/pasted) your older text. Row 264: “Simon criteria” are “Simon Broome criteria”, “Dutch Network Diagnostic Criteria” are “Dutch Lipid Clinic Network criteria”. Row 301: “According to the… (ACMG)” – there are VCEP criteria for LDLR published in 2022 (PMID: 34906454). Row 337: Missing space between “Thr” and “mutant”. Rows 384 – 566: “Discussion”. This is NOT discussion! Presented information are rather encyclopedic information about LDLR, LDLR protein, LDLR cycle and pathogenic variants in LDLR than discussed results of this study. Why did not you discuss results of assays for Gly343Ser published here PMID: 25647241 or here PMID: 37397863 for Ala627Thr? Please, COMPLETELY revise the text. Row 520: p.Arg53fs? Why Arg53fs? This is the reason: PMID: 34786791? In my opinion, you overwrote (copy/pasted) your older text. Row 529: We → we Row 548: Severity → severity Row 714: Check the reference [39]. Row 822: Table 1, Head of second column: ago → Age Comment: It is necessary to mention that the authors are minimally oriented in the field of LDLR or FH. Errors on line 93 or 264 are clear evidence of this. It is necessary to completely revise the body of the manuscript. Please clearly explain how the errors on Rows 218 and 520 occurred. Reviewer #2: The current study is interesting with novel and important findings. The authors used a sound methodological approach with adequate results and discussion. Here are some comments for improving the manuscript: In the abstract: -In materials and methods section – please mention the number of family members subjected to Sanger sequencing. -In results section - please replace “Western blotting was showed that….” with “Western blotting has showed that……” -In conclusion section – please replace “This study show….” with “This study shows……” In methods: -P.12 Line 128: The line “It will start in July 2022 and end in December 2023” needs modification and to be in the past tense. -Please separate the exome sequencing section from the sanger sequencing one. -Please mention the number of family members subjected to Sanger sequencing and if there any other investigations have been done to them or not. ******** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: Yes: Hoda Y. Abdallah ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0310547.r001
Revision 1
24 Jul 2024 Author Response Dear editors, Thank you for your letter and for the reviewers’ comments concerning our manuscript entitled “Analysis of low-density lipoprotein receptor gene mutations in a family with familial hypercholesterolemia”(Submission ID number PONE-D-24-12858). Those comments are all valuable and very helpful for revising and improving our manuscript, as well as the important guiding significance to our researches. We have studied comments carefully and have made correction which we hope meet with approval. Revised portion are marked in red in the manuscript. The main corrections in the manuscript and the responds to the reviewer’s comments are listed below this letter. We would like to express our great appreciation to you and reviewers for comments on our manuscript. If you have any questions, please do not hesitate to contact me. With best wishes, Yours sincerely, Fan Lin Jie-Wei Luo Hong-Li 2024-7-10 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 Re: Thank you very much for your comments, we have already revised the manuscript and file name according to PLOS ONE's style requirements. 2. Thank you for submitting the above manuscript to PLOS ONE. During our internal evaluation of the manuscript, we found significant text overlap between your submission and previous work in the [introduction, conclusion, etc.]. We would like to make you aware that copying extracts from previous publications, especially outside the methods section, word-for-word is unacceptable. In addition, the reproduction of text from published reports has implications for the copyright that may apply to the publications. Please revise the manuscript to rephrase the duplicated text, cite your sources, and provide details as to how the current manuscript advances on previous work. Please note that further consideration is dependent on the submission of a manuscript that addresses these concerns about the overlap in text with published work. We will carefully review your manuscript upon resubmission and further consideration of the manuscript is dependent on the text overlap being addressed in full. Please ensure that your revision is thorough as failure to address the concerns to our satisfaction may result in your submission not being considered further. Re: Thank you very much for your comments, we have completely revised the introduction, discussion and conclusion sections in the manuscript. 3. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. Re: Sorry, we have corrected the grant numbers and ensured that all information now accurately reflects the funding sources for our study. 4. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels. In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. Re: Thank you for your guidance regarding the submission requirements for blot and gel results. We have reviewed PLOS ONE's updated policies on reporting requirements for blots and gels and have prepared our manuscript accordingly. 5. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript. Re: Thank you for your comments, we have deleted ethics statement in other section besides the Methods. 6. Please include complete captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. Re: Thank you for your comments, since we have revised the manuscript, there is currently no supporting information in the manuscript. Review Comments to the Author Reviewer 1 The authors reported variants in LDLR gene in a Chinese family with FH. In silico analysis and functional assays were perform. Some major issues need to be addressed. Major comments: 1.Row 27 (and in whole body of manuscript): LDLR - gene (genes) name should be writen in italics. Re: Thank you for your comments, we have already revised it in whole body of manuscript. 2.Row 32: Rather genotype-phenotype associations“ than „genetic-phenotypic associations“. Re: Thank you for your comments, we have already revised it. 3.Rows 49-51: Conclusions“: Presented information are well known for many years and cannot be presented as conclusions of this study. Please, completely revise the text. Re: Thank you for your comments, we have already revised the conclusions section completely. 4.Row 69: Rather “caused by pathogenic variations” than “caused by variations”. Re: Thank you for your comments, we have already revised it. 5.Row 77: Rather “common population” than “average people”. Re: Thank you for your comments, we have already revised it. 6.Row 86: The author is writing about the apolipoprotein APOB, not the gene, so italics cannot be used. Re: Thank you for your comments, we have already revised it. 7.Row 93: 1951? Joseph Leonard Goldstein (* 18. April 1940) and Michael Stuart Brown (* 13. April 1941), so at the age of 11 and 10? – reference [17] is from 1974. Re: Very sorry, the correct statement is 1974, rather than 1951. We apologize for our mistake and have already revised it. 8.Row 176: Use italics for LDLR. Re: Thank you for your comments, we have already revised it. 9.Row 176: Which “Target genes…”. Re: Thank you for your comments, the target gene refers to the LDLR gene carrying the c.1027G>A mutation and c.1879G>A mutation. 10.Row 218: …of PROS1? Why PROS1? This is the reason: PMID: 34496879? In my opinion, you overwrote (copy/pasted) your older text. Re: Very sorry, we accidentally pasted our older text (PMID: 34496879). We apologize for our carelessness and we have already revised it. 11.Row 264: “Simon criteria” are “Simon Broome criteria”, “Dutch Network Diagnostic Criteria” are “Dutch Lipid Clinic Network criteria”. Re: Thank you for your comments, we have already revised it. 12.Row 301: “According to the… (ACMG)” – there are VCEP criteria for LDLR published in 2022 (PMID: 34906454). Re: Thank you for your comments, we have already revised it in the manuscript according to the VCEP criteria for LDLR published in 2022. 13. Row 337: Missing space between “Thr” and “mutant”. Re: Thank you for your comments, we have already revised it. 14.Rows 384 – 566: “Discussion”. This is NOT discussion! Presented information are rather encyclopedic information about LDLR, LDLR protein, LDLR cycle and pathogenic variants in LDLR than discussed results of this study. Why did not you discuss results of assays for Gly343Ser published here PMID: 25647241 or here PMID: 37397863 for Ala627Thr? Please, COMPLETELY revise the text. Re: Thank you for your comments, we have revised the discussion section completely. 15.Row 520: p.Arg53fs? Why Arg53fs? This is the reason: PMID: 34786791? In my opinion, you overwrote (copy/pasted) your older text. Re: Very sorry, we accidentally pasted our older text (PMID: 34786791). We apologize for our carelessness and we have already revised it. 16.Row 529: We → we Re: Thank you for your comments, we have already revised it. 17.Row 548: Severity → severity Re: Thank you for your comments, we have already revised it. 18.Row 714: Check the reference [39]. Re: Thank you for your comments, due to a complete revision of the discussion, the content citing reference [39] has been deleted. 19.Row 822: Table 1, Head of second column: ago → Age Re: Thank you for your comments, we have already revised it. 20.Comment: It is necessary to mention that the authors are minimally oriented in the field of LDLR or FH. Errors on line 93 or 264 are clear evidence of this. It is necessary to completely revise the body of the manuscript. Please clearly explain how the errors on Rows 218 and 520 occurred. Re: Very sorry, we deeply apologize for the oversight of pasting content from our previous publications during the manuscript preparation process. We have made the necessary corrections and have thoroughly revised the introduction, discussion and conclusion sections of the paper. Reviewer #2: The current study is interesting with novel and important findings. The authors used a sound methodological approach with adequate results and discussion. Here are some comments for improving the manuscript: In the abstract: -In materials and methods section – please mention the number of family members subjected to Sanger sequencing. Re: Thank you for your comments, we have mentioned the number of family members subjected to Sanger sequencing in materials and methods section. -In results section - please replace “Western blotting was showed that….” with “Western blotting has showed that……” Re: Thank you for your comments, we have already revised it. -In conclusion section – please replace “This study show….” with “This study shows……” Re: Thank you for your comments, we have thoroughly revised the conclusion section of the manuscript. In methods: -P.12 Line 128: The line “It will start in July 2022 and end in December 2023” needs modification and to be in the past tense. Re: Thank you for your comments, but the line actually was not mentioned in the manuscript. -Please separate the exome sequencing section from the sanger sequencing one. Re: Thank you for your comments, we have divided the exome sequencing section and the Sanger sequencing section into two parts. -Please mention the number of family members subjected to Sanger sequencing and if there any other investigations have been done to them or not. Re: Thank you for your comments, fourteen family members subjected to Sanger sequencing have been mentioned in methods. And all of them performed investigations including routine physical examination, blood biochemistry, electrocardiogram, carotid ultrasound, renal artery ultrasound, echocardiography, and coronary CTA, which has been mentioned in the Research subject section. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0310547.r002
6 Aug 2024 Decision Letter - Nejat Mahdieh, Editor PONE-D-24-12858R1Analysis of low-density lipoprotein receptor gene mutations in a family with familial hypercholesterolemiaPLOS ONE Dear Dr. Luo, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Sep 20 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Nejat Mahdieh 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: (No Response) Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: No Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The authors reported variants in LDLR gene in a Chinese family with FH. In silico analysis and functional assays were perform. Some minor issues need to be addressed. Row 104: Who is the proband? Male, 53-year-old Chinese Han? Or Fig 1a, proband = II2, female!? Row 179 petri dish → Petri dish. Rows 312 - 313 …have both been → …have been both. Row 315: …is classified under the PS3 criteria… I do not understand, what author want to say. G1027A is classified as Pathogenic (modified) for Familial Hypercholesterolemia by applying evidence codes (PM2, PP3, PS3, PP4, PS4, PP1_Strong, PM5, PM3, BS4) according to VCEP (https://erepo.clinicalgenome.org/evrepo/ui/interpretation/2fc03ee7-785f-44c9-bac0-10c93ad52227). Row 316: …is classified as PS4 – the same as Row 315. I do not understand, what author want to say. PS4 (The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls) is only one of VCEP criteria met. Row 337: …Pur, … → …Puro,… Row 354: Missing space between “Thr” and “mutant”. Row 369: …of the LDLR. Maybe for clarify … of the mutant (or mutated) LDLR. Row 382: Rredictprotein → Predictprotein Row 389: LDLR-deficient disease? Please rephrase this part. Row 553: In my opinion, Gly + Ser + Ala +Thr is not necessary to clarify. Row 615: Please check reference 11 and 16 = duplicity. Row 620: Please check reference 13 and 17 = duplicity. Row 669: Strom → Strøm. Reviewer #2: The authors have responded adequately for all the requested comments and the manuscript is suitable for publishing in its current form. ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: Yes: Hoda Y. Abdallah ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0310547.r003
Revision 2
26 Aug 2024 Author Response Dear editors, Thank you for your letter and for the reviewers’ comments concerning our manuscript entitled “Analysis of low-density lipoprotein receptor gene mutations in a family with familial hypercholesterolemia”(Submission ID number PONE-D-24-12858). Those comments are all valuable and very helpful for revising and improving our manuscript, as well as the important guiding significance to our researches. We have studied comments carefully and have made correction which we hope meet with approval. Revised portion are marked in red in the manuscript. The main corrections in the manuscript and the responds to the reviewer’s comments are listed below this letter. We would like to express our great appreciation to you and reviewers for comments on our manuscript. If you have any questions, please do not hesitate to contact me. With best wishes, Yours sincerely, Fan Lin Jie-Wei Luo Hong-Li 2024-8-17 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. Re: Thank you very much for your comments, we have already revised the reference list and we have not found any retracted articles among our references. If you identify any, please inform us promptly. Review Comments to the Author Reviewer #1 The authors reported variants in LDLR gene in a Chinese family with FH. In silico analysis and functional assays were perform. Some minor issues need to be addressed. 1.Row 104: Who is the proband? Male, 53-year-old Chinese Han? Or Fig 1a, proband = II2, female!? Re: Very sorry, the proband is indeed II-2 in Fig 1a, a female. We apologize for our mistake and have already revised it. 2.Row 179 petri dish → Petri dish. Re: Thank you for your comments, we have already revised it. 3.Rows 312 - 313 …have both been → …have been both. Re: Thank you for your comments, we have already revised it. 4.Row 315: …is classified under the PS3 criteria… I do not understand, what author want to say. G1027A is classified as Pathogenic (modified) for Familial Hypercholesterolemia by applying evidence codes (PM2, PP3, PS3, PP4, PS4, PP1_Strong, PM5, PM3, BS4) according to VCEP (https://erepo.clinicalgenome.org/evrepo/ui/interpretation/2fc03ee7-785f-44c9-bac0-10c93ad52227). Re: Thank you for your comments, we have already revised it. 5.Row 316: …is classified as PS4 – the same as Row 315. I do not understand, what author want to say. PS4 (The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls) is only one of VCEP criteria met. Re: Thank you for your comments, we have already revised it. 6.Row 337: …Pur, … → …Puro,… Re: Thank you for your comments, we have already revised it. 7.Row 354: Missing space between “Thr” and “mutant”. Re: Thank you for your comments, we have already revised it. 8.Row 369: …of the LDLR. Maybe for clarify … of the mutant (or mutated) LDLR. Re: Thank you for your comments, we have already revised it. 9.Row 382: Rredictprotein → Predictprotein Re: Thank you for your comments, we have already revised it. 10.Row 389: LDLR-deficient disease? Please rephrase this part. Re: Thank you for your comments, we have already revised it. 11.Row 553: In my opinion, Gly + Ser + Ala +Thr is not necessary to clarify. Re: Thank you for your comments, we have already deleted it. 12.Row 615: Please check reference 11 and 16 = duplicity. Re: Thank you for your comments, we have already revised the reference list. Row 620: Please check reference 13 and 17 = duplicity. Re: Thank you for your comments, we have already revised the reference list. Row 669: Strom → Strøm. Re: Thank you for your comments, we have already deleted it. Reviewer #2: The authors have responded adequately for all the requested comments and the manuscript is suitable for publishing in its current form. Re: Very thank you for your comments. Attachments Attachment Submitted filename: Response to Reviewers (1).docx https://doi.org/10.1371/journal.pone.0310547.r004
3 Sep 2024 Decision Letter - Nejat Mahdieh, Editor Analysis of low-density lipoprotein receptor gene mutations in a family with familial hypercholesterolemia PONE-D-24-12858R2 Dear Dr. Luo, 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. If you have any questions relating to publication charges, 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, Nejat Mahdieh Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0310547.r005
Formally Accepted
3 Oct 2024 Acceptance Letter - Nejat Mahdieh, Editor PONE-D-24-12858R2 PLOS ONE Dear Dr. Luo, 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 If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks 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. 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. Nejat Mahdieh Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0310547.r006

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