<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD Journal Publishing DTD v2.0 20040830//EN" "journalpublishing.dtd"><article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="2.0" xml:lang="en" article-type="reviewer-report"><front><journal-meta><journal-id journal-id-type="nlm-ta">JMIRx Med</journal-id><journal-id journal-id-type="publisher-id">xmed</journal-id><journal-id journal-id-type="index">34</journal-id><journal-title>JMIRx Med</journal-title><abbrev-journal-title>JMIRx Med</abbrev-journal-title><issn pub-type="epub">2563-6316</issn><publisher><publisher-name>JMIR Publications</publisher-name><publisher-loc>Toronto, Canada</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">v6i1e70039</article-id><article-id pub-id-type="doi">10.2196/70039</article-id><article-categories><subj-group subj-group-type="heading"><subject>Peer-Review Report</subject></subj-group></article-categories><title-group><article-title>Peer Review of &#x201C;Identifying Safeguards Disabled by Epstein-Barr Virus Infections in Genomes From Patients With Breast Cancer: Chromosomal Bioinformatics Analysis&#x201D;</article-title></title-group><contrib-group><contrib contrib-type="author"><collab>Anonymous</collab></contrib></contrib-group><contrib-group><contrib contrib-type="editor"><name name-style="western"><surname>Schwartz</surname><given-names>Amy</given-names></name></contrib></contrib-group><pub-date pub-type="collection"><year>2025</year></pub-date><pub-date pub-type="epub"><day>29</day><month>1</month><year>2025</year></pub-date><volume>6</volume><elocation-id>e70039</elocation-id><history><date date-type="received"><day>13</day><month>12</month><year>2024</year></date><date date-type="accepted"><day>13</day><month>12</month><year>2024</year></date></history><copyright-statement>&#x00A9; Anonymous. Originally published in JMIRx Med (<ext-link ext-link-type="uri" xlink:href="https://med.jmirx.org">https://med.jmirx.org</ext-link>), 29.1.2025. </copyright-statement><copyright-year>2025</copyright-year><license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by/4.0/"><p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">https://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work, first published in JMIRx Med, is properly cited. The complete bibliographic information, a link to the original publication on <ext-link ext-link-type="uri" xlink:href="https://med.jmirx.org/">https://med.jmirx.org/</ext-link>, as well as this copyright and license information must be included.</p></license><self-uri xlink:type="simple" xlink:href="https://xmed.jmir.org/2025/1/e70039"/><related-article related-article-type="companion" ext-link-type="doi" xlink:href="10.1101/2023.07.03.23292185v1" xlink:title="Preprint (medRxiv)" xlink:type="simple">https://www.medrxiv.org/content/10.1101/2023.07.03.23292185v1</related-article><related-article related-article-type="companion" ext-link-type="doi" xlink:href="10.2196/69307" xlink:title="Authors' Response to Peer-Review Reports" xlink:type="simple">https://med.jmirx.org/2025/1/e69307</related-article><related-article related-article-type="companion" ext-link-type="doi" xlink:href="10.2196/50712" xlink:title="Published Article" xlink:type="simple">https://med.jmirx.org/2025/1/e50712</related-article><kwd-group><kwd>breast</kwd><kwd>cancer</kwd><kwd>oncology</kwd><kwd>ovarian</kwd><kwd>virus</kwd><kwd>viral</kwd><kwd>Epstein-Barr</kwd><kwd>herpes</kwd><kwd>bioinformatics</kwd><kwd>chromosome</kwd><kwd>gene</kwd><kwd>genetic</kwd><kwd>genetics</kwd><kwd>chromosomal</kwd><kwd>DNA</kwd><kwd>genomic</kwd><kwd>BRCA</kwd><kwd>metastasis</kwd><kwd>biology</kwd></kwd-group></article-meta></front><body><p><italic>This is the peer-review report for &#x201C;Identifying Safeguards Disabled by Epstein-Barr Virus Infections in Genomes From Patients With Breast Cancer: Chromosomal Bioinformatics Analysis.&#x201D;</italic></p><sec id="s2"><title>Round 1 Review</title><sec id="s1-1"><title>Review Report With Major Revisions for the Paper</title><p>Title: &#x201C;Herpesvirus infections eliminate safeguards against breast cancer and its metastasis: comparable to hereditary breast cancers&#x201D;</p></sec><sec id="s1-2"><title>Summary</title><p>The paper [<xref ref-type="bibr" rid="ref1">1</xref>] hypothesizes that Epstein-Barr virus (EBV) infections promote breast cancer by disabling cancer safeguards. It is a bioinformatics analysis of public information from about 2100 breast cancers. The study finds that breast and ovarian cancer breakpoints cluster around EBV-associated cancer breakpoints, suggesting a significant role of EBV in promoting these cancers. The paper also identifies similarities in the molecular and cellular disruptions caused by EBV with those found in hereditary breast cancers.</p></sec><sec id="s1-3"><title>Major Revisions Needed</title><sec id="s1-3-1"><title>Clarification of Hypotheses and Objectives</title><p>The hypothesis, while intriguing, needs clearer articulation. Specifically, the connection between EBV and breast cancer needs more explicit theoretical underpinning. Clarify the objectives and expected outcomes of the study at the outset.</p></sec><sec id="s1-3-2"><title>Methodological Rigor and Data Sources</title><p>While the bioinformatics approach is robust, it would benefit from a more detailed description of the methods and algorithms used. Additionally, the selection criteria for the breast cancer data should be justified more thoroughly to avoid selection bias.</p></sec><sec id="s1-3-3"><title>Statistical Analysis</title><p>The statistical methods used need more comprehensive detailing. For complex analyses, ensure the statistical assumptions and any transformations of data are clearly explained. Include more information on the statistical tests used for hypothesis testing and the justification for their use.</p></sec><sec id="s1-3-4"><title>Comparative Analysis</title><p>The comparison between hereditary breast cancers and those potentially caused by EBV is insightful. However, a more detailed comparative analysis would strengthen the argument. This could include molecular or genetic profiling comparisons.</p></sec><sec id="s1-3-5"><title>Discussion on Contradictory or Supporting Evidence</title><p>The discussion section should address not only the supporting evidence but also any contradictory findings in the literature. This balance is crucial for a nuanced understanding of the subject.</p></sec><sec id="s1-3-6"><title>Implications and Future Research Directions</title><p>The implications of these findings are profound but need clearer articulation. Discuss the potential impact on breast cancer treatment and prevention strategies. Also, outline future research directions, particularly in clinical or experimental studies, to confirm these bioinformatics findings.</p></sec><sec id="s1-3-7"><title>References</title><p>Please add more background information about breast cancer (please cite: 1. Cao Y, Efetov S, He M, et al. Updated clinical perspectives and challenges of chimeric antigen receptor-T cell therapy in colorectal cancer and invasive breast cancer. Arch Immunol Ther Exp (Warsz). Aug 11, 2023;71(1):19. [doi: 10.1007/s00005-023-00684-x] [Medline: 37566162]; and 2. Liu Y, Lu S, Sun Y, et al. Deciphering the role of QPCTL in glioma progression and cancer immunotherapy. Front Immunol. Mar 29, 2023;14:1166377. [doi: 10.3389/fimmu.2023.1166377] [Medline: 37063864]).</p></sec></sec><sec id="s1-4"><title>Concluding Remarks</title><p>The paper presents a novel and potentially significant hypothesis linking EBV to breast cancer. However, it requires major revisions to enhance its methodological rigor, clarity, and comprehensiveness. Addressing these concerns will significantly strengthen the manuscript&#x2019;s impact and contribution to the field.</p></sec></sec></body><back><fn-group><fn fn-type="conflict"><p>None declared.</p></fn></fn-group><glossary><title>Abbreviations</title><def-list><def-item><term id="abb1">EBV</term><def><p>Epstein-Barr virus</p></def></def-item></def-list></glossary><ref-list><title>References</title><ref id="ref1"><label>1</label><nlm-citation citation-type="journal"><person-group person-group-type="author"><name name-style="western"><surname>Friedenson</surname><given-names>B</given-names> </name></person-group><article-title>Identifying safeguards disabled by Epstein-Barr virus infections in genomes from patients with breast cancer: chromosomal bioinformatics analysis</article-title><source>JMIRx Med</source><year>2025</year><volume>6</volume><fpage>e50712</fpage><pub-id pub-id-type="doi">10.2196/50712</pub-id></nlm-citation></ref></ref-list></back></article>