Clinical and Genetic Spectrum of Dual Rare Genetic Diseases Revealed by Whole-Exome Sequencing in 14 Pediatric Patients

Clinical and Genetic Spectrum of Dual Rare Genetic Diseases Revealed by Whole-Exome Sequencing in 14 Pediatric Patients | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Clinical and Genetic Spectrum of Dual Rare Genetic Diseases Revealed by Whole-Exome Sequencing in 14 Pediatric Patients Minjun Zhao, Fuwei Li, Xiangpeng Lu, Hong Zheng, Xilong Du This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8320803/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 5 You are reading this latest preprint version Abstract Background : Dual molecular diagnoses, defined as the coexistence of pathogenic variants in two distinct disease-causing genes, challenge the traditional single-gene model of Mendelian inheritance. With the advent of whole-exome sequencing (WES), such complex genotypes are increasingly recognized. Objective : To investigate the clinical and genetic spectrum of dual rare genetic diseases in pediatric patients and to assess the diagnostic utility of WES in detecting diverse variant types. Methods : A retrospective analysis was conducted on 872 children with suspected rare genetic disorders who underwent proband or trio-based WES from January 2019 to February 2025. Variants were classified according to American College of Medical Genetics and Genomics(ACMG) guidelines. Dual diagnoses were confirmed when two independent pathogenic or likely pathogenic variants, each explaining part of the phenotype, were identified. Results : Among 872 patients, 370 (42.4%) received a molecular diagnosis, and 14 (3.8%) were confirmed with dual molecular diagnoses. Autosomal dominant (AD) disorders were most frequent (85.7%), de novo variants represented 57.14% (8 out of 14 cases). Six patients (42.9%) harbored combinations of single nucleotide variant (SNV) and other variant types, including exon deletions, paternal uniparental disomy (UPD15). Clinically, 14.3% of cases were phenotypically distinct, while 85.7% were phenotypically overlapping. Conclusion : Dual molecular diagnoses occur in approximately 3.8% of molecularly diagnosed patients and frequently involve de novo dominant variants. WES effectively detects multiple variant types (including SNV, CNV, exon deletions , UPD, and mosaicism) providing crucial insights for precise diagnosis, management, and genetic counseling in children with complex phenotypes. Dual molecular diagnosis whole-exome sequencing rare genetic diseases pediatric genetics Full Text Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Minor revision 23 Mar, 2026 Reviewers agreed at journal 14 Mar, 2026 Reviewers invited by journal 05 Mar, 2026 Editor assigned by journal 12 Dec, 2025 First submitted to journal 10 Dec, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8320803","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":601414565,"identity":"b68b72e2-d841-4c89-8bf4-8046d2b9bca2","order_by":0,"name":"Minjun Zhao","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAu0lEQVRIiWNgGAWjYHCCBIaEHzU8/MzMhx8Qr+VjzzE5yXa2NAOirWGcwcZsbHCeR0GCKOXy0w48YObhYUvcfJiHwYChxiaasA2zExKYeSxkErcd5j3wgOFYWm4DIS3M0iAtQFu2HeZLMGBsOExYCxtYCxtz4uZmHgMJorTwALVAvM9MrBYJoBZwIEscBgZyAjF+kZ+dA43K/sOHH3yosSGsBei09B9wdgJh5SDAfoA4daNgFIyCUTByAQBZ7jkPBXxCGQAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0009-0006-1257-1937","institution":"Henan University of Chinese Medicine","correspondingAuthor":true,"prefix":"","firstName":"Minjun","middleName":"","lastName":"Zhao","suffix":""},{"id":601414566,"identity":"15de89ef-9f01-4981-893c-34c94c3e70fc","order_by":1,"name":"Fuwei Li","email":"","orcid":"","institution":"Chigene(Beijing)Translational Medical Research Center Co.Ltd.","correspondingAuthor":false,"prefix":"","firstName":"Fuwei","middleName":"","lastName":"Li","suffix":""},{"id":601414567,"identity":"acff205f-0ee0-4385-85c0-61f84c24e3ac","order_by":2,"name":"Xiangpeng Lu","email":"","orcid":"","institution":"The First Affiliated Hospital of Henan University of Traditional Chinese Medicine","correspondingAuthor":false,"prefix":"","firstName":"Xiangpeng","middleName":"","lastName":"Lu","suffix":""},{"id":601414568,"identity":"9888c434-7dea-410b-b891-e154250713cd","order_by":3,"name":"Hong Zheng","email":"","orcid":"","institution":"The First Affiliated Hospital of Henan University of Traditional Chinese Medicine","correspondingAuthor":false,"prefix":"","firstName":"Hong","middleName":"","lastName":"Zheng","suffix":""},{"id":601414569,"identity":"25578ba2-e67b-4dae-a1ac-8af5c5486bdd","order_by":4,"name":"Xilong Du","email":"","orcid":"","institution":"Chigene(Beijing)Translational Medical Research Center Co. Ltd.","correspondingAuthor":false,"prefix":"","firstName":"Xilong","middleName":"","lastName":"Du","suffix":""}],"badges":[],"createdAt":"2025-12-09 19:16:24","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8320803/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8320803/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":104368255,"identity":"2ef4ed2d-5eb8-40a1-bcf7-1b131628ff26","added_by":"auto","created_at":"2026-03-11 03:55:56","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":437539,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8320803/v1_covered_f0c4d4fd-911d-4586-938a-1dbc2ff01d96.pdf"}],"financialInterests":"","formattedTitle":"Clinical and Genetic Spectrum of Dual Rare Genetic Diseases Revealed by Whole-Exome Sequencing in 14 Pediatric Patients","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"orphanet-journal-of-rare-diseases","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"ojrd","sideBox":"Learn more about [Orphanet Journal of Rare Diseases](http://ojrd.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/ojrd/default.aspx","title":"Orphanet Journal of Rare Diseases","twitterHandle":"@bmc","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"BMC/SO AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Dual molecular diagnosis, whole-exome sequencing, rare genetic diseases, pediatric genetics","lastPublishedDoi":"10.21203/rs.3.rs-8320803/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8320803/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e:\u0026nbsp;Dual molecular diagnoses, defined as the coexistence of pathogenic variants in two distinct disease-causing genes, challenge the traditional single-gene model of Mendelian inheritance. With the advent of whole-exome sequencing (WES), such complex genotypes are increasingly recognized.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eObjective\u003c/strong\u003e:\u0026nbsp;To investigate the clinical and genetic spectrum of dual rare genetic diseases in pediatric patients and to assess the diagnostic utility of WES in detecting diverse variant types.\u0026nbsp;\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethods\u003c/strong\u003e:\u0026nbsp;A retrospective analysis was conducted on 872 children with suspected rare genetic disorders who underwent proband or trio-based WES from January 2019 to February 2025. Variants were classified according to American College of Medical Genetics and Genomics(ACMG) guidelines. Dual diagnoses were confirmed when two independent pathogenic or likely pathogenic variants, each explaining part of the phenotype, were identified.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e: Among 872 patients, 370 (42.4%) received a molecular diagnosis, and 14 (3.8%) were confirmed with dual molecular diagnoses. Autosomal dominant (AD) disorders were most frequent (85.7%),\u0026nbsp;de novo variants represented 57.14% (8 out of 14 cases). Six patients (42.9%) harbored combinations of single nucleotide variant\u0026nbsp;(SNV) and other variant types, including exon deletions, paternal uniparental disomy (UPD15). Clinically, 14.3% of cases were phenotypically distinct, while 85.7% were phenotypically overlapping.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusion\u003c/strong\u003e:\u0026nbsp;Dual molecular diagnoses occur in approximately 3.8% of molecularly diagnosed patients and frequently involve de novo dominant variants. WES effectively detects multiple variant types (including SNV, CNV, exon deletions , UPD, and mosaicism) providing crucial insights for precise diagnosis, management, and genetic counseling in children with complex phenotypes.\u003c/p\u003e","manuscriptTitle":"Clinical and Genetic Spectrum of Dual Rare Genetic Diseases Revealed by Whole-Exome Sequencing in 14 Pediatric Patients","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-11 03:55:35","doi":"10.21203/rs.3.rs-8320803/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Minor revision","date":"2026-03-23T04:36:18+00:00","index":"","fulltext":""},{"type":"reviewerAgreed","content":"","date":"2026-03-14T09:57:53+00:00","index":0,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-03-05T16:16:01+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-12-12T13:48:10+00:00","index":"","fulltext":""},{"type":"submitted","content":"Orphanet Journal of Rare Diseases","date":"2025-12-11T03:49:17+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"orphanet-journal-of-rare-diseases","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"ojrd","sideBox":"Learn more about [Orphanet Journal of Rare Diseases](http://ojrd.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/ojrd/default.aspx","title":"Orphanet Journal of Rare Diseases","twitterHandle":"@bmc","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"BMC/SO AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"d4a3a814-06c1-4681-a733-406f6eed606e","owner":[],"postedDate":"March 11th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-05-06T10:52:11+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-11 03:55:35","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8320803","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8320803","identity":"rs-8320803","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}