[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-seo-364548-105":3,"detail-sidebar-cat-0-en-105":81,"doc-detail-364548-en":130},{"code":4,"msg":5,"data":6},0,"ok",{"site_id":7,"language":8,"slug":9,"title":10,"keywords":11,"description":12,"schema_data":13,"social_meta":74,"head_meta":76,"extra_data":78,"updated_unix":80},105,"en","tracking-the-evolution-of-cutaneous-melanoma-by-multiparameter-flow-sorting-and-genomic-profiling","Tracking the Evolution of Cutaneous Melanoma by Multiparameter Flow Sorting and Genomic Profiling","","Intratumoral heterogeneity and clonal evolution drive melanoma progression and metastasis, yet variable tumor cellularity reduces sensitivity when characterizing clonal evolution. This study integrates fluorescence-activated cell sorting (FACS) with whole-exome sequencing (WES) to analyze clonal composition across seven melanoma biopsies from three patients, each with matched primary and metastatic samples. A multiparameter ploidy sorting strategy enriches tumor populations using DNA ploidy and melanoma biomarkers (SOX10 or S100). Tumor purity increases from 70% (range 19–88%) to 91% (range 87–96%) post-sorting. Results reveal substantial inter- and intratumor heterogeneity, including two genomically distinct clonal populations within one primary site that generate different metastases.",{"@graph":14,"@context":73},[15,34,56],{"@type":16,"itemListElement":17},"BreadcrumbList",[18,23,27,31],{"item":19,"name":20,"@type":21,"position":22},"https://docshare.wps.com","Home","ListItem",1,{"item":24,"name":25,"@type":21,"position":26},"https://docshare.wps.com/document/","Document",2,{"item":28,"name":29,"@type":21,"position":30},"https://docshare.wps.com/document/healthcare/","Healthcare",3,{"item":32,"name":10,"@type":21,"position":33},"https://docshare.wps.com/document/tracking-the-evolution-of-cutaneous-melanoma-by-multiparameter-flow-sorting-and-genomic-profiling/364548/",4,{"url":32,"name":10,"@type":35,"image":36,"author":41,"headline":10,"publisher":44,"fileFormat":47,"inLanguage":8,"description":12,"dateModified":48,"datePublished":49,"encodingFormat":47,"isAccessibleForFree":50,"interactionStatistic":51},"DigitalDocument",{"url":37,"@type":38,"width":39,"height":40},"https://docshare.wps.com/thumbnails/tracking-the-evolution-of-cutaneous-melanoma-by-multiparameter-flow-sorting-and-genomic-profiling/364548.png","ImageObject",300,407,{"name":42,"@type":43},"Liam","Person",{"url":19,"name":45,"@type":46},"DocShare","Organization","application/pdf","2026-11-02","2026-09-23",true,{"@type":52,"interactionType":53,"userInteractionCount":55},"InteractionCounter",{"@type":54},"ViewAction",10,{"@type":57,"mainEntity":58},"FAQPage",[59,65,69],{"name":60,"@type":61,"acceptedAnswer":62},"Why is intratumoral heterogeneity important in melanoma studies?","Question",{"text":63,"@type":64},"Intratumoral heterogeneity and clonal evolution are pivotal in melanoma progression and metastasis. Variable tumor cellularity can limit the sensitivity and accuracy of detecting clonal evolution.","Answer",{"name":66,"@type":61,"acceptedAnswer":67},"What methods does the study combine to study melanoma evolution?",{"text":68,"@type":64},"The study combines fluorescence-activated cell sorting (FACS) with whole-exome sequencing (WES) to investigate clonal composition and evolutionary patterns.",{"name":70,"@type":61,"acceptedAnswer":71},"How does multiparameter sorting affect tumor purity?",{"text":72,"@type":64},"Using a multiparameter ploidy sorting approach, the mean tumor purity increases from 70% (range 19–88%) in unsorted material to 91% (range 87–96%) after sorting.","https://schema.org",{"og:url":32,"og:type":75,"og:title":10,"og:site_name":45,"og:description":12},"article",{"robots":77,"canonical":32},"index,follow",{"doc_id":79,"site_id":7},364548,1790486926,{"code":4,"msg":82,"data":83},"success",[84,88,92,96,101,106,110,115,120,123,126],{"id":22,"doc_module":4,"doc_module_name":25,"category_name":85,"show_sort_weight":86,"slug":87},"Story & Novel",90,"story-novel",{"id":26,"doc_module":4,"doc_module_name":25,"category_name":89,"show_sort_weight":90,"slug":91},"Literature",80,"literature",{"id":33,"doc_module":4,"doc_module_name":25,"category_name":93,"show_sort_weight":94,"slug":95},"Exam",70,"exam",{"id":97,"doc_module":4,"doc_module_name":25,"category_name":98,"show_sort_weight":99,"slug":100},5,"Comic",60,"comic",{"id":102,"doc_module":4,"doc_module_name":25,"category_name":103,"show_sort_weight":104,"slug":105},6,"Technology",50,"technology",{"id":107,"doc_module":4,"doc_module_name":25,"category_name":29,"show_sort_weight":108,"slug":109},7,40,"healthcare",{"id":111,"doc_module":4,"doc_module_name":25,"category_name":112,"show_sort_weight":113,"slug":114},8,"Research & Report",30,"research-report",{"id":116,"doc_module":4,"doc_module_name":25,"category_name":117,"show_sort_weight":118,"slug":119},9,"Religion & Spirituality",20,"religion-spirituality",{"id":118,"doc_module":4,"doc_module_name":25,"category_name":121,"show_sort_weight":118,"slug":122},"World Cup","world-cup",{"id":55,"doc_module":4,"doc_module_name":25,"category_name":124,"show_sort_weight":55,"slug":125},"Lifestyle","lifestyle",{"id":127,"doc_module":4,"doc_module_name":25,"category_name":128,"show_sort_weight":97,"slug":129},19,"General","general",{"code":4,"msg":82,"data":131},{"doc_id":79,"user_id":132,"nickname":42,"user_avatar":133,"doc_module":4,"category_id":107,"category_name":29,"doc_title":10,"doc_description":12,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":55,"is_deleted":4,"is_public":22,"is_downloadable":22,"audit_status":22,"page_count":139,"language":140,"language_code":8,"site_id":7,"html_lang":8,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":12,"update_tm":144,"read_time":145},8796095461564,"https://ap-avatar.wpscdn.com/davatar_155a257f0dc6eb9ab79c44ca47cae57d","Article  \nTracking the Evolution of Cutaneous Melanoma by Multiparameter Flow Sorting and Genomic Profiling  \nLuca Roma 1, *,†, Thomas Lorber 1,†, Sabrina Rau 1, Michael T. Barrett 2,‡, Caner Ercan 1, Federica Panebianco 1, Salvatore Piscuoglio 3, Katharina Glatz 1, Lukas Bubendorf 1,§ and Christian Ruiz 1,§  \nAcademic Editor: Alfonso Baldi  \nReceived: 20 January 2025  \nRevised: 14 February 2025  \nAccepted: 17 February 2025  \nPublished: 19 February 2025  \nCitation: Roma, L.; Lorber, T.; Rau, S.; Barrett, M.T.; Ercan, C.; Panebianco, F.; Piscuoglio, S.; Glatz, K.; Bubendorf, L.; Ruiz, C. Tracking the Evolution of Cutaneous Melanoma by Multiparameter Flow Sorting and Genomic Profiling. Int. J. Mol. Sci. 2025, 26, 1758. [https://doi.org/](https://doi.org/)[ ](https://doi.org/)[10.3390/ijms26041758](10.3390/ijms26041758)  \nCopyright: © 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ([https://creativecommons.org/](https://creativecommons.org/)[ ](https://creativecommons.org/)[licenses/by/4.0/](licenses/by/4.0/)) .  \n1 Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, CH-4031 Basel, Switzerland  \n2 Department of Research, Mayo Clinic in Arizona, Scottsdale, AZ 85259, USA  \n3 IRCCS Humanitas Research Hospital, 20089 Rozzano, Milan, Italy  \n* Correspondence: luca.roma@usb.ch or [luca.roma@unibas.ch](luca.roma@unibas.ch)[ ](luca.roma@unibas.ch)† These authors contributed equally to this work.  \n‡ Current address: Binary Genomics, Phoenix, AZ 85004, USA.  \n§ These authors contributed equally to this work.  \nAbstract: Intratumoral heterogeneity and clonal evolution are pivotal in the progression and metastasis of melanoma. However, when combined with variable tumor cellularity, intratumoral heterogeneity limits the sensitivity and accuracy of uncovering a cancer’sclonal evolution. In this study, we combined fluorescence-activated cell sorting (FACS) with whole-exome sequencing (WES) to investigate the clonal composition and evolutionary patterns in seven melanoma biopsies obtained from three patients, each having both primary site and metastatic samples. We employed a multiparameter ploidy sorting approach to isolate tumor populations based on DNA ploidy and melanoma biomarkers (SOX10 or S100), enabling us to investigate clonal evolution with high resolution. Our approach increased the mean tumor purity from 70%(range 19–88%) in unsorted material to 91%(range 87–96%) post-sorting. Our findings revealed significant inter-and intratumor heterogeneity, with one patient exhibiting two genomically distinct clonal tumor populations within a single primary site biopsy, each giving rise to different metastases. Our findings highlight the critical role of intratumoral heterogeneity and clonal evolution in melanoma, especially when analyzing tumor trajectories. The unique combination of multiparameter FACS and WES provides a powerful method for identifying clonal populations and reconstructing clonal evolution. This study provides valuable insights into the clonal architecture of melanoma and lays the groundwork for future research with larger patient groups.  \nKeywords: FACS; WES; melanoma; bioinformatics; omics data  \n1. Introduction  \nThe genomic landscape of melanoma features numerous genomic alterations with key driver mutations in genes, such as BRAF (45%), NRAS (17%), and KIT (9%), leading to dysregulated cell growth and survival pathways [1,2] . Detecting BRAF mutation is vital in advanced melanoma patients for the effective use of BRAF–MEK inhibitors. Despite their success, long-term survival rates remain relatively low [3,4]: only 22% and 19% of the patients treated with first-line BRAF–MEK inhibitors reached 3-year survival and 4-year survival, respectively [3] . Immune checkpoint inhibitors (ICIs) represent a breakthrough in the treatment of melanoma, w","cbCaijmbsVVuCOpo","https://ap.wps.com/l/cbCaijmbsVVuCOpo","pdf",1561356,15,"English","# Introduction\n## Abstract","[{\"question\":\"Why is intratumoral heterogeneity important in melanoma studies?\",\"answer\":\"Intratumoral heterogeneity and clonal evolution are pivotal in melanoma progression and metastasis. Variable tumor cellularity can limit the sensitivity and accuracy of detecting clonal evolution.\"},{\"question\":\"What methods does the study combine to study melanoma evolution?\",\"answer\":\"The study combines fluorescence-activated cell sorting (FACS) with whole-exome sequencing (WES) to investigate clonal composition and evolutionary patterns.\"},{\"question\":\"How does multiparameter sorting affect tumor purity?\",\"answer\":\"Using a multiparameter ploidy sorting approach, the mean tumor purity increases from 70% (range 19–88%) in unsorted material to 91% (range 87–96%) after sorting.\"}]","Tracking the Evolution of Cutaneous Melanoma by Multiparameter Flow Sorting and Genomic Profiling | PDF",1790158037,38]