[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"detail-sidebar-cat-0-en-105":3,"doc-seo-378488-105":59,"doc-detail-378488-en":131},{"code":4,"msg":5,"data":6},0,"success",[7,13,18,23,28,33,38,43,48,51,55],{"id":8,"doc_module":4,"doc_module_name":9,"category_name":10,"show_sort_weight":11,"slug":12},1,"Document","Story & Novel",90,"story-novel",{"id":14,"doc_module":4,"doc_module_name":9,"category_name":15,"show_sort_weight":16,"slug":17},2,"Literature",80,"literature",{"id":19,"doc_module":4,"doc_module_name":9,"category_name":20,"show_sort_weight":21,"slug":22},4,"Exam",70,"exam",{"id":24,"doc_module":4,"doc_module_name":9,"category_name":25,"show_sort_weight":26,"slug":27},5,"Comic",60,"comic",{"id":29,"doc_module":4,"doc_module_name":9,"category_name":30,"show_sort_weight":31,"slug":32},6,"Technology",50,"technology",{"id":34,"doc_module":4,"doc_module_name":9,"category_name":35,"show_sort_weight":36,"slug":37},7,"Healthcare",40,"healthcare",{"id":39,"doc_module":4,"doc_module_name":9,"category_name":40,"show_sort_weight":41,"slug":42},8,"Research & Report",30,"research-report",{"id":44,"doc_module":4,"doc_module_name":9,"category_name":45,"show_sort_weight":46,"slug":47},9,"Religion & Spirituality",20,"religion-spirituality",{"id":46,"doc_module":4,"doc_module_name":9,"category_name":49,"show_sort_weight":46,"slug":50},"World Cup","world-cup",{"id":52,"doc_module":4,"doc_module_name":9,"category_name":53,"show_sort_weight":52,"slug":54},10,"Lifestyle","lifestyle",{"id":56,"doc_module":4,"doc_module_name":9,"category_name":57,"show_sort_weight":24,"slug":58},19,"General","general",{"code":4,"msg":60,"data":61},"ok",{"site_id":62,"language":63,"slug":64,"title":65,"keywords":66,"description":67,"schema_data":68,"social_meta":124,"head_meta":126,"extra_data":128,"updated_unix":130},105,"en","liquid-biopsy-epigenomic-profiling-for-cancer-subtyping","Liquid biopsy epigenomic profiling for cancer subtyping","","Liquid biopsy assays using circulating tumor DNA (ctDNA) are increasingly used in cancer care, but they have limited ability to characterize transcriptional programs and their dynamic changes. The study introduces an immunoprecipitation-based method for comprehensive epigenomic profiling from 1 ml of patient plasma, targeting histone modifications and DNA methylation. Across 433 individuals spanning 15 cancers, 1,268 epigenomic profiles provide a proxy for transcriptional activity, enabling inference of diagnostic and drug-target expression, assessment of targetable transcription factors, and detection of epigenetic resistance mechanisms.",{"@graph":69,"@context":123},[70,84,106],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":35,"@type":76,"position":81},"https://docshare.wps.com/document/healthcare/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/liquid-biopsy-epigenomic-profiling-for-cancer-subtyping/378488/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/liquid-biopsy-epigenomic-profiling-for-cancer-subtyping/378488.png","ImageObject",300,407,{"name":92,"@type":93},"Blitz","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-30","2026-09-24",true,{"@type":102,"interactionType":103,"userInteractionCount":105},"InteractionCounter",{"@type":104},"ViewAction",12,{"@type":107,"mainEntity":108},"FAQPage",[109,115,119],{"name":110,"@type":111,"acceptedAnswer":112},"What clinical problem does the method address in ctDNA testing?","Question",{"text":113,"@type":114},"It addresses ctDNA assays’ limited ability to identify transcriptional programs and their disease-associated dynamics compared with tumor tissue readouts.","Answer",{"name":116,"@type":111,"acceptedAnswer":117},"How does the assay perform epigenomic profiling from patient samples?",{"text":118,"@type":114},"It uses an immunoprecipitation-based approach to enrich DNA fragments carrying specific epigenetic marks, followed by high-throughput sequencing to quantify promoter activity, enhancer activity, and DNA methylation.",{"name":120,"@type":111,"acceptedAnswer":121},"What kinds of clinically actionable information does plasma epigenomic profiling enable?",{"text":122,"@type":114},"It can infer expression levels of diagnostic markers and drug targets, measure activity of therapeutically targetable transcription factors, and detect epigenetic mechanisms of resistance.","https://schema.org",{"og:url":83,"og:type":125,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":127,"canonical":83},"index,follow",{"doc_id":129,"site_id":62},378488,1790706434,{"code":4,"msg":5,"data":132},{"doc_id":129,"user_id":133,"nickname":92,"user_avatar":134,"doc_module":4,"category_id":34,"category_name":35,"doc_title":65,"doc_description":67,"doc_content":135,"file_id":136,"file_url":137,"file_type":138,"file_size":139,"view_count":105,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":140,"language":141,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":142,"faqs":143,"seo_title":144,"seo_description":67,"update_tm":145,"read_time":146},24464137899374,"https://us-avatar.wpscdn.com/davatar_3d24733baf745e90a7e4bdd5f77d97b2","nature medicine  \nBrief Communication [https://doi.org/10.1038/s41591-023-02605-z](https://doi.org/10.1038/s41591-023-02605-z)  \nLiquid biopsy epigenomic profiling for cancer subtyping  \nReceived: 15 July 2023  \nAccepted: 21 September 2023  \n\n| Published online: 21 October 2023 |\n| --- |\n|  Check for updates |\n\nSylvan C. Baca1,2,3,19, Ji-Heui Seo1,2,19, Matthew P. Davidsohn1,2, Brad Fortunato1,2,3, Karl Semaan1,3, Shahabbedin Sotudian  1,2,3, Gitanjali Lakshminarayanan1,2, Miklos Diossy4, Xintao Qiu  1,2, Talal ElZarif1,2, Hunter Savignano1,2,  \nJohn Canniff1,2, Ikenna Madueke1,2, Renee MariaSaliby  1,2, Ziwei Zhang1,2,3, Rong Li  1,2, Yijia Jiang1,2, Len Taing1,2, Mark Awad5, Cindy H. Chau  6,  \nJames A. DeCaprio  1,7, William D. Figg  6, Tim F. Greten  8, Aaron N. Hata  9,10, F. Stephen Hodi1, Melissa E. Hughes1, Keith L. Ligon  1,11, Nancy Lin1,  \nKimmie Ng  1, Matthew G. Oser  1, Catherine Meador9,10, HeatherA. Parsons  1, Mark M. Pomerantz1,2, Arun Rajan  12, Jerome Ritz  1, Manisha Thakuria13,14, Sara M. Tolaney  1, Patrick Y. Wen15,16, Henry Long  1,2, Jacob E. Berchuck  1,2, Zoltan Szallasi  4,17,18, Toni K. Choueiri  1 & Matthew L. Freedman  1,2,3   \nAlthough circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypesand their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1 ml of patient plasma. Using an immunoprecipitation-based approach targeting histone modificationsand DNA methylation, we measured 1,268 epigenomic profilesin plasma from 433 individuals with oneof 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling has the potential to unlock clinically actionable information that is currently accessible only via direct tissue sampling.  \nCirculating tumor DNA (ctDNA) analysis is gaining traction in clinical oncology asa minimally invasive means to detect targetable alterationsand monitor cancer recurrence or persistence. Most clinical ctDNA assays focus on genomic alterations, limiting their ability to detect clinically important features of cancer that are measured from tumor tissues, such as histologic subtypes and expression of key genes. To overcome this limitation, recent efforts have focused on measuring epigenomic features from ctDNA (for example, DNA methylation1,2) or inferring epigenomic features from nucleosome positioning3–5or DNA fragmentation patterns6. Most recently, profiling histone modifications  \nfrom circulating nucleosomes has advanced the ability to measure gene regulation from plasma7,8. Histone modifications provide a dynamic  \nreadout of transcriptional programs and cellular states in cancer9.  \nDespite advances in epigenomic profiling, current approaches provide a limited view of gene regulation. To address this deficit, we developed anassay that measures multiple facets of gene regulation. Using an immunoprecipitation-based approach, our assay enriches DNA fragments from regulatory elements (REs) bearing specific epigenetic marks. We used antibodies targeting methylated DNA, H3K4me3 (a histone modification associated with promoter activity) and  \nA full list of affiliations appears at the end of the paper. [e-mail:](e-mail: matthew_freedman@dfci.harvard.edu)[ matthew_freedman@dfci.harvard.edu](e-mail: matthew_freedman@dfci.harvard.edu)  \nNature Medicine | Volume 29 | November 2023 | 2737–2741 2737  \nBrief Communication [https://doi.org/10.1038/s41591-023-02605-z](https://doi.org/10.1038/s41591-023-02605-z)  \nf  \nH3K4me3 signal (arbit rar","cbCaipW1NX1D6GwW","https://ap.wps.com/l/cbCaipW1NX1D6GwW","pdf",8147063,23,"English","# Overview of the method\n## Profiling from plasma via immunoprecipitation and sequencing\n## Epigenomic datasets and correlations with ctDNA\n## Functional readouts: promoter and enhancer activity, DNA methylation\n## Linking plasma epigenomic signals to gene expression","[{\"question\":\"What clinical problem does the method address in ctDNA testing?\",\"answer\":\"It addresses ctDNA assays’ limited ability to identify transcriptional programs and their disease-associated dynamics compared with tumor tissue readouts.\"},{\"question\":\"How does the assay perform epigenomic profiling from patient samples?\",\"answer\":\"It uses an immunoprecipitation-based approach to enrich DNA fragments carrying specific epigenetic marks, followed by high-throughput sequencing to quantify promoter activity, enhancer activity, and DNA methylation.\"},{\"question\":\"What kinds of clinically actionable information does plasma epigenomic profiling enable?\",\"answer\":\"It can infer expression levels of diagnostic markers and drug targets, measure activity of therapeutically targetable transcription factors, and detect epigenetic mechanisms of resistance.\"}]","Liquid biopsy epigenomic profiling for cancer subtyping | PDF",1790230287,58]