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Stroma abundance can also complicate genomic analysis by reducing detection of somatic mutations. This study performs computational tumor purity analysis on hepatic colorectal cancer metastases using whole-exome sequencing, evaluating ABSOLUTE, Sequenza, and PureCN. Median purity estimates were 30% for metastases versus 94% for matching tumor organoids, with organoid-enriched variant allele frequencies showing positive correlation with computational purity.",{"@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/metastatic-colorectal-adenocarcinoma-tumor-purity-assessment-from-whole-exome-sequencing-data/385668/",{"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/metastatic-colorectal-adenocarcinoma-tumor-purity-assessment-from-whole-exome-sequencing-data/385668.png","ImageObject",300,407,{"name":92,"@type":93},"Ivy","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-31","2026-09-24",true,{"@type":102,"interactionType":103,"userInteractionCount":105},"InteractionCounter",{"@type":104},"ViewAction",17,{"@type":107,"mainEntity":108},"FAQPage",[109,115,119],{"name":110,"@type":111,"acceptedAnswer":112},"What is the goal of this study on metastatic colorectal adenocarcinoma tumor purity?","Question",{"text":113,"@type":114},"To estimate the proportion of stroma embedded in hepatic colorectal cancer metastases using computational tumor purity analysis based on whole-exome sequencing data.","Answer",{"name":116,"@type":111,"acceptedAnswer":117},"Which in silico tumor purity tools were assessed?",{"text":118,"@type":114},"ABSOLUTE, Sequenza, and PureCN were used to generate computational purity estimates for the metastatic specimens.",{"name":120,"@type":111,"acceptedAnswer":121},"How did computational purity estimates compare between patient tumors and matching organoids?",{"text":122,"@type":114},"All computational methods reported a median tumor purity of 30% for metastatic specimens, while matching tumor organoids showed a much higher median purity estimate of 94%.","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},385668,1790470589,{"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},549758252649,"https://ap-avatar.wpscdn.com/avatar/8000253669c5317157?_k=1778319167496531819","PLOS ONE  \nOPEN ACCESS  \nCitation: Tbeileh N, Timmerman L, Mattis AN, Toriguchi K, Kasai Y, Corvera C, et al. (2023) Metastatic colorectal adenocarcinoma tumor purity assessment from whole exome sequencing data. PLoS ONE 18(4): e0271354 . [https://doi.org/](https://doi.org/)[ ](https://doi.org/)[10.1371/journal.pone](10.1371/journal.pone).0271354  \nEditor: Elizabeth Christie, Peter MacCallum Cancer Institute, AUSTRALIA  \nReceived: December 21, 2021  \nAccepted: June 28, 2022  \nPublished: April 6, 2023  \nPeer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here:  \n[https://doi.org/10.1371/journal.pone.0271354](https://doi.org/10.1371/journal.pone.0271354)  \n[Copyright:](Copyright:) © [2023 Tbeileh](2023 Tbeileh) et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.  \nData Availability Statement: All relevant data are within the paper. Whole-exome sequences of patients cannot be made publicly available for patient confidentiality reasons. This data is  \nRESEARCH ARTICLE  \nMetastatic colorectal adenocarcinoma tumor purity assessment from whole exome sequencing data  \nNoura Tbeileh1,2¤a, Luika Timmerman2 *, Aras N. Mattis2,3,4, Kan Toriguchi1,2¤b, Yosuke Kasai1,2¤c, Carlos Corvera1,2, Eric Nakakura1,2, Kenzo Hirose1,2, David  \nB. Donner1,2, Robert S. Warren1,2☯*, Eveliina Karelehto1,2☯  \n1 Department of Surgery, University of California, San Francisco, San Francisco, California, United States of America, 2 UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America, 3 Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America, 4 Liver Center, University of California, San Francisco, San Francisco, California, United States of America  \n☯ These authors contributed equally to this work.  \n¤a Current address: University of California, San Diego, San Diego, California, United States of America ¤b Current address: Department of Gastroenterological Surgery, Hyogo College of Medicine, Hyogo, Japan ¤c Current address: Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan * [robert.warren@ucsf.edu](robert.warren@ucsf.edu) (RSW); [luika.timmerman@ucsf.edu](luika.timmerman@ucsf.edu) (LT)  \nAbstract  \nTumors rich in stroma are associated with advanced stage and poor prognosis in colorectal adenocarcinoma (CRC) . Abundance of stromal cells also has implications for genomic analysis of patient tumors as it may prevent detection of somatic mutations. As part of our efforts to interrogate stroma-cancer cell interactions and to identify actionable therapeutic targets in metastatic CRC, we aimed to determine the proportion of stroma embedded in hepatic CRC metastases by performing computational tumor purity analysis based on whole exome sequencing data (WES) . Unlike previous studies focusing on histopathologically prescreened samples, we used an unbiased in-house collection of tumor specimens. WES from CRC liver metastasis samples were utilized to evaluate stromal content and to assess the performance of three in silico tumor purity tools, ABSOLUTE, Sequenza and PureCN. Matching tumor derived organoids were analyzed as a high purity control as they are enriched in cancer cells. Computational purity estimates were compared to those from a histopathological assessment conducted by a board-certified pathologist. According to all computational methods, metastatic specimens had a median tumor purity of 30% whereas the organoids were enriched for cancer cells with a median purity estimate of 94% . In line with this, va","cbCaifoPDoZPLozG","https://ap.wps.com/l/cbCaifoPDoZPLozG","pdf",2093400,14,"English","# Abstract\n# Introduction","[{\"question\":\"What is the goal of this study on metastatic colorectal adenocarcinoma tumor purity?\",\"answer\":\"To estimate the proportion of stroma embedded in hepatic colorectal cancer metastases using computational tumor purity analysis based on whole-exome sequencing data.\"},{\"question\":\"Which in silico tumor purity tools were assessed?\",\"answer\":\"ABSOLUTE, Sequenza, and PureCN were used to generate computational purity estimates for the metastatic specimens.\"},{\"question\":\"How did computational purity estimates compare between patient tumors and matching organoids?\",\"answer\":\"All computational methods reported a median tumor purity of 30% for metastatic specimens, while matching tumor organoids showed a much higher median purity estimate of 94%.\"}]","Metastatic colorectal adenocarcinoma tumor purity assessment from whole exome sequencing data | PDF",1790270505,35]