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This study examines the genomic landscape of HCC in Egyptian patients using whole exome sequencing. Thirteen HCC patients were analyzed, including living donor liver transplantation and surgical resection cases. Mutational signatures, significantly mutated genes, and pathway enrichments are assessed, alongside low-frequency variant profiles across HCC and non-HCC tissues, with emphasis on Tier 1 and Tier 2 clinically actionable targets.",{"@graph":69,"@context":122},[70,84,105],{"@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":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/genomic-landscape-of-hepatocellular-carcinoma-in-egyptian-patients-by-whole-exome-sequencing/333619/",{"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/genomic-landscape-of-hepatocellular-carcinoma-in-egyptian-patients-by-whole-exome-sequencing/333619.png","ImageObject",300,407,{"name":92,"@type":93},"Liam","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-27","2026-09-21",true,{"@type":102,"interactionType":103,"userInteractionCount":24},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"What is the main goal of the study on Egyptian HCC patients?","Question",{"text":112,"@type":113},"To explore the genomic landscape of hepatocellular carcinoma in Egyptian patients using whole exome sequencing.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"How were participants analyzed in the whole exome sequencing approach?",{"text":117,"@type":113},"Whole exome sequencing (Ion Torrent) was performed on 13 HCC patients, including cases undergoing living donor liver transplantation and surgical resection.",{"name":119,"@type":110,"acceptedAnswer":120},"What categories of variants and pathways were emphasized in the results?",{"text":121,"@type":113},"The study reports mutational signatures, significantly mutated genes, Tier 1 and Tier 2 variants, and KEGG pathway enrichments in HCC and compares them with non-HCC tissues.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},333619,1790668370,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":24,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":56,"language":139,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":140,"faqs":141,"seo_title":142,"seo_description":67,"update_tm":143,"read_time":144,"preview_page_count":4},8796095461564,"https://ap-avatar.wpscdn.com/davatar_155a257f0dc6eb9ab79c44ca47cae57d","Kassem etal. BMC Medical Genomics (2024) 17:202 [https://doi.org/10.1186/s12920-024-01965-w](https://doi.org/10.1186/s12920-024-01965-w)  \nBMC Medical Genomics  \n RESEARCH Open Access  \nGenomic landscape of hepatocellular  \ncarcinoma in Egyptian patients by whole exome sequencing  \nPerihan Hamdy Kassem1, Iman Fawzy Montasser2*, Ramy Mohamed Mahmoud 1, Rasha Ahmed Ghorab1, Dina A. AbdelHakam 1, Marium EL Sayed Ahmad Fathi1, Marwa A. Abdel Wahed1, Khaled Mohey1, Mariam Ibrahim4, Mohamed El Hadidi5,6, Yasmine M. Masssoud2, Manar Salah2, Arwa Abugable7, Mohamad Bahaa3, Sherif El Khamisy7 and Mahmoud El Meteini3  \nAbstract  \nBackground Hepatocellular carcinoma (HCC) is the most common primary liver cancer. Chronic hepatitis and liver cirrhosis lead to accumulation of genetic alterations driving HCC pathogenesis. This study is designed to explore genomic landscape of HCC in Egyptian patients by whole exome sequencing.  \nMethods Whole exome sequencing using Ion Torrent was done on 13 HCC patients, who underwent surgical intervention (7 patients underwent living donor liver transplantation (LDLT) and 6 patients had surgical resection} .  \nResults Mutational signature was mostly S1, S5, S6, and S12 in HCC. Analysis of highly mutated genes in both HCCand Non-HCC revealed the presence of highly mutated genes in HCC (AHNAK2, MUC6, MUC16, TTN, ZNF17, FLG, MUC12, OBSCN, PDE4DIP, MUC5b, and HYDIN) . Among the 26 significantly mutated HCC genes—identified across 10 genome sequencing studies—in addition to TCGA, APOB and RP1L1 showed the highest number of mutations in both HCC and Non-HCC tissues. Tier 1, Tier 2 variants inTCGA SMGs in HCC and Non-HCC (TP53, PIK3CA, CDKN2A, and BAP1) . Cancer Genome Landscape analysis revealed Tier 1 and Tier 2 variants in HCC (MSH2) and in Non-HCC (KMT2D and ATM) . For KEGG analysis, the significantly annotated clusters in HCC were Notch signaling, Wnt signaling, PI3K-AKT pathway, Hippo signaling, Apelin signaling, Hedgehog (Hh) signaling, and MAPK signaling, in addition to ECM-receptor interaction, focal adhesion, and calcium signaling. Tier 1 and Tier 2 variants KIT, KMT2D, NOTCH1, KMT2C, PIK3CA, KIT, SMARCA4, ATM, PTEN, MSH2, and PTCH1 were low frequency variants in both HCC and Non-HCC. Conclusion Our results are in accordance with previous studies in HCC regarding highly mutated genes, TCGA and specifically enriched pathways in HCC. Analysis for clinical interpretation of variants revealed the presence of Tier 1 and Tier 2 variants that represent potential clinically actionable targets. The use of sequencing techniques to detect structural variants and novel techniques as single cell sequencing together with multiomics transcriptomics, metagenomics will integrate the molecular pathogenesis of HCC in Egyptian patients.  \nKeywords Hepatocelleular carcinoma (HCC), Living Donor Liver Transplantation (LDLT), Whole exome sequencing, Mutational signature  \n*Correspondence:  \nIman Fawzy Montasser  \n[imanfawzy2@gmail.com](imanfawzy2@gmail.com)  \nFull list of author information is available at the end of the article  \n© The Author(s) 2024, corrected publication 2024. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, ","cbCaie2q4BsbhFf0","https://ap.wps.com/l/cbCaie2q4BsbhFf0","pdf",2858350,"English","# Abstract\n## Background\n## Methods\n## Results\n## Conclusion\n# Introduction\n## Genomic drivers and epidemiology in Egypt\n## Unmet needs and liquid biopsy context","[{\"question\":\"What is the main goal of the study on Egyptian HCC patients?\",\"answer\":\"To explore the genomic landscape of hepatocellular carcinoma in Egyptian patients using whole exome sequencing.\"},{\"question\":\"How were participants analyzed in the whole exome sequencing approach?\",\"answer\":\"Whole exome sequencing (Ion Torrent) was performed on 13 HCC patients, including cases undergoing living donor liver transplantation and surgical resection.\"},{\"question\":\"What categories of variants and pathways were emphasized in the results?\",\"answer\":\"The study reports mutational signatures, significantly mutated genes, Tier 1 and Tier 2 variants, and KEGG pathway enrichments in HCC and compares them with non-HCC tissues.\"}]","Genomic landscape of hepatocellular carcinoma in Egyptian patients by whole exome sequencing | PDF",1790003287,48]