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Immunotherapy has witnessed considerable success in recent years as a treatment for tumors. However, due to the heterogeneity of diseases, only a fraction of patients exhibit a positive response to immune checkpoint inhibitor (ICI) therapy. Various single-gene-based biomarkers and tumor mutational burden (TMB) have been proposed for predicting clinical responses to ICI; however, their predictive ability is limited. We propose the utilization of the Text Graph Convolutional Network (GCN) method to comprehensively assess the impact of multiple genes, aiming to improve the predictive capability for ICI response. We developed TG468, a Text GCN model framing drug response prediction as a text classification task. By combining natural language processing (NLP) and graph neural network techniques, TG468 effectively handles sparse and high-dimensional exome sequencing data. As a result, TG468 can distinguish survival time for patients who received ICI therapy and outperforms single gene biomarkers, TMB and some classical machine learning models. Additionally, TG468\u2019s prediction results facilitate the identification of immune status differences among specific patient types in the Cancer Genome Atlas dataset, providing a rationale for the model\u2019s predictions. Our approach represents a pioneering use of a GCN model to analyze exome data in patients undergoing ICI therapy and offers inspiration for future research using NLP technology to analyze exome sequencing data.<\/jats:p>","DOI":"10.1093\/bib\/bbae017","type":"journal-article","created":{"date-parts":[[2024,1,15]],"date-time":"2024-01-15T00:16:50Z","timestamp":1705277810000},"source":"Crossref","is-referenced-by-count":1,"title":["TG468: a text graph convolutional network for predicting clinical response to immune checkpoint inhibitor therapy"],"prefix":"10.1093","volume":"25","author":[{"given":"Kun","family":"Wang","sequence":"first","affiliation":[{"name":"School of Life Sciences , Division of Life Sciences and Medicine, , Hefei 230026 , China"},{"name":"University of Science and Technology of China , Division of Life Sciences and Medicine, , Hefei 230026 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiangshan","family":"Shi","sequence":"additional","affiliation":[{"name":"Drug Discovery and Design Center , State Key Laboratory of Drug Research, ; 555 Zuchongzhi Road, Shanghai 201203 , China"},{"name":"Shanghai Institute of Materia Medica Chinese Academy of Sciences , State Key Laboratory of Drug Research, ; 555 Zuchongzhi Road, Shanghai 201203 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaochu","family":"Tong","sequence":"additional","affiliation":[{"name":"Drug Discovery and Design Center , State Key Laboratory of Drug Research, ; 555 Zuchongzhi Road, Shanghai 201203 , China"},{"name":"Shanghai Institute of Materia Medica Chinese Academy of Sciences , State Key Laboratory of Drug Research, ; 555 Zuchongzhi Road, Shanghai 201203 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ning","family":"Qu","sequence":"additional","affiliation":[{"name":"Drug Discovery and Design Center , State Key Laboratory of Drug Research, ; 555 Zuchongzhi Road, Shanghai 201203 , China"},{"name":"Shanghai Institute of Materia Medica Chinese Academy of Sciences , State Key Laboratory of Drug Research, ; 555 Zuchongzhi Road, Shanghai 201203 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiangtai","family":"Kong","sequence":"additional","affiliation":[{"name":"Drug Discovery and Design Center , State Key Laboratory of Drug Research, ; 555 Zuchongzhi Road, Shanghai 201203 , China"},{"name":"Shanghai Institute of Materia Medica Chinese Academy of Sciences , State Key Laboratory of Drug Research, ; 555 Zuchongzhi Road, Shanghai 201203 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shengkun","family":"Ni","sequence":"additional","affiliation":[{"name":"Drug Discovery and Design Center , State Key Laboratory of Drug Research, ; 555 Zuchongzhi Road, Shanghai 201203 , China"},{"name":"Shanghai Institute of Materia Medica Chinese Academy of Sciences , State Key Laboratory of Drug Research, ; 555 Zuchongzhi Road, Shanghai 201203 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Xing","sequence":"additional","affiliation":[{"name":"Lingang Laboratory , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9547-0643","authenticated-orcid":false,"given":"Xutong","family":"Li","sequence":"additional","affiliation":[{"name":"Drug Discovery and Design Center , State Key Laboratory of Drug Research, , 555 Zuchongzhi Road, Shanghai 201203 , China"},{"name":"Shanghai Institute of Materia Medica, Chinese Academy of Sciences , State Key Laboratory of Drug Research, , 555 Zuchongzhi Road, Shanghai 201203 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3323-3092","authenticated-orcid":false,"given":"Mingyue","family":"Zheng","sequence":"additional","affiliation":[{"name":"School of Life Sciences , Division of Life Sciences and Medicine, , Hefei 230026 , China"},{"name":"University of Science and Technology of China , Division of Life Sciences and Medicine, , Hefei 230026 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,2,23]]},"reference":[{"issue":"4","key":"2024022316133891300_ref1","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1016\/j.cell.2017.01.017","article-title":"Primary, adaptive, and acquired resistance to cancer immunotherapy","volume":"168","author":"Sharma","year":"2017","journal-title":"Cell"},{"key":"2024022316133891300_ref2","doi-asserted-by":"crossref","DOI":"10.1111\/cpr.13283","article-title":"PAPPA2 mutation as a novel indicator 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