Journal Article
. 2018 Oct; 28(11):1747-1756.
doi: 10.1101/gr.239244.118.

Maftools: efficient and comprehensive analysis of somatic variants in cancer

Anand Mayakonda 1 De-Chen Lin 2 Yassen Assenov 3 Christoph Plass 3 H Phillip Koeffler 1 
Affiliations
  • PMID: 30341162
  •     59 References
  •     351 citations

Abstract

Numerous large-scale genomic studies of matched tumor-normal samples have established the somatic landscapes of most cancer types. However, the downstream analysis of data from somatic mutations entails a number of computational and statistical approaches, requiring usage of independent software and numerous tools. Here, we describe an R Bioconductor package, Maftools, which offers a multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools only requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files. With the implementation of well-established statistical and computational methods, Maftools facilitates data-driven research and comparative analysis to discover novel results from publicly available data sets. In the present study, using three of the well-annotated cohorts from The Cancer Genome Atlas (TCGA), we describe the application of Maftools to reproduce known results. More importantly, we show that Maftools can also be used to uncover novel findings through integrative analysis.

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Xuanchen Zhou, Jie Han, +5 authors, Shuai Xu.
Front Oncol, 2020 Jun 18; 10. PMID: 32547941    Free PMC article.
Whole genome sequencing analysis identifies recurrent structural alterations in esophageal squamous cell carcinoma.
Munmee Dutta, Hidewaki Nakagawa, +12 authors, Masashi Fujita.
PeerJ, 2020 Jul 04; 8. PMID: 32617189    Free PMC article.
Conditionally Reprogrammed Cells from Patient-Derived Xenograft to Model Neuroendocrine Prostate Cancer Development.
Xinpei Ci, Jun Hao, +8 authors, Yuzhuo Wang.
Cells, 2020 Jun 10; 9(6). PMID: 32512818    Free PMC article.
Well-Differentiated Papillary Mesothelioma of the Peritoneum Is Genetically Distinct from Malignant Mesothelioma.
Raunak Shrestha, Noushin Nabavi, +10 authors, Andrew Churg.
Cancers (Basel), 2020 Jun 18; 12(6). PMID: 32545767    Free PMC article.
Construction of a Comprehensive Multiomics Map of Hepatocellular Carcinoma and Screening of Possible Driver Genes.
Ziyu Liu, Yan Lin, +4 authors, Rong Liang.
Front Genet, 2020 Jul 17; 11. PMID: 32670354    Free PMC article.
Increased number of subclones in lung squamous cell carcinoma elicits overexpression of immune related genes.
Myung Jin Song, Sang Hoon Lee, Eun Young Kim, Yoon Soo Chang.
Transl Lung Cancer Res, 2020 Jul 18; 9(3). PMID: 32676328    Free PMC article.
Prognostic value of an autophagy-related gene expression signature for endometrial cancer patients.
Hui Wang, Xiaoling Ma, +4 authors, Wenjun Cheng.
Cancer Cell Int, 2020 Jul 21; 20. PMID: 32684843    Free PMC article.
Establishment of a novel cell cycle-related prognostic signature predicting prognosis in patients with endometrial cancer.
Jinhui Liu, Jie Mei, +2 authors, Yan Zhang.
Cancer Cell Int, 2020 Jul 24; 20. PMID: 32699528    Free PMC article.
A DNA Methylation-Based Panel for the Prognosis and Dagnosis of Patients With Breast Cancer and Its Mechanisms.
Xiao-Ping Liu, Jinxuan Hou, +3 authors, Sheng Li.
Front Mol Biosci, 2020 Aug 01; 7. PMID: 32733914    Free PMC article.
Recurrent Neoantigens in Colorectal Cancer as Potential Immunotherapy Targets.
Chao Chen, Songming Liu, Ruokai Qu, Bo Li.
Biomed Res Int, 2020 Aug 01; 2020. PMID: 32733937    Free PMC article.
Identification of the key genes and characterizations of Tumor Immune Microenvironment in Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC).
Lemeng Zhang, Jianhua Chen, +3 authors, Changqie Pan.
J Cancer, 2020 Aug 04; 11(17). PMID: 32742444    Free PMC article.
Characterization of Neoantigen Load Subgroups in Gynecologic and Breast Cancers.
Yue Zhu, Xiaowei Meng, +3 authors, Fei Wang.
Front Bioeng Biotechnol, 2020 Aug 06; 8. PMID: 32754579    Free PMC article.
Overexpression of MUC16 predicts favourable prognosis in MUC16-mutant cervical cancer related to immune response.
Hao Wang, Chao Yan, Hong Ye.
Exp Ther Med, 2020 Aug 09; 20(2). PMID: 32765681    Free PMC article.
Somatic Mutation Profiling in Premalignant Lesions of Vulvar Squamous Cell Carcinoma.
Sebastian Zięba, Anne-Floor W Pouwer, +7 authors, Magdalena Kowalewska.
Int J Mol Sci, 2020 Jul 16; 21(14). PMID: 32664330    Free PMC article.
A Pilot Study for the Feasibility of Exome-Sequencing in Circulating Tumor Cells Versus Single Metastatic Biopsies in Breast Cancer.
Pushpinder Kaur, Daniel Campo, +6 authors, Julie E Lang.
Int J Mol Sci, 2020 Jul 12; 21(14). PMID: 32650480    Free PMC article.
The Somatic Mutation Landscape and RNA Prognostic Markers in Stomach Adenocarcinoma.
Xiulei Zhang, Peiming Zheng, +2 authors, Guangzhi Liu.
Onco Targets Ther, 2020 Aug 18; 13. PMID: 32801780    Free PMC article.
Clinical implications of prospective genomic profiling of metastatic breast cancer patients.
Courtney T van Geelen, Peter Savas, +11 authors, Sherene Loi.
Breast Cancer Res, 2020 Aug 20; 22(1). PMID: 32811538    Free PMC article.
Spontaneous mutations in the single TTN gene represent high tumor mutation burden.
Ji-Hye Oh, Se Jin Jang, +5 authors, Chang Ohk Sung.
NPJ Genom Med, 2020 Aug 22; 5. PMID: 32821429    Free PMC article.
Genome-wide identification of CpG island methylator phenotype related gene signature as a novel prognostic biomarker of gastric cancer.
Zhuo Zeng, Daxing Xie, Jianping Gong.
PeerJ, 2020 Aug 22; 8. PMID: 32821544    Free PMC article.
CVCDAP: an integrated platform for molecular and clinical analysis of cancer virtual cohorts.
Xiaoqing Guan, Meng Cai, +3 authors, Jianmin Wu.
Nucleic Acids Res, 2020 May 26; 48(W1). PMID: 32449936    Free PMC article.
Identifying CpG methylation signature as a promising biomarker for recurrence and immunotherapy in non-small-cell lung carcinoma.
Ruihan Luo, Jing Song, +6 authors, Longke Ran.
Aging (Albany NY), 2020 Jul 30; 12(14). PMID: 32723974    Free PMC article.
The Potential of Five Immune-Related Prognostic Genes to Predict Survival and Response to Immune Checkpoint Inhibitors for Soft Tissue Sarcomas Based on Multi-Omic Study.
Hui-Yun Gu, Lu-Lu Lin, +3 authors, Ren-Xiong Wei.
Front Oncol, 2020 Aug 28; 10. PMID: 32850416    Free PMC article.
Immunogenomic Profiling and Classification of Prostate Cancer Based on HIF-1 Signaling Pathway.
Jukun Song, Weiming Chen, +3 authors, Jianguo Zhu.
Front Oncol, 2020 Aug 28; 10. PMID: 32850440    Free PMC article.
Immune Cytolytic Activity as an Indicator of Immune Checkpoint Inhibitors Treatment for Prostate Cancer.
Ze Gao, Yiran Tao, +7 authors, Hai Huang.
Front Bioeng Biotechnol, 2020 Aug 28; 8. PMID: 32850758    Free PMC article.
RNA processing genes characterize RNA splicing and further stratify colorectal cancer.
Xiaofan Lu, Yujie Zhou, +8 authors, Fangrong Yan.
Cell Prolif, 2020 Jul 01; 53(8). PMID: 32596958    Free PMC article.
Analyzing and validating the prognostic value and mechanism of colon cancer immune microenvironment.
Xinyi Wang, Jinzhong Duanmu, +2 authors, Qunguang Jiang.
J Transl Med, 2020 Aug 30; 18(1). PMID: 32859214    Free PMC article.
Association of MUC16 Mutation With Response to Immune Checkpoint Inhibitors in Solid Tumors.
Lei Zhang, Xiaohong Han, Yuankai Shi.
JAMA Netw Open, 2020 Aug 28; 3(8). PMID: 32845327    Free PMC article.
Identification of an immune-related gene-based signature to predict prognosis of patients with gastric cancer.
Xiang-Ting Qiu, Yu-Cui Song, +3 authors, Jing He.
World J Gastrointest Oncol, 2020 Sep 04; 12(8). PMID: 32879664    Free PMC article.
Pre-Existing Tumoral B Cell Infiltration and Impaired Genome Maintenance Correlate with Response to Chemoradiotherapy in Locally Advanced Rectal Cancer.
Juan M Sendoya, Soledad Iseas, +19 authors, Andrea S Llera.
Cancers (Basel), 2020 Aug 14; 12(8). PMID: 32784964    Free PMC article.
Impact of Somatic Mutations in Non-Small-Cell Lung Cancer: A Retrospective Study of a Chinese Cohort.
Hai-Bo Shen, Jie Li, +4 authors, Tian-Jun Hu.
Cancer Manag Res, 2020 Sep 05; 12. PMID: 32884354    Free PMC article.
HPV-related methylation-based reclassification and risk stratification of cervical cancer.
Si Yang, Ying Wu, +10 authors, Huafeng Kang.
Mol Oncol, 2020 May 15; 14(9). PMID: 32408396    Free PMC article.
Multi-omics Data Analyses Construct TME and Identify the Immune-Related Prognosis Signatures in Human LUAD.
Yuwei Zhang, Minglei Yang, +6 authors, Qi Liao.
Mol Ther Nucleic Acids, 2020 Aug 18; 21. PMID: 32805489    Free PMC article.
Prognosis of Lung Adenocarcinoma Patients With NTRK3 Mutations to Immune Checkpoint Inhibitors.
Yuchun Niu, Anqi Lin, +5 authors, Jian Zhang.
Front Pharmacol, 2020 Sep 10; 11. PMID: 32903385    Free PMC article.
Discovery of Prognostic Signature Genes for Overall Survival Prediction in Gastric Cancer.
Changyuan Meng, Shusen Xia, +3 authors, Tong Zhou.
Comput Math Methods Med, 2020 Sep 11; 2020. PMID: 32908579    Free PMC article.
ATM Mutations Benefit Bladder Cancer Patients Treated With Immune Checkpoint Inhibitors by Acting on the Tumor Immune Microenvironment.
Ruibin Yi, Anqi Lin, +3 authors, Jian Zhang.
Front Genet, 2020 Sep 15; 11. PMID: 32922441    Free PMC article.
The genomic landscape of Mongolian hepatocellular carcinoma.
Julián Candia, Enkhjargal Bayarsaikhan, +8 authors, Xin Wei Wang.
Nat Commun, 2020 Sep 03; 11(1). PMID: 32873799    Free PMC article.
Next-Generation Sequencing Characterizes the Landscape of Somatic Mutations and Pathways in Metastatic Bile Tract Carcinoma.
Qi Li, Qifan Zhang, +5 authors, Jinzhang Chen.
J Oncol, 2020 Sep 22; 2020. PMID: 32952556    Free PMC article.
Development of Autophagy Signature-Based Prognostic Nomogram for Refined Glioma Survival Prognostication.
Yuxiang Fan, Xinyu Peng, Baoqin Li, Gang Zhao.
Biomed Res Int, 2020 Sep 24; 2020. PMID: 32964017    Free PMC article.
Identification of RNA: 5-Methylcytosine Methyltransferases-Related Signature for Predicting Prognosis in Glioma.
Peng Wang, Miaojing Wu, +5 authors, Kai Huang.
Front Oncol, 2020 Sep 26; 10. PMID: 32974125    Free PMC article.
Development and Validation of a Tumor Mutation Burden-Related Immune Prognostic Model for Lower-Grade Glioma.
Wen Yin, Xingjun Jiang, +9 authors, Guihua Tang.
Front Oncol, 2020 Sep 26; 10. PMID: 32974146    Free PMC article.
Long Non-Coding RNA Profile Study Identifies an Immune-Related lncRNA Prognostic Signature for Kidney Renal Clear Cell Carcinoma.
Zhuolun Sun, Changying Jing, Chutian Xiao, Tengcheng Li.
Front Oncol, 2020 Sep 26; 10. PMID: 32974157    Free PMC article.
CoMut: visualizing integrated molecular information with comutation plots.
Jett Crowdis, Meng Xiao He, Brendan Reardon, Eliezer M Van Allen.
Bioinformatics, 2020 Jun 06; 36(15). PMID: 32502231    Free PMC article.
MUC4, MUC16, and TTN genes mutation correlated with prognosis, and predicted tumor mutation burden and immunotherapy efficacy in gastric cancer and pan-cancer.
Yue Yang, Jieyun Zhang, +3 authors, Weijian Guo.
Clin Transl Med, 2020 Sep 09; 10(4). PMID: 32898332    Free PMC article.
Favorable Immune Microenvironment in Patients with EGFR and MAPK Co-Mutations.
Wang Yang, Naifei Chen, +4 authors, Jiuwei Cui.
Lung Cancer (Auckl), 2020 Sep 29; 11. PMID: 32982525    Free PMC article.
Biomarkers of the Response to Immune Checkpoint Inhibitors in Metastatic Urothelial Carcinoma.
Siteng Chen, Ning Zhang, +3 authors, Junhua Zheng.
Front Immunol, 2020 Sep 29; 11. PMID: 32983112    Free PMC article.
Mucinous Adenocarcinoma of the Rectum: A Whole Genome Sequencing Study.
Ian S Reynolds, Valentina Thomas, +6 authors, Simon J Furney.
Front Oncol, 2020 Sep 29; 10. PMID: 32984045    Free PMC article.
A Prognostic Prediction Model Developed Based on Four CpG Sites and Weighted Correlation Network Analysis Identified DNAJB1 as a Novel Biomarker for Pancreatic Cancer.
Lingming Kong, Peng Liu, +5 authors, Xiaodong Tan.
Front Oncol, 2020 Sep 29; 10. PMID: 32984053    Free PMC article.
Analysis of genomic and transcriptomic variations as prognostic signature for lung adenocarcinoma.
Talip Zengin, Tuğba Önal-Süzek.
BMC Bioinformatics, 2020 Oct 02; 21(Suppl 14). PMID: 32998690    Free PMC article.
Identification of an Immune Signature Predicting Prognosis Risk and Lymphocyte Infiltration in Colon Cancer.
Xinyu Li, Dacheng Wen, +3 authors, Hao Chen.
Front Immunol, 2020 Oct 06; 11. PMID: 33013820    Free PMC article.
Characteristics of mutational signatures of unknown etiology.
Xiaoju Hu, Zhuxuan Xu, Subhajyoti De.
NAR Cancer, 2020 Oct 06; 2(3). PMID: 33015626    Free PMC article.
Low mutation burden and differential tumor-infiltrating immune cells correlate with lymph node metastasis in colorectal cancer.
Xiao Huang, Wei Cai, Li Liu, Wenliang Yuan.
Int J Clin Exp Pathol, 2020 Oct 13; 13(9). PMID: 33042330    Free PMC article.
Trastuzumab plus docetaxel and capecitabine as a first-line treatment for HER2-positive advanced gastric or gastroesophageal junction cancer: a phase II, multicenter, open-label, single-arm study.
Feng Wang, Tian-Shu Liu, +14 authors, Rui-Hua Xu.
Am J Cancer Res, 2020 Oct 13; 10(9). PMID: 33042632    Free PMC article.
Whole-exome sequencing of long-term, never relapse exceptional responders of trastuzumab-treated HER2+ metastatic breast cancer.
Naomi Walsh, Charlotte Andrieu, +5 authors, John Crown.
Br J Cancer, 2020 Jul 28; 123(8). PMID: 32713940    Free PMC article.
Molecular stratification of endometrioid ovarian carcinoma predicts clinical outcome.
Robert L Hollis, John P Thomson, +12 authors, C Simon Herrington.
Nat Commun, 2020 Oct 07; 11(1). PMID: 33020491    Free PMC article.
Construction of a Prognostic Immune Signature for Squamous-Cell Lung Cancer to Predict Survival.
Rui-Lian Chen, Jing-Xu Zhou, +8 authors, Li-Zhu Lin.
Front Immunol, 2020 Oct 20; 11. PMID: 33072067    Free PMC article.
Significance of Tumor Mutation Burden in Immune Infiltration and Prognosis in Cutaneous Melanoma.
Kai Kang, Fucun Xie, +2 authors, Xiang Wang.
Front Oncol, 2020 Oct 20; 10. PMID: 33072607    Free PMC article.
Distinct Mutation Patterns Reveal Melanoma Subtypes and Influence Immunotherapy Response in Advanced Melanoma Patients.
Franz J Hilke, Tobias Sinnberg, +10 authors, Andrea Forschner.
Cancers (Basel), 2020 Aug 23; 12(9). PMID: 32825510    Free PMC article.
CTLA4 has a profound impact on the landscape of tumor-infiltrating lymphocytes with a high prognosis value in clear cell renal cell carcinoma (ccRCC).
Shiyi Liu, Feiyan Wang, +10 authors, Yanxiang Cheng.
Cancer Cell Int, 2020 Oct 30; 20. PMID: 33117084    Free PMC article.
Comprehensive Analysis of Prognostic Markers for Acute Myeloid Leukemia Based on Four Metabolic Genes.
Yuanyuan Zhang, Shengling Ma, +2 authors, Yu Hu.
Front Oncol, 2020 Oct 30; 10. PMID: 33117716    Free PMC article.
Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma.
Wenshuai Liu, Hanxing Tong, +16 authors, Yuhong Zhou.
BMC Cancer, 2020 Oct 30; 20(1). PMID: 33115433    Free PMC article.
Whole-genome sequencing of 508 patients identifies key molecular features associated with poor prognosis in esophageal squamous cell carcinoma.
Yongping Cui, Hongyan Chen, +35 authors, Zhihua Liu.
Cell Res, 2020 May 14; 30(10). PMID: 32398863    Free PMC article.
Identification and validation of a combined hypoxia and immune index for triple-negative breast cancer.
Shaoquan Zheng, Yutian Zou, +6 authors, Xiaoming Xie.
Mol Oncol, 2020 Jun 11; 14(11). PMID: 32521117    Free PMC article.
Landscape of active enhancers developed de novo in cirrhosis and conserved in hepatocellular carcinoma.
Yao Yang, Xiaoyu Deng, +9 authors, Youcai Deng.
Am J Cancer Res, 2020 Nov 10; 10(10). PMID: 33163263    Free PMC article.
Targeted sequencing reveals the somatic mutation landscape in a Swedish breast cancer cohort.
Argyri Mathioudaki, Viktor Ljungström, +9 authors, Kerstin Lindblad-Toh.
Sci Rep, 2020 Nov 11; 10(1). PMID: 33168853    Free PMC article.
DNA Methylation-Based Panel Predicts Survival of Patients With Clear Cell Renal Cell Carcinoma and Its Correlations With Genomic Metrics and Tumor Immune Cell Infiltration.
Xiao-Ping Liu, Lingao Ju, +3 authors, Xinghuan Wang.
Front Cell Dev Biol, 2020 Nov 13; 8. PMID: 33178689    Free PMC article.
Butyrate enhances the efficacy of radiotherapy via FOXO3A in colorectal cancer patient‑derived organoids.
Misun Park, Junhye Kwon, +5 authors, Younjoo Kim.
Int J Oncol, 2020 Nov 12; 57(6). PMID: 33173975    Free PMC article.
Whole Genome Sequencing Identifies Key Genes in Spinal Schwannoma.
Xin Gao, Li Zhang, +7 authors, Jianru Xiao.
Front Genet, 2020 Nov 17; 11. PMID: 33193598    Free PMC article.
Integration of the Tumor Mutational Burden and Tumor Heterogeneity Identify an Immunological Subtype of Melanoma With Favorable Survival.
Yanmei Gao, Chunhe Yang, +3 authors, Yadong Yang.
Front Oncol, 2020 Nov 17; 10. PMID: 33194669    Free PMC article.
Molecular Profiling Reveals Common and Specific Development Processes in Different Types of Gynecologic Cancers.
Yuanli Guo, Junfeng Liu, +10 authors, Shan Chen.
Front Oncol, 2020 Nov 17; 10. PMID: 33194730    Free PMC article.
Epigenetic age acceleration of early stage hepatocellular carcinoma tightly associated with hepatitis B virus load, immunoactivation, and improved survival.
Xiaole Fan, Hongxin Yuan, +4 authors, Hui Zhao.
Cancer Biol Ther, 2020 Sep 12; 21(10). PMID: 32914683    Free PMC article.
An Epithelial-Mesenchymal Transition (EMT) Preoperative Nomogram for Prediction of Lymph Node Metastasis in Bladder Cancer (BLCA).
Rui Cao, Bo Ma, +3 authors, Lushun Yuan.
Dis Markers, 2020 Nov 19; 2020. PMID: 33204364    Free PMC article.
The Clinical Kinase Index: A Method to Prioritize Understudied Kinases as Drug Targets for the Treatment of Cancer.
Derek Essegian, Rimpi Khurana, Vasileios Stathias, Stephan C Schürer.
Cell Rep Med, 2020 Nov 19; 1(7). PMID: 33205077    Free PMC article.
Identification of long-term survival-associated gene in breast cancer.
Shipeng Ning, Hui Li, +10 authors, Da Pang.
Aging (Albany NY), 2020 Oct 21; 12(20). PMID: 33080569    Free PMC article.
Ex vivo culture of circulating tumour cells derived from non-small cell lung cancer.
Joanna Kapeleris, Arutha Kulasinghe, +6 authors, Chamindie Punyadeera.
Transl Lung Cancer Res, 2020 Nov 20; 9(5). PMID: 33209602    Free PMC article.
Molecular Landscape and Actionable Alterations in a Genomically Guided Cancer Clinical Trial: National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH).
Keith T Flaherty, Robert J Gray, +23 authors, NCI-MATCH team.
J Clin Oncol, 2020 Oct 14; 38(33). PMID: 33048619    Free PMC article.
Germline mutational profile of Chinese patients under 70 years old with colorectal cancer.
Teng-Jia Jiang, Fang Wang, +9 authors, Feng Wang.
Cancer Commun (Lond), 2020 Sep 12; 40(11). PMID: 32914570    Free PMC article.
Characterization of the Immune Cell Infiltration Landscape in Head and Neck Squamous Cell Carcinoma to Aid Immunotherapy.
Xinhai Zhang, Mengqi Shi, Tielou Chen, Boxin Zhang.
Mol Ther Nucleic Acids, 2020 Nov 25; 22. PMID: 33230435    Free PMC article.
Prognostic Role of Tumor Mutation Burden Combined With Immune Infiltrates in Skin Cutaneous Melanoma Based on Multi-Omics Analysis.
Junya Yan, Xiaowen Wu, +2 authors, Shundong Cang.
Front Oncol, 2020 Nov 27; 10. PMID: 33240814    Free PMC article.
Lower mutant-allele tumor heterogeneity is a biomarker in FGFR3-mutant bladder cancer for better prognosis.
Yuying Han, Xu Liu, +2 authors, Zhengguo Ji.
World J Surg Oncol, 2020 Nov 28; 18(1). PMID: 33243261    Free PMC article.
Immunological classification of gliomas based on immunogenomic profiling.
Qiushi Feng, Lin Li, Mengyuan Li, Xiaosheng Wang.
J Neuroinflammation, 2020 Nov 29; 17(1). PMID: 33246490    Free PMC article.
SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events.
Erik N Bergstrom, Mi Ni Huang, +4 authors, Ludmil B Alexandrov.
BMC Genomics, 2019 Sep 01; 20(1). PMID: 31470794    Free PMC article.
Exploring the Pathological Mechanism of Bladder Cancer Based on Tumor Mutational Burden Analysis.
Yao Ma, Xiao-Fei Feng, Wan-Xia Yang, Chong-Ge You.
Biomed Res Int, 2019 Sep 20; 2019. PMID: 31534952    Free PMC article.
Genetic investigation of nodal melanocytic nevi in cases of giant congenital melanocytic nevus.
Y Cao, X Yang, +4 authors, D-M Lin.
Histol Histopathol, 2020 Jul 31; 35(10). PMID: 32729623
Mouse-human co-clinical trials demonstrate superior anti-tumour effects of buparlisib (BKM120) and cetuximab combination in squamous cell carcinoma of head and neck.
Hye Ryun Kim, Han Na Kang, +19 authors, Byoung Chul Cho.
Br J Cancer, 2020 Sep 24; 123(12). PMID: 32963347    Free PMC article.
CCL5-dependent mast cell infiltration into the tumor microenvironment in clear cell renal cell carcinoma patients.
Tianjie Liu, Qing Xia, +10 authors, Shan Xu.
Aging (Albany NY), 2020 Nov 13; 12(21). PMID: 33177244    Free PMC article.
Discovering novel driver mutations from pan-cancer analysis of mutational and gene expression profiles.
Houriiyah Tegally, Kevin H Kensler, +3 authors, Shakuntala Baichoo.
PLoS One, 2020 Nov 25; 15(11). PMID: 33232371    Free PMC article.
Correlation of genetic alterations by whole-exome sequencing with clinical outcomes of glioblastoma patients from the Lebanese population.
Fadi S Saadeh, Rami Z Morsi, +7 authors, Hazem I Assi.
PLoS One, 2020 Nov 26; 15(11). PMID: 33237934    Free PMC article.
Tumor evolutionary trajectories during the acquisition of invasiveness in early stage lung adenocarcinoma.
Siwei Wang, Mulong Du, +14 authors, Rong Yin.
Nat Commun, 2020 Nov 29; 11(1). PMID: 33247113    Free PMC article.
Major Histocompatibility Complex Genes as Therapeutic Opportunity for Immune Cold Molecular Cancer Subtypes.
Paweł Karpiński, Łukasz Łaczmański, Maria M Sąsiadek.
J Immunol Res, 2020 Dec 08; 2020. PMID: 33282963    Free PMC article.
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Assessment of hazard immune-related genes and tumor immune infiltrations in renal cell carcinoma.
Hongxi Chen, Jinliang Xie, Peng Jin.
Am J Transl Res, 2020 Dec 15; 12(11). PMID: 33312353    Free PMC article.
Multi-omics analysis reveals the genetics and immune landscape of dexamethasone responsive genes in cancer microenvironment.
Yu Shen, Ying C Wu, Lixiong Gu.
Ann Transl Med, 2020 Dec 15; 8(21). PMID: 33313161    Free PMC article.
Multi-Omics Analysis Reveals Novel Subtypes and Driver Genes in Glioblastoma.
Yang Yuan, Pan Qi, +3 authors, Mao Qing.
Front Genet, 2020 Dec 17; 11. PMID: 33324446    Free PMC article.
The Significance of Secreted Phosphoprotein 1 in Multiple Human Cancers.
Tengteng Wei, Guoshu Bi, +9 authors, Donglin Zhu.
Front Mol Biosci, 2020 Dec 17; 7. PMID: 33324676    Free PMC article.
Somatic alterations and mutational burden are potential predictive factors for metachronous development of early gastric cancer.
Kazuhiro Sakuta, Yu Sasaki, +12 authors, Yoshiyuki Ueno.
Sci Rep, 2020 Dec 18; 10(1). PMID: 33328548    Free PMC article.
Prognostic Biomarker TP53 Mutations for Immune Checkpoint Blockade Therapy and Its Association With Tumor Microenvironment of Lung Adenocarcinoma.
Xinqing Lin, Liqiang Wang, +4 authors, Chengzhi Zhou.
Front Mol Biosci, 2020 Dec 18; 7. PMID: 33330629    Free PMC article.
SYNE1 mutation may enhance the response to immune checkpoint blockade therapy in clear cell renal cell carcinoma patients.
Pengju Li, Jeifei Xiao, +3 authors, Wei Chen.
Aging (Albany NY), 2020 Oct 09; 12(19). PMID: 33031058    Free PMC article.
Association of clock-like mutational signature with immune checkpoint inhibitor outcome in patients with melanoma and NSCLC.
Wei Chong, Zhe Wang, +8 authors, Hao Chen.
Mol Ther Nucleic Acids, 2020 Dec 19; 23. PMID: 33335795    Free PMC article.
Metabolism-Associated Molecular Classification of Colorectal Cancer.
Meng Zhang, Hai-Zhou Wang, +3 authors, Qiu Zhao.
Front Oncol, 2020 Dec 22; 10. PMID: 33344254    Free PMC article.
Targeted Sequencing of Pancreatic Adenocarcinomas from Patients with Metachronous Pulmonary Metastases.
Viktor Hlavac, Beatrice Mohelnikova-Duchonova, +4 authors, Pavel Soucek.
Genes (Basel), 2020 Dec 02; 11(12). PMID: 33255265    Free PMC article.
Clinical and Genetic Tumor Characteristics of Responding and Non-Responding Patients to PD-1 Inhibition in Hepatocellular Carcinoma.
Stephan Spahn, Daniel Roessler, +13 authors, Michael Bitzer.
Cancers (Basel), 2020 Dec 24; 12(12). PMID: 33353145    Free PMC article.
Genetic alterations associated with 18F-fluorodeoxyglucose positron emission tomography/computed tomography in head and neck squamous cell carcinoma.
Sangwon Han, Jungsu S Oh, Hyo Sang Lee, Jae Seung Kim.
Transl Oncol, 2020 Dec 29; 14(2). PMID: 33359902    Free PMC article.
Identification of Driver Genes Regulating the T-Cell-Infiltrating Levels in Hepatocellular Carcinoma.
Yi Cai, Ying Tian, +8 authors, Zhengxia Yang.
Front Genet, 2021 Jan 01; 11. PMID: 33381145    Free PMC article.
ANTXR1 Is a Prognostic Biomarker and Correlates With Stromal and Immune Cell Infiltration in Gastric Cancer.
Xiaodong Huang, Jie Zhang, Yongbin Zheng.
Front Mol Biosci, 2021 Jan 02; 7. PMID: 33385012    Free PMC article.
Immune signature-based risk stratification and prediction of immune checkpoint inhibitor's efficacy for lung adenocarcinoma.
Ming Yi, Anping Li, +3 authors, Kongming Wu.
Cancer Immunol Immunother, 2021 Jan 03; 70(6). PMID: 33386920    Free PMC article.
Defining muscle-invasive bladder cancer immunotypes by introducing tumor mutation burden, CD8+ T cells, and molecular subtypes.
Zihao Chen, Guojun Liu, +5 authors, Zhifeng Wang.
Hereditas, 2021 Jan 04; 158(1). PMID: 33388091    Free PMC article.
Sequential fate-switches in stem-like cells drive the tumorigenic trajectory from human neural stem cells to malignant glioma.
Xiaofei Wang, Ran Zhou, +18 authors, Yuan Wang.
Cell Res, 2021 Jan 05; 31(6). PMID: 33390587    Free PMC article.
Tumor Mutation Burden, Immune Cell Infiltration, and Construction of Immune-Related Genes Prognostic Model in Head and Neck Cancer.
Ai-Min Jiang, Meng-Di Ren, +8 authors, Yu Yao.
Int J Med Sci, 2021 Jan 05; 18(1). PMID: 33390791    Free PMC article.
Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer.
Miho Oka, Liu Xu, +9 authors, Masahide Seki.
Genome Biol, 2021 Jan 06; 22(1). PMID: 33397462    Free PMC article.
PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer.
Zheng Li, Yaming Li, Xiaolong Wang, Qifeng Yang.
Cancer Cell Int, 2021 Jan 08; 21(1). PMID: 33407498    Free PMC article.
Immune landscape and prognostic immune-related genes in KRAS-mutant colorectal cancer patients.
Jungang Liu, Xiaoliang Huang, +11 authors, Weizhong Tang.
J Transl Med, 2021 Jan 09; 19(1). PMID: 33413474    Free PMC article.
Survival prediction and response to immune checkpoint inhibitors: A prognostic immune signature for hepatocellular carcinoma.
Ying Xu, Zheng Wang, Fufeng Li.
Transl Oncol, 2020 Nov 28; 14(1). PMID: 33246289    Free PMC article.
OncoVar: an integrated database and analysis platform for oncogenic driver variants in cancers.
Tao Wang, Shasha Ruan, +7 authors, Fengbiao Mao.
Nucleic Acids Res, 2020 Nov 13; 49(D1). PMID: 33179738    Free PMC article.
Inflammatory Proteins HMGA2 and PRTN3 as Drivers of Vulvar Squamous Cell Carcinoma Progression.
Agnieszka Fatalska, Natalia Rusetska, +7 authors, Magdalena Kowalewska.
Cancers (Basel), 2020 Dec 31; 13(1). PMID: 33374674    Free PMC article.
Analysis of the TCGA Dataset Reveals that Subsites of Laryngeal Squamous Cell Carcinoma are Molecularly Distinct.
Alana Sorgini, Hugh Andrew Jinwook Kim, +17 authors, Anthony C Nichols.
Cancers (Basel), 2021 Jan 06; 13(1). PMID: 33396315    Free PMC article.
Genomic and clinical characteristics of MET exon14 alterations in a large cohort of Chinese cancer patients revealed distinct features and a novel resistance mechanism for crizotinib.
Tianli Cheng, Zhongping Gu, +5 authors, Wei Hong.
J Cancer, 2021 Jan 07; 12(3). PMID: 33403024    Free PMC article.
Upregulation of RAC3 in bladder cancer predicts adverse clinical outcome and increased tumor immune response.
Song Ou-Yang, Ji-Hong Liu, Qin-Zhang Wang.
Int J Clin Exp Pathol, 2021 Jan 12; 13(12). PMID: 33425095    Free PMC article.
Identification of immune-based prostate cancer subtypes using mRNA expression.
Jukun Song, Wei Wang, +5 authors, Jianguo Zhu.
Biosci Rep, 2020 Dec 09; 41(1). PMID: 33289508    Free PMC article.
Exploration of the relationship between tumor mutation burden and immune infiltrates in colon adenocarcinoma.
Rong Ouyang, Zhongzhuan Li, +4 authors, Jiean Huang.
Int J Med Sci, 2021 Jan 14; 18(3). PMID: 33437203    Free PMC article.
Genome diversity in Ukraine.
Taras K Oleksyk, Walter W Wolfsberger, +27 authors, Volodymyr Smolanka.
Gigascience, 2021 Jan 14; 10(1). PMID: 33438729    Free PMC article.
miRNA-Based Feature Classifier Is Associated with Tumor Mutational Burden in Head and Neck Squamous Cell Carcinoma.
Yu Xia, Qi Wang, +4 authors, Xiaofeng Duan.
Biomed Res Int, 2021 Jan 26; 2020. PMID: 33490233    Free PMC article.
Tumour microenvironment (TME) characterization identified prognosis and immunotherapy response in muscle-invasive bladder cancer (MIBC).
Rui Cao, Lushun Yuan, +2 authors, Ye Tian.
Cancer Immunol Immunother, 2020 Jul 04; 70(1). PMID: 32617668
m6A regulator-based methylation modification patterns characterized by distinct tumor microenvironment immune profiles in colon cancer.
Wei Chong, Liang Shang, +10 authors, Hao Chen.
Theranostics, 2021 Jan 28; 11(5). PMID: 33500720    Free PMC article.
Identification of a Five-Autophagy-Related-lncRNA Signature as a Novel Prognostic Biomarker for Hepatocellular Carcinoma.
Xiaoyu Deng, Qinghua Bi, +7 authors, Yao Yang.
Front Mol Biosci, 2021 Jan 29; 7. PMID: 33505990    Free PMC article.
Mining The Cancer Genome Atlas database for tumor mutation burden and its clinical implications in gastric cancer.
Dong-Yan Zhao, Xi-Zhen Sun, Shu-Kun Yao.
World J Gastrointest Oncol, 2021 Jan 30; 13(1). PMID: 33510848    Free PMC article.
Tumor mutation burden in connection with immune-related survival in uterine corpus endometrial carcinoma.
Ling Zhao, Xueshu Fu, +3 authors, Jun Gao.
Cancer Cell Int, 2021 Jan 30; 21(1). PMID: 33509222    Free PMC article.
Neoadjuvant PD-L1 plus CTLA-4 blockade in patients with cisplatin-ineligible operable high-risk urothelial carcinoma.
Jianjun Gao, Neema Navai, +28 authors, Padmanee Sharma.
Nat Med, 2020 Oct 14; 26(12). PMID: 33046869
CARD11 alteration as a candidate biomarker of skin cutaneous melanoma treated with immune checkpoint blockade.
Yutian Si, Anqi Lin, +3 authors, Jian Zhang.
Am J Transl Res, 2021 Feb 03; 13(1). PMID: 33527024    Free PMC article.
Whole genome sequencing of skull-base chordoma reveals genomic alterations associated with recurrence and chordoma-specific survival.
Jiwei Bai, Jianxin Shi, +26 authors, Xiaohong R Yang.
Nat Commun, 2021 Feb 05; 12(1). PMID: 33536423    Free PMC article.
KRAS mutations are negatively correlated with immunity in colon cancer.
Xiaorui Fu, Xinyi Wang, +2 authors, Qunguang Jiang.
Aging (Albany NY), 2020 Dec 01; 13(1). PMID: 33254149    Free PMC article.
Mutational Signatures Driven by Epigenetic Determinants Enable the Stratification of Patients with Gastric Cancer for Therapeutic Intervention.
Jaqueline Ramalho Buttura, Monize Nakamoto Provisor Santos, +14 authors, Israel Tojal da Silva.
Cancers (Basel), 2021 Jan 31; 13(3). PMID: 33513945    Free PMC article.
Integrated Bioinformatical Analysis Identifies GIMAP4 as an Immune-Related Prognostic Biomarker Associated With Remodeling in Cervical Cancer Tumor Microenvironment.
Fangfang Xu, Jiacheng Shen, Shaohua Xu.
Front Cell Dev Biol, 2021 Feb 09; 9. PMID: 33553190    Free PMC article.
Development and External Validation of a Novel Immune Checkpoint-Related Gene Signature for Prediction of Overall Survival in Hepatocellular Carcinoma.
Enfa Zhao, Shimin Chen, Ying Dang.
Front Mol Biosci, 2021 Feb 09; 7. PMID: 33553243    Free PMC article.
Whole-exome mutational landscape of neuroendocrine carcinomas of the gallbladder.
Fatao Liu, Yongsheng Li, +14 authors, Yingbin Liu.
Signal Transduct Target Ther, 2021 Feb 11; 6(1). PMID: 33563892    Free PMC article.
Isolating live cell clones from barcoded populations using CRISPRa-inducible reporters.
Christian Umkehrer, Felix Holstein, +11 authors, Anna C Obenauf.
Nat Biotechnol, 2020 Jul 29; 39(2). PMID: 32719478
Identification of a prognostic and therapeutic immune signature associated with hepatocellular carcinoma.
Yanan Peng, Chang Liu, +7 authors, Qiu Zhao.
Cancer Cell Int, 2021 Feb 12; 21(1). PMID: 33568167    Free PMC article.
Survival outcomes are associated with genomic instability in luminal breast cancers.
Lydia King, Andrew Flaus, Emma Holian, Aaron Golden.
PLoS One, 2021 Feb 04; 16(2). PMID: 33534788    Free PMC article.
A comparative genomics analysis of lung adenocarcinoma for Chinese population by using panel of recurrent mutations.
Wanlin Li, Min Wu, +4 authors, Renhua Guo.
J Biomed Res, 2020 Dec 22; 35(1). PMID: 33342770    Free PMC article.
The role of an immune signature for prognosis and immunotherapy response in endometrial cancer.
Yue Meng, Yuebo Yang, +3 authors, Chuan Hu.
Am J Transl Res, 2021 Feb 18; 13(2). PMID: 33594308    Free PMC article.
A Deep Look into the Program of Rapid Tumor Growth of Hepatocellular Carcinoma.
Jie Wang, Yi Lou, +7 authors, Jin Yang.
J Clin Transl Hepatol, 2021 Feb 20; 9(1). PMID: 33604252    Free PMC article.
Identification of a novel immune microenvironment signature predicting survival and therapeutic options for bladder cancer.
Yilin Yan, Zhengnan Huang, +4 authors, Bing Shen.
Aging (Albany NY), 2021 Jan 08; 13(2). PMID: 33408272    Free PMC article.
Development of a novel immune-related lncRNA signature as a prognostic classifier for endometrial carcinoma.
Jinhui Liu, Jie Mei, +4 authors, Yan Zhang.
Int J Biol Sci, 2021 Feb 23; 17(2). PMID: 33613104    Free PMC article.
Construction and validation of an N6-methyladenosine-associated prognostic signature in hepatocellular carcinoma.
Peng Zhu, Qianqian Ren, +3 authors, Zhao Gong.
Oncol Lett, 2021 Feb 23; 21(3). PMID: 33613710    Free PMC article.
MicroRNAs Expression Patterns Predict Tumor Mutational Burden in Colorectal Cancer.
Jiahao Huang, Haizhou Liu, +5 authors, Weizhong Tang.
Front Oncol, 2021 Feb 27; 10. PMID: 33634010    Free PMC article.
Mutational Landscape of Virus- and UV-Associated Merkel Cell Carcinoma Cell Lines Is Comparable to Tumor Tissue.
Kai Horny, Patricia Gerhardt, +3 authors, Jürgen C Becker.
Cancers (Basel), 2021 Feb 11; 13(4). PMID: 33562873    Free PMC article.
Long Non-coding RNA Expression Patterns in Stomach Adenocarcinoma Serve as an Indicator of Tumor Mutation Burden and Are Associated With Tumor-Infiltrating Lymphocytes and Microsatellite Instability.
Dongdong Yang, Jinling Yu, +3 authors, Jing Hu.
Front Cell Dev Biol, 2021 Mar 02; 9. PMID: 33644056    Free PMC article.
Identification of candidate genes encoding tumor-specific neoantigens in early- and late-stage colon adenocarcinoma.
Chong Wang, Wenhua Xue, Haohao Zhang, Yang Fu.
Aging (Albany NY), 2021 Jan 12; 13(3). PMID: 33428592    Free PMC article.
Identification of Potential Driver Genes Based on Multi-Genomic Data in Cervical Cancer.
Yuexun Xu, Hui Luo, Qunchao Hu, Haiyan Zhu.
Front Genet, 2021 Mar 06; 12. PMID: 33664766    Free PMC article.
Comprehensive Profiling of Genomic and Transcriptomic Differences between Risk Groups of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma.
Talip Zengin, Tuğba Önal-Süzek.
J Pers Med, 2021 Mar 07; 11(2). PMID: 33672117    Free PMC article.
Syngeneic tobacco carcinogen-induced mouse lung adenocarcinoma model exhibits PD-L1 expression and high tumor mutational burden.
Laura P Stabile, Vinod Kumar, +8 authors, Christopher J Bakkenist.
JCI Insight, 2020 Dec 23; 6(3). PMID: 33351788    Free PMC article.
Comprehensive analysis of tumor mutation burden and immune microenvironment in gastric cancer.
Jie Yu, QianYun Zhang, +5 authors, JinLong Yu.
Biosci Rep, 2021 Jan 26; 41(2). PMID: 33492335    Free PMC article.
Identification of FPR3 as a Unique Biomarker for Targeted Therapy in the Immune Microenvironment of Breast Cancer.
Jian Qi, Yu Liu, +5 authors, Wulin Yang.
Front Pharmacol, 2021 Mar 09; 11. PMID: 33679387    Free PMC article.
The association of sex-biased ATRX mutation in female gastric cancer patients with enhanced immunotherapy-related anticancer immunity.
You Ge, Feiran Wei, +5 authors, Pingmin Wei.
BMC Cancer, 2021 Mar 09; 21(1). PMID: 33678158    Free PMC article.
DNA damage response as a prognostic indicator in metastatic breast cancer via mutational analysis.
Guohua Rong, Zongbi Yi, +4 authors, Binghe Xu.
Ann Transl Med, 2021 Mar 13; 9(3). PMID: 33708847    Free PMC article.
Identification and validation of a prognostic signature and combination drug therapy for immunotherapy of head and neck squamous cell carcinoma.
Weijie Qiang, Yifei Dai, Xiaoyan Xing, Xiaobo Sun.
Comput Struct Biotechnol J, 2021 Mar 16; 19. PMID: 33717423    Free PMC article.
Mutational signatures in squamous cell carcinoma of the lung.
Atsushi Osoegawa, Kazuki Takada, +8 authors, Masaki Mori.
J Thorac Dis, 2021 Mar 16; 13(2). PMID: 33717580    Free PMC article.
Analysis of mutations in cutaneous squamous cell carcinoma reveals novel genes and mutations associated with patient-specific characteristics and metastasis: a systematic review.
Marissa B Lobl, Dillon Clarey, +2 authors, Ashley Wysong.
Arch Dermatol Res, 2021 Mar 19;. PMID: 33735396
An immune-related gene signature for predicting survival and immunotherapy efficacy in hepatocellular carcinoma.
Yifei Dai, Weijie Qiang, +3 authors, Dong Wang.
Cancer Immunol Immunother, 2020 Oct 23; 70(4). PMID: 33089373
An integrated model of N6-methyladenosine regulators to predict tumor aggressiveness and immune evasion in pancreatic cancer.
Zhijun Zhou, Junxia Zhang, +14 authors, Min Li.
EBioMedicine, 2021 Mar 14; 65. PMID: 33714027    Free PMC article.
Granzyme family acts as a predict biomarker in cutaneous melanoma and indicates more benefit from anti-PD-1 immunotherapy.
Xia Wu, Xiaojie Wang, +3 authors, Jianzhong Zhang.
Int J Med Sci, 2021 Mar 23; 18(7). PMID: 33746582    Free PMC article.
Analysis of m6A-Related Signatures in the Tumor Immune Microenvironment and Identification of Clinical Prognostic Regulators in Adrenocortical Carcinoma.
Yi Jin, Zhanwang Wang, +7 authors, Ke Cao.
Front Immunol, 2021 Mar 23; 12. PMID: 33746977    Free PMC article.
Characterization of Tumor Microenvironment in Lung Adenocarcinoma Identifies Immune Signatures to Predict Clinical Outcomes and Therapeutic Responses.
Donglai Chen, Yifei Wang, +7 authors, Yongbing Chen.
Front Oncol, 2021 Mar 23; 11. PMID: 33747907    Free PMC article.
Identification of tumor mutation burden-related hub genes and the underlying mechanism in melanoma.
Chuan Zhang, Dan Dang, +2 authors, Xianling Cong.
J Cancer, 2021 Mar 25; 12(8). PMID: 33758620    Free PMC article.
Multi-omics analysis of tumor angiogenesis characteristics and potential epigenetic regulation mechanisms in renal clear cell carcinoma.
Wenzhong Zheng, Shiqiang Zhang, +4 authors, Mengqiang Li.
Cell Commun Signal, 2021 Mar 26; 19(1). PMID: 33761933    Free PMC article.
Effect of NCOR1 Mutations on Immune Microenvironment and Efficacy of Immune Checkpoint Inhibitors in Patient with Bladder Cancer.
Anqi Lin, Zhengang Qiu, Jian Zhang, Peng Luo.
Front Immunol, 2021 Mar 26; 12. PMID: 33763074    Free PMC article.
SPINK7 expression changes accompanied by HER2, P53 and RB1 can be relevant in predicting oral squamous cell carcinoma at a molecular level.
Gina Pennacchiotti, Fabio Valdés-Gutiérrez, +11 authors, Flavia Alejandra Bruna.
Sci Rep, 2021 Mar 27; 11(1). PMID: 33767253    Free PMC article.
Prognosis and Genomic Landscape of Liver Metastasis in Patients With Breast Cancer.
Chonglin Tian, Sujing Liu, Yongsheng Wang, Xianrang Song.
Front Oncol, 2021 Mar 30; 11. PMID: 33777740    Free PMC article.
Comprehensive Analysis of Ferroptosis Regulators in Lung Adenocarcinomas Identifies Prognostic and Immunotherapy-Related Biomarkers.
Sijin Sun, Wei Guo, +9 authors, Jie He.
Front Mol Biosci, 2021 Mar 30; 8. PMID: 33778001    Free PMC article.
FAT3 Mutation Is Associated With Tumor Mutation Burden and Poor Prognosis in Esophageal Cancer.
Zixin Guo, Xin Yan, +6 authors, Weidong Hu.
Front Oncol, 2021 Apr 06; 11. PMID: 33816234    Free PMC article.
Molecular characterization of long-term survivors of hepatocellular carcinoma.
Junwei Shen, Jing Hu, +3 authors, Jue Li.
Aging (Albany NY), 2021 Mar 10; 13(5). PMID: 33686022    Free PMC article.
Artificial intelligence prediction model for overall survival of clear cell renal cell carcinoma based on a 21-gene molecular prognostic score system.
Qiliang Peng, Yi Shen, +4 authors, Jin Zhu.
Aging (Albany NY), 2021 Mar 10; 13(5). PMID: 33686949    Free PMC article.
Identification and validation of a glycolysis-associated multiomics prognostic model for hepatocellular carcinoma.
Tuo Deng, Qian Ye, +7 authors, Yi Wang.
Aging (Albany NY), 2021 Mar 10; 13(5). PMID: 33686959    Free PMC article.
Identification of PIK3CA multigene mutation patterns associated with superior prognosis in stomach cancer.
Yu Yu, Zhuoming Xie, Mingxin Zhao, Xiaohua Lian.
BMC Cancer, 2021 Apr 09; 21(1). PMID: 33827485    Free PMC article.
Multiomics Analysis of Genetics and Epigenetics Reveals Pathogenesis and Therapeutic Targets for Atrial Fibrillation.
Li Liu, Jianjun Huang, +10 authors, Xingshou Pan.
Biomed Res Int, 2021 Apr 10; 2021. PMID: 33834070    Free PMC article.
Gene expression and immune infiltration in melanoma patients with different mutation burden.
Liwei Wang, Fu Chen, +3 authors, Zhengjian Yan.
BMC Cancer, 2021 Apr 11; 21(1). PMID: 33836680    Free PMC article.
Aberrations of Chromosomes 1 and 16 in Breast Cancer: A Framework for Cooperation of Transcriptionally Dysregulated Genes.
Anna Provvidenza Privitera, Vincenza Barresi, Daniele Filippo Condorelli.
Cancers (Basel), 2021 Apr 04; 13(7). PMID: 33808143    Free PMC article.
TTN/OBSCN 'Double-Hit' predicts favourable prognosis, 'immune-hot' subtype and potentially better immunotherapeutic efficacy in colorectal cancer.
Zaoqu Liu, Libo Wang, +6 authors, Xinwei Han.
J Cell Mol Med, 2021 Feb 25; 25(7). PMID: 33624434    Free PMC article.
Enhancing the landscape of colorectal cancer using targeted deep sequencing.
Chul Seung Lee, In Hye Song, +5 authors, Sung Hak Lee.
Sci Rep, 2021 Apr 16; 11(1). PMID: 33854094    Free PMC article.
Prediction of overall survival and response to immune checkpoint inhibitors: An immune-related signature for gastric cancer.
Zheng Wang, Xiang Li, Ying Xu.
Transl Oncol, 2021 Mar 31; 14(6). PMID: 33784584    Free PMC article.
Establishment and validation of an eight-gene metabolic-related prognostic signature model for lung adenocarcinoma.
Weishuang Ma, Jiaming Liang, +2 authors, Zisheng Chen.
Aging (Albany NY), 2021 Feb 24; 13(6). PMID: 33619235    Free PMC article.
Mucin 4 mutation is associated with tumor mutation burden and promotes antitumor immunity in colon cancer patients.
Linglong Peng, Yang Li, +5 authors, Jijian Wang.
Aging (Albany NY), 2021 Mar 15; 13(6). PMID: 33714943    Free PMC article.
Multiomics Analysis of Transcriptome, Epigenome, and Genome Uncovers Putative Mechanisms for Dilated Cardiomyopathy.
Li Liu, Jianjun Huang, +15 authors, Zhaohe Huang.
Biomed Res Int, 2021 Apr 17; 2021. PMID: 33860048    Free PMC article.
A Comprehensive Investigation to Reveal the Relationship Between Plasmacytoid Dendritic Cells and Breast Cancer by Multiomics Data Analysis.
Saisai Tian, Li Yan, +4 authors, Weidong Zhang.
Front Cell Dev Biol, 2021 Apr 20; 9. PMID: 33869191    Free PMC article.
An integrative analysis of the age-associated multi-omic landscape across cancers.
Kasit Chatsirisupachai, Tom Lesluyes, +2 authors, João Pedro de Magalhães.
Nat Commun, 2021 Apr 22; 12(1). PMID: 33879792    Free PMC article.
Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data.
François Fauteux, Anuradha Surendra, +2 authors, Jennifer J Hill.
Sci Rep, 2021 Apr 24; 11(1). PMID: 33888829    Free PMC article.
RB1 and TP53 co-mutations correlate strongly with genomic biomarkers of response to immunity checkpoint inhibitors in urothelial bladder cancer.
Ramon Gonzalez Manzano, Ana Catalan-Latorre, Antonio Brugarolas.
BMC Cancer, 2021 Apr 22; 21(1). PMID: 33879103    Free PMC article.
ARID2 deficiency promotes tumor progression and is associated with higher sensitivity to chemotherapy in lung cancer.
Thaidy Moreno, Beatriz Monterde, +17 authors, Ignacio Varela.
Oncogene, 2021 Mar 21; 40(16). PMID: 33742126    Free PMC article.
Identification of NTRK3 as a potential prognostic biomarker associated with tumor mutation burden and immune infiltration in bladder cancer.
Zhao Zhang, Yongbo Yu, +5 authors, Haitao Niu.
BMC Cancer, 2021 Apr 26; 21(1). PMID: 33894748    Free PMC article.
Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.
Karsten Krug, Eric J Jaehnig, +44 authors, Clinical Proteomic Tumor Analysis Consortium.
Cell, 2020 Nov 20; 183(5). PMID: 33212010    Free PMC article.
Using The Cancer Genome Atlas data to refine the 8th edition of the American Joint Committee on Cancer staging for papillary thyroid carcinoma.
Anello Marcello Poma, Elisabetta Macerola, +3 authors, Fulvio Basolo.
Endocrine, 2020 Sep 12; 72(1). PMID: 32915437    Free PMC article.
Comprehensive omic characterization of breast cancer in Mexican-Hispanic women.
Sandra L Romero-Cordoba, Ivan Salido-Guadarrama, +8 authors, Alfredo Hidalgo-Miranda.
Nat Commun, 2021 Apr 16; 12(1). PMID: 33854067    Free PMC article.
Radiomic profiling of clear cell renal cell carcinoma reveals subtypes with distinct prognoses and molecular pathways.
Peng Lin, Yi-Qun Lin, +4 authors, Hong Yang.
Transl Oncol, 2021 Apr 17; 14(7). PMID: 33862522    Free PMC article.
Robust Prediction of Immune Checkpoint Inhibition Therapy for Non-Small Cell Lung Cancer.
Jiehan Jiang, Zheng Jin, +9 authors, Kui Xiao.
Front Immunol, 2021 May 01; 12. PMID: 33927719    Free PMC article.
SLF1 polymorphism predicts response to oxaliplatin-based adjuvant chemotherapy in patients with colon cancer.
Xiaohong Han, Zheng Wang, +7 authors, Yuankai Shi.
Am J Cancer Res, 2021 May 06; 11(4). PMID: 33948371    Free PMC article.
Genomic Alteration Characterization in Colorectal Cancer Identifies a Prognostic and Metastasis Biomarker: FAM83A|IDO1.
Zaoqu Liu, Yuyuan Zhang, +5 authors, Xinwei Han.
Front Oncol, 2021 May 08; 11. PMID: 33959500    Free PMC article.
Hypoxia Constructing the Prognostic Model of Colorectal Adenocarcinoma and Related to the Immune Microenvironment.
Yuanyuan Zhang, Feng Yang, +6 authors, Guangyuan Hu.
Front Cell Dev Biol, 2021 May 08; 9. PMID: 33959617    Free PMC article.
Identification of Prognostic Glycolysis-Related lncRNA Signature in Tumor Immune Microenvironment of Hepatocellular Carcinoma.
Yang Bai, Haiping Lin, +2 authors, Shi'an Yu.
Front Mol Biosci, 2021 May 11; 8. PMID: 33968985    Free PMC article.
Identification of prognosis-related molecular subgroups based on DNA methylation in pancreatic cancer.
Xiaoli Yin, Lingming Kong, Peng Liu.
Clin Epigenetics, 2021 May 14; 13(1). PMID: 33980289    Free PMC article.
Comprehensive analysis of tumor microenvironment and identification of an immune signature to predict the prognosis and immunotherapeutic response in lung squamous cell carcinoma.
Jinlong Wu, Chengfeng Xu, +4 authors, Mingsong Wang.
Ann Transl Med, 2021 May 15; 9(7). PMID: 33987267    Free PMC article.
Glioma-Associated Stromal Cells Stimulate Glioma Malignancy by Regulating the Tumor Immune Microenvironment.
Xiangming Cai, Feng Yuan, +4 authors, Chiyuan Ma.
Front Oncol, 2021 May 18; 11. PMID: 33996602    Free PMC article.
Decreased ATM Function Causes Delayed DNA Repair and Apoptosis in Common Variable Immunodeficiency Disorders.
Chantal E Hargreaves, Silvia Salatino, +7 authors, Smita Y Patel.
J Clin Immunol, 2021 May 20; 41(6). PMID: 34009545    Free PMC article.
Association between Smoking History and Tumor Mutation Burden in Advanced Non-Small Cell Lung Cancer.
Xinan Wang, Biagio Ricciuti, +6 authors, David C Christiani.
Cancer Res, 2021 Mar 04; 81(9). PMID: 33653773    Free PMC article.
Distinct patterns of somatic genomic alterations and mutational signatures in central and peripheral-type small-cell lung cancer.
Lei Wang, Jing Wang, +4 authors, Caicun Zhou.
Transl Lung Cancer Res, 2021 May 21; 10(4). PMID: 34012790    Free PMC article.
Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes.
Shixiang Wang, Huimin Li, +6 authors, Xue-Song Liu.
PLoS Genet, 2021 May 05; 17(5). PMID: 33945534    Free PMC article.
MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations.
Mengni Liu, Jianyu Chen, +6 authors, Qi Zhao.
Gigascience, 2021 May 22; 10(5). PMID: 34018555    Free PMC article.
Analysis of multi-omics differences in left-side and right-side colon cancer.
Yanyi Huang, Jinzhong Duanmu, +3 authors, Qunguang Jiang.
PeerJ, 2021 May 25; 9. PMID: 34026368    Free PMC article.
Identification of immune subtypes of cervical squamous cell carcinoma predicting prognosis and immunotherapy responses.
Yimin Li, Shun Lu, +2 authors, Jinyi Lang.
J Transl Med, 2021 May 26; 19(1). PMID: 34030694    Free PMC article.
Identification of biomarkers complementary to homologous recombination deficiency for improving the clinical outcome of ovarian serous cystadenocarcinoma.
Zhiwen Shi, Qingguo Zhao, +5 authors, Keqin Hua.
Clin Transl Med, 2021 May 29; 11(5). PMID: 34047476    Free PMC article.
Characterization of the Immune Cell Infiltration Profile in Pancreatic Carcinoma to Aid in Immunotherapy.
De Luo, Fei Kuang, +7 authors, Song Su.
Front Oncol, 2021 Jun 01; 11. PMID: 34055645    Free PMC article.
Evidence of Cooperation between Hippo Pathway and RAS Mutation in Thyroid Carcinomas.
Thaise Nayane Ribeiro Carneiro, Larissa Valdemarin Bim, +5 authors, Janete Maria Cerutti.
Cancers (Basel), 2021 Jun 03; 13(10). PMID: 34065786    Free PMC article.
Cell-Free DNA Analysis by Whole-Exome Sequencing for Hepatocellular Carcinoma: A Pilot Study in Thailand.
Pattapon Kunadirek, Natthaya Chuaypen, +5 authors, Pisit Tangkijvanich.
Cancers (Basel), 2021 Jun 03; 13(9). PMID: 34066484    Free PMC article.
Multi-Omics Perspective Reveals the Different Patterns of Tumor Immune Microenvironment Based on Programmed Death Ligand 1 (PD-L1) Expression and Predictor of Responses to Immune Checkpoint Blockade across Pan-Cancer.
Kaitang Huang, Meiling Hu, +4 authors, Hongli Du.
Int J Mol Sci, 2021 Jun 03; 22(10). PMID: 34068143    Free PMC article.
Association of RYR2 Mutation With Tumor Mutation Burden, Prognosis, and Antitumor Immunity in Patients With Esophageal Adenocarcinoma.
Zaoqu Liu, Long Liu, +6 authors, Xinwei Han.
Front Genet, 2021 Jun 04; 12. PMID: 34079583    Free PMC article.
Potential Impact of ALKBH5 and YTHDF1 on Tumor Immunity in Colon Adenocarcinoma.
Guanyu Yan, Yue An, +3 authors, Mingjun Sun.
Front Oncol, 2021 Jun 04; 11. PMID: 34079761    Free PMC article.
2-kupl: mapping-free variant detection from DNA-seq data of matched samples.
Yunfeng Wang, Haoliang Xue, +2 authors, Daniel Gautheret.
BMC Bioinformatics, 2021 Jun 07; 22(1). PMID: 34090332    Free PMC article.
Integrated molecular characterisation of endometrioid ovarian carcinoma identifies opportunities for stratification.
Robert L Hollis, Barbara Stanley, +10 authors, C Simon Herrington.
NPJ Precis Oncol, 2021 Jun 04; 5(1). PMID: 34079052    Free PMC article.
Development and Interpretation of a Genomic Instability Derived lncRNAs Based Risk Signature as a Predictor of Prognosis for Clear Cell Renal Cell Carcinoma Patients.
Huiying Yang, Xiaoling Xiong, Hua Li.
Front Oncol, 2021 Jun 08; 11. PMID: 34094983    Free PMC article.
Ubiquitin-related molecular classification and risk stratification of hepatocellular carcinoma.
Si Yang, Bowen Yao, +11 authors, Zhijun Dai.
Mol Ther Oncolytics, 2021 Jun 08; 21. PMID: 34095460    Free PMC article.

;. PMID: 34098941
Genomic insights into the pathogenesis of Epstein-Barr virus-associated diffuse large B-cell lymphoma by whole-genome and targeted amplicon sequencing.
Niklas Gebauer, Axel Künstner, +17 authors, Alfred C Feller.
Blood Cancer J, 2021 May 28; 11(5). PMID: 34039950    Free PMC article.
Multi-Omics Data Analyses Construct a Six Immune-Related Genes Prognostic Model for Cervical Cancer in Tumor Microenvironment.
Fangfang Xu, Jiacheng Shen, Shaohua Xu.
Front Genet, 2021 Jun 11; 12. PMID: 34108992    Free PMC article.
Association Between FSIP2 Mutation and an Improved Efficacy of Immune Checkpoint Inhibitors in Patients With Skin Cutaneous Melanoma.
Haoxuan Ying, Anqi Lin, +2 authors, Peng Luo.
Front Mol Biosci, 2021 Jun 12; 8. PMID: 34113648    Free PMC article.
Analysis of the genomic landscape of yolk sac tumors reveals mechanisms of evolution and chemoresistance.
Xuan Zong, Ying Zhang, +7 authors, Jiaxin Yang.
Nat Commun, 2021 Jun 13; 12(1). PMID: 34117242    Free PMC article.
Prognostic Genetic Biomarkers Based on Oncogenic Signaling Pathways for Outcome Prediction in Patients with Oral Cavity Squamous Cell Carcinoma.
Wen-Lang Fan, Lan-Yan Yang, +3 authors, Chun-Ta Liao.
Cancers (Basel), 2021 Jun 03; 13(11). PMID: 34070941    Free PMC article.
AID Contributes to Accelerated Disease Progression in the TCL1 Mouse Transplant Model for CLL.
Maria Schubert, Franz Josef Gassner, +7 authors, Roland Geisberger.
Cancers (Basel), 2021 Jun 03; 13(11). PMID: 34073525    Free PMC article.
Immunological Significance of Prognostic DNA Methylation Sites in Hepatocellular Carcinoma.
Qianhui Xu, Yuanbo Hu, +8 authors, Wen Huang.
Front Mol Biosci, 2021 Jun 15; 8. PMID: 34124163    Free PMC article.
Identification of autophagy-related genes signature predicts chemotherapeutic and immunotherapeutic efficiency in bladder cancer (BLCA).
Rui Cao, Bo Ma, +3 authors, Lushun Yuan.
J Cell Mol Med, 2021 May 08; 25(12). PMID: 33960661    Free PMC article.
Development and validation of an individualized immune prognostic model in stage I-III lung squamous cell carcinoma.
Qi-Fan Yang, Di Wu, +5 authors, Li Liu.
Sci Rep, 2021 Jun 18; 11(1). PMID: 34135424    Free PMC article.
Association of IDH mutation and 1p19q co-deletion with tumor immune microenvironment in lower-grade glioma.
Wanzun Lin, Xianxin Qiu, +4 authors, Jiade J Lu.
Mol Ther Oncolytics, 2021 Jun 19; 21. PMID: 34141867    Free PMC article.
Exploration of the Role of m6 A RNA Methylation Regulators in Malignant Progression and Clinical Prognosis of Ovarian Cancer.
Qinglv Wei, Dan Yang, +5 authors, Ping Yi.
Front Genet, 2021 Jun 22; 12. PMID: 34149801    Free PMC article.
Correlation Between the Evolution of Somatic Alterations During Lymphatic Metastasis and Clinical Outcome in Penile Squamous Cell Carcinoma.
Jian Cao, Chun-He Yang, +3 authors, Shu-Suan Jiang.
Front Oncol, 2021 Jun 22; 11. PMID: 34150614    Free PMC article.
A Poliovirus Receptor (CD155)-Related Risk Signature Predicts the Prognosis of Bladder Cancer.
Cong Luo, Wenrui Ye, +4 authors, Xiongbing Zu.
Front Oncol, 2021 Jun 22; 11. PMID: 34150627    Free PMC article.
What Is Abnormal in Normal Karyotype Acute Myeloid Leukemia in Children? Analysis of the Mutational Landscape and Prognosis of the TARGET-AML Cohort.
Morten Krogh Herlin, Sara A Yones, +2 authors, Henrik Hasle.
Genes (Basel), 2021 Jun 03; 12(6). PMID: 34064268    Free PMC article.
Catenin Alpha-2 Mutation Changes the Immune Microenvironment in Lung Adenocarcinoma Patients Receiving Immune Checkpoint Inhibitors.
Yang Wen, Anqi Lin, +4 authors, Jian Zhang.
Front Pharmacol, 2021 Jun 25; 12. PMID: 34163353    Free PMC article.
DIVIS: Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation.
Xiaoyu He, Yu Zhang, +6 authors, Beifang Niu.
Front Oncol, 2021 Jun 26; 11. PMID: 34168993    Free PMC article.
Identification of COL3A1 variants associated with sporadic thoracic aortic dissection: a case-control study.
Yanghui Chen, Yang Sun, +13 authors, Dao Wen Wang.
Front Med, 2021 May 29; 15(3). PMID: 34047934
The Pyroptosis-Related Signature Predicts Prognosis and Indicates Immune Microenvironment Infiltration in Gastric Cancer.
Wei Shao, Zongcheng Yang, +4 authors, Jihui Jia.
Front Cell Dev Biol, 2021 Jun 29; 9. PMID: 34179006    Free PMC article.
The Genomic Landscape of Actinic Keratosis.
Jason Thomson, Findlay Bewicke-Copley, +8 authors, Jun Wang.
J Invest Dermatol, 2021 Jan 23; 141(7). PMID: 33482222    Free PMC article.
Regulatory Network Analysis of Mutated Genes Based on Multi-Omics Data Reveals the Exclusive Features in Tumor Immune Microenvironment Between Left-Sided and Right-Sided Colon Cancer.
Tianfei Yi, Yuwei Zhang, +16 authors, Qi Liao.
Front Oncol, 2021 Jul 03; 11. PMID: 34211853    Free PMC article.
Characterization of a ferroptosis and iron-metabolism related lncRNA signature in lung adenocarcinoma.
Jie Yao, Xiao Chen, +3 authors, Yiqing Qu.
Cancer Cell Int, 2021 Jul 05; 21(1). PMID: 34217273    Free PMC article.
Prognostic value of tumor immune cell infiltration patterns in colon adenocarcinoma based on systematic bioinformatics analysis.
Hao Xu, Qianhui Xu, Lu Yin.
Cancer Cell Int, 2021 Jul 05; 21(1). PMID: 34217290    Free PMC article.
Multi-omics analysis reveals prognostic value of tumor mutation burden in hepatocellular carcinoma.
Qianhui Xu, Hao Xu, +5 authors, Wen Huang.
Cancer Cell Int, 2021 Jul 05; 21(1). PMID: 34217320    Free PMC article.
Investigation of Genetic Determinants of Glioma Immune Phenotype by Integrative Immunogenomic Scale Analysis.
Binghao Zhao, Yuekun Wang, +3 authors, Wenbin Ma.
Front Immunol, 2021 Jul 06; 12. PMID: 34220791    Free PMC article.
A Novel Immune-Related Prognostic Signature in Head and Neck Squamous Cell Carcinoma.
Yi Zhang, Ping Chen, +4 authors, Hongliang Zhong.
Front Genet, 2021 Jul 06; 12. PMID: 34220923    Free PMC article.
Comprehensive Characterization of Integrin Subunit Genes in Human Cancers.
Kaisa Cui, Xiaohan Wu, +6 authors, Zhaohui Huang.
Front Oncol, 2021 Jul 06; 11. PMID: 34222028    Free PMC article.
Upregulation of ARNTL2 is associated with poor survival and immune infiltration in clear cell renal cell carcinoma.
Song Wang, Xueyou Ma, +9 authors, Liping Xie.
Cancer Cell Int, 2021 Jul 05; 21(1). PMID: 34217271    Free PMC article.
TENT4A Non-Canonical Poly(A) Polymerase Regulates DNA-Damage Tolerance via Multiple Pathways That Are Mutated in Endometrial Cancer.
Umakanta Swain, Gilgi Friedlander, +8 authors, Zvi Livneh.
Int J Mol Sci, 2021 Jul 03; 22(13). PMID: 34203408    Free PMC article.
An m6A-Related Prognostic Biomarker Associated With the Hepatocellular Carcinoma Immune Microenvironment.
Yingxi Du, Yarui Ma, +4 authors, Xiaobing Wang.
Front Pharmacol, 2021 Jul 13; 12. PMID: 34248650    Free PMC article.
Tumor Mutation Burden Predicts Relapse in Papillary Thyroid Carcinoma With Changes in Genes and Immune Microenvironment.
Mengli Guo, Zhen Chen, +7 authors, Bo Xu.
Front Endocrinol (Lausanne), 2021 Jul 13; 12. PMID: 34248843    Free PMC article.
Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis.
Shixiang Wang, Ziyu Tao, Tao Wu, Xue-Song Liu.
Bioinformatics, 2020 Dec 04; 37(11). PMID: 33270873    Free PMC article.
Relationship of HER2 Alteration and Microsatellite Instability Status in Colorectal Adenocarcinoma.
Miao-Zhen Qiu, Cai-Yun He, +10 authors, Rui-Hua Xu.
Oncologist, 2021 Apr 13; 26(7). PMID: 33844372    Free PMC article.
Identification of Prognostic Related Genes of Tumor Microenvironment Derived From Esophageal Cancer Patients.
Wei Yuan, Jiaqin Yan, +4 authors, Mingzhi Zhang.
Pathol Oncol Res, 2021 Jul 15; 27. PMID: 34257539    Free PMC article.
A novel ferroptosis phenotype-related clinical-molecular prognostic signature for hepatocellular carcinoma.
Tuo Deng, Bingren Hu, +8 authors, Yi Wang.
J Cell Mol Med, 2021 Jun 05; 25(14). PMID: 34085405    Free PMC article.
A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma.
Fei Li, Dongcen Ge, Shu-Lan Sun.
BMC Pulm Med, 2021 Jul 15; 21(1). PMID: 34256754    Free PMC article.
Comprehensive characterization of distinct genetic alterations in metastatic breast cancer across various metastatic sites.
Soojin Cha, Esak Lee, Hong-Hee Won.
NPJ Breast Cancer, 2021 Jul 18; 7(1). PMID: 34272397    Free PMC article.
IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures.
Dongqiang Zeng, Zilan Ye, +12 authors, Wangjun Liao.
Front Immunol, 2021 Jul 20; 12. PMID: 34276676    Free PMC article.
Exome sequencing identifies novel somatic variants in African American esophageal squamous cell carcinoma.
Hayriye Verda Erkizan, Shrey Sukhadia, +4 authors, Robert G Wadleigh.
Sci Rep, 2021 Jul 22; 11(1). PMID: 34285259    Free PMC article.
Exploration of the Important Role of Microfibril-Associated Protein 4 Gene in Oral Squamous Cell Carcinoma.
Ying Han, Kun Xia, Tong Su.
Med Sci Monit, 2021 Jul 03; 27. PMID: 34210950    Free PMC article.
A Transcriptome-Wide Isoform Landscape of Melanocytic Nevi and Primary Melanomas Identifies Gene Isoforms Associated with Malignancy.
Siras Hakobyan, Henry Loeffler-Wirth, +2 authors, Manfred Kunz.
Int J Mol Sci, 2021 Jul 21; 22(13). PMID: 34281234    Free PMC article.
Analyzing the characteristics of immune cell infiltration in lung adenocarcinoma via bioinformatics to predict the effect of immunotherapy.
Yi Liao, Dingxiu He, Fuqiang Wen.
Immunogenetics, 2021 Jul 25;. PMID: 34302518
Significance of Tumor Mutation Burden Combined With Immune Infiltrates in the Progression and Prognosis of Advanced Gastric Cancer.
Xiong Guo, Xiaolong Liang, +4 authors, Ziwei Wang.
Front Genet, 2021 Jul 27; 12. PMID: 34306002    Free PMC article.
Comprehensive Molecular Analyses of a Novel Mutational Signature Classification System with Regard to Prognosis, Genomic Alterations, and Immune Landscape in Glioma.
Zaoqu Liu, Taoyuan Lu, +3 authors, Xinwei Han.
Front Mol Biosci, 2021 Jul 27; 8. PMID: 34307451    Free PMC article.
Genomic Analysis of Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma.
Fereshteh Izadi, Benjamin P Sharpe, +11 authors, On Behalf Of Occams.
Cancers (Basel), 2021 Jul 25; 13(14). PMID: 34298611    Free PMC article.
Molecular correlates of immune cytolytic subgroups in colorectal cancer by integrated genomics analysis.
Constantinos Roufas, Ilias Georgakopoulos-Soares, Apostolos Zaravinos.
NAR Cancer, 2021 Jul 29; 3(1). PMID: 34316699    Free PMC article.
Identification and Validation of Immune Molecular Subtypes in Pancreatic Ductal Adenocarcinoma: Implications for Prognosis and Immunotherapy.
Ruiyu Li, Yangzhige He, +5 authors, Zhiyong Liang.
Front Immunol, 2021 Aug 03; 12. PMID: 34335594    Free PMC article.
Multi-Omics Data Integration Analysis of an Immune-Related Gene Signature in LGG Patients With Epilepsy.
Quan Cheng, Weiwei Duan, +6 authors, Zhiwei Xia.
Front Cell Dev Biol, 2021 Aug 03; 9. PMID: 34336837    Free PMC article.
EPHA5 mutation predicts the durable clinical benefit of immune checkpoint inhibitors in patients with lung adenocarcinoma.
Weimei Huang, Anqi Lin, +7 authors, Jian Zhang.
Cancer Gene Ther, 2020 Aug 08; 28(7-8). PMID: 32759987
Prognostic Implications of Immune-Related Gene Pairs Signatures in Bladder Cancer.
Hui Xiong, Hui Gao, +9 authors, Weiting Kang.
J Oncol, 2021 Aug 07; 2021. PMID: 34354750    Free PMC article.
A Patient-Derived Organoid-Based Radiosensitivity Model for the Prediction of Radiation Responses in Patients with Rectal Cancer.
Misun Park, Junhye Kwon, +7 authors, Ui Sup Shin.
Cancers (Basel), 2021 Aug 08; 13(15). PMID: 34359661    Free PMC article.
Establishment of a novel CNV-related prognostic signature predicting prognosis in patients with breast cancer.
Wei Hu, Mingyue Li, +5 authors, Liang Li.
J Ovarian Res, 2021 Aug 09; 14(1). PMID: 34364397    Free PMC article.
Immune infiltration phenotypes of prostate adenocarcinoma and their clinical implications.
Zehua Ma, Xiankui Cheng, +6 authors, Wei Xue.
Cancer Med, 2021 Jun 16; 10(15). PMID: 34128342    Free PMC article.
Integrative analysis of immune molecular subtypes and microenvironment characteristics of bladder cancer.
Jinlong Cao, Jianpeng Li, +6 authors, Junqiang Tian.
Cancer Med, 2021 Jun 25; 10(15). PMID: 34165261    Free PMC article.
Molecular profiling of soft-tissue sarcomas with FoundationOne® Heme identifies potential targets for sarcoma therapy: a single-centre experience.
Susanne Scheipl, Iva Brcic, +12 authors, Joanna Szkandera.
Ther Adv Med Oncol, 2021 Aug 10; 13. PMID: 34367342    Free PMC article.
Cancer Stemness Associated With Prognosis and the Efficacy of Immunotherapy in Adrenocortical Carcinoma.
Xiaoxi Shi, Yuanlin Liu, +5 authors, Shijie Xin.
Front Oncol, 2021 Aug 10; 11. PMID: 34367952    Free PMC article.
The Landscape of Genetic Alterations Stratified Prognosis in Oriental Pancreatic Cancer Patients.
Shiwei Guo, Xiaohan Shi, +16 authors, Gang Jin.
Front Oncol, 2021 Aug 10; 11. PMID: 34368001    Free PMC article.
Identification of a Prognostic Signature Associated With the Homeobox Gene Family for Bladder Cancer.
Bingqi Dong, Jiaming Liang, +6 authors, Tiejun Yang.
Front Mol Biosci, 2021 Aug 10; 8. PMID: 34368227    Free PMC article.
Comparison of Genomic Characterization in Upper Tract Urothelial Carcinoma and Urothelial Carcinoma of the Bladder.
Kaiwei Yang, Wei Yu, +8 authors, Zhisong He.
Oncologist, 2021 May 30; 26(8). PMID: 34050578    Free PMC article.
A High Epigenetic Risk Score Shapes the Non-Inflamed Tumor Microenvironment in Breast Cancer.
Dong Zhang, Yingnan Wang, Qifeng Yang.
Front Mol Biosci, 2021 Aug 13; 8. PMID: 34381812    Free PMC article.
Kidney cancer biomarkers and targets for therapeutics: survivin (BIRC5), XIAP, MCL-1, HIF1α, HIF2α, NRF2, MDM2, MDM4, p53, KRAS and AKT in renal cell carcinoma.
Fengzhi Li, Ieman A M Aljahdali, +3 authors, Xiang Ling.
J Exp Clin Cancer Res, 2021 Aug 14; 40(1). PMID: 34384473    Free PMC article.
Review.
Identification of CXCL10-Relevant Tumor Microenvironment Characterization and Clinical Outcome in Ovarian Cancer.
Jing Jin, Yi Li, +2 authors, Qijie Zhao.
Front Genet, 2021 Aug 14; 12. PMID: 34386037    Free PMC article.
Downregulation of CCL22 and mutated NOTCH1 in tongue and mouth floor squamous cell carcinoma results in decreased Th2 cell recruitment and expression, predicting poor clinical outcome.
Xuejie Li, Zheqi Liu, +2 authors, Wei Cao.
BMC Cancer, 2021 Aug 16; 21(1). PMID: 34391381    Free PMC article.
An immune-related prognostic signature for thyroid carcinoma to predict survival and response to immune checkpoint inhibitors.
Pu Wu, Wei Sun, Hao Zhang.
Cancer Immunol Immunother, 2021 Aug 17;. PMID: 34398303
The Prognostic Value of the DNA Repair Gene Signature in Head and Neck Squamous Cell Carcinoma.
Ruijie Ming, Enhao Wang, +3 authors, Hongjun Xiao.
Front Oncol, 2021 Aug 17; 11. PMID: 34395285    Free PMC article.
TP53 Mutation Related and Directly Regulated lncRNA Prognosis Markers in Hepatocellular Carcinoma.
Xiulei Zhang, Zhihao Fu, Xiao Zhang.
Onco Targets Ther, 2021 Aug 20; 14. PMID: 34408439    Free PMC article.
A Novel Inflammatory lncRNAs Prognostic Signature for Predicting the Prognosis of Low-Grade Glioma Patients.
Zijin Xiang, Xueru Chen, Qiaoli Lv, Xiangdong Peng.
Front Genet, 2021 Aug 20; 12. PMID: 34408772    Free PMC article.
Comprehensive Characterization of RNA Processing Factors in Gastric Cancer Identifies a Prognostic Signature for Predicting Clinical Outcomes and Therapeutic Responses.
Shenghan Lou, Fanzheng Meng, +3 authors, Yingwei Xue.
Front Immunol, 2021 Aug 21; 12. PMID: 34413861    Free PMC article.
Two Similar Signatures for Predicting the Prognosis and Immunotherapy Efficacy of Stomach Adenocarcinoma Patients.
Taohua Yue, Shuai Zuo, +7 authors, Pengyuan Wang.
Front Cell Dev Biol, 2021 Aug 21; 9. PMID: 34414187    Free PMC article.
Predictive Value of the TP53/PIK3CA/ATM Mutation Classifier for Patients With Bladder Cancer Responding to Immune Checkpoint Inhibitor Therapy.
Yi-Hui Pan, Jia-Xing Zhang, +5 authors, Jun-Hang Luo.
Front Immunol, 2021 Aug 24; 12. PMID: 34421886    Free PMC article.
Identification of Distinct Molecular Patterns and a Four-Gene Signature in Colon Cancer Based on Invasion-Related Genes.
Yunfei Dong, Tao Shang, +2 authors, Zhi Chen.
Front Genet, 2021 Aug 24; 12. PMID: 34421995    Free PMC article.
Robust Prognostic Subtyping of Muscle-Invasive Bladder Cancer Revealed by Deep Learning-Based Multi-Omics Data Integration.
Xiaolong Zhang, Jiayin Wang, +5 authors, Xiaoyan Zhu.
Front Oncol, 2021 Aug 24; 11. PMID: 34422643    Free PMC article.
Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated With Outcomes.
Hussein A Abbas, Vakul Mohanty, +15 authors, Steven M Kornblau.
Front Oncol, 2021 Aug 24; 11. PMID: 34422660    Free PMC article.
Identification of a Costimulatory Molecule Gene Signature to Predict Survival and Immunotherapy Response in Head and Neck Squamous Cell Carcinoma.
Ling Aye, Xiaole Song, +6 authors, Dehui Wang.
Front Cell Dev Biol, 2021 Aug 27; 9. PMID: 34434928    Free PMC article.
m6A RNA Methylation Regulator YTHDF1 Correlated With Immune Microenvironment Predicts Clinical Outcomes and Therapeutic Efficacy in Breast Cancer.
Ying Hu, Qinwen Pan, +6 authors, Jun Jiang.
Front Med (Lausanne), 2021 Aug 27; 8. PMID: 34434939    Free PMC article.
Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity.
S Y Cindy Yang, Scott C Lien, +24 authors, Trevor J Pugh.
Nat Commun, 2021 Aug 28; 12(1). PMID: 34446728
Utilizing Patient-Derived Epithelial Ovarian Cancer Tumor Organoids to Predict Carboplatin Resistance.
Justin W Gorski, Zhuwei Zhang, +7 authors, Jill M Kolesar.
Biomedicines, 2021 Aug 28; 9(8). PMID: 34440225    Free PMC article.
Identification of putative actionable alterations in clinically relevant genes in breast cancer.
Pushpinder Kaur, Tania B Porras, +4 authors, Julie E Lang.
Br J Cancer, 2021 Aug 30;. PMID: 34455425
DNA Damage Repair Profiles Alteration Characterize a Hepatocellular Carcinoma Subtype With Unique Molecular and Clinicopathologic Features.
Peng Lin, Rui-Zhi Gao, +2 authors, Hong Yang.
Front Immunol, 2021 Aug 31; 12. PMID: 34456923    Free PMC article.
Genomic analysis uncovers prognostic and immunogenic characteristics of ferroptosis for clear cell renal cell carcinoma.
Dan Bai, Huhu Feng, +4 authors, Hiroshi Sugiyama.
Mol Ther Nucleic Acids, 2021 Aug 31; 25. PMID: 34458004    Free PMC article.
The Identification of the Metabolism Subtypes of Skin Cutaneous Melanoma Associated With the Tumor Microenvironment and the Immunotherapy.
Ronghua Yang, Zhengguang Wang, +5 authors, Sitong Zhou.
Front Cell Dev Biol, 2021 Aug 31; 9. PMID: 34458265    Free PMC article.
Pan-Cancer Analysis of Genomic and Prognostic Characteristics Associated With Coronavirus Disease 2019 Regulators.
Jian Zhang, Huali Jiang, +6 authors, Jiacai Ye.
Front Med (Lausanne), 2021 Aug 31; 8. PMID: 34458283    Free PMC article.
Molecular and functional profiling identifies therapeutically targetable vulnerabilities in plasmablastic lymphoma.
Fabian Frontzek, Annette M Staiger, +41 authors, Georg Lenz.
Nat Commun, 2021 Sep 02; 12(1). PMID: 34465776
Acquisition of aneuploidy drives mutant p53-associated gain-of-function phenotypes.
Lindsay N Redman-Rivera, Timothy M Shaver, +8 authors, Jennifer A Pietenpol.
Nat Commun, 2021 Sep 02; 12(1). PMID: 34465782