Visualization of the Effect of Assay Size on the Error Profile of Tumor Mutational Burden Measurement

Bailey, Nathanael G.

doi:10.3390/genes13030432

Cited by 2 publications

(1 citation statement)

References 25 publications

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“…Tumor mutational burden (TMB) can be used to evaluate the response to immunotherapy [27]. Microsatellite instability (MSI) status was associated with DNA mismatch repair(MMR) and can be as a biomarker in tumor immunotherapy and can evaluate the prognosis of tumors [28].…”

Section: Tmb Msi Mmr Gene Mutation and Dna Methyltransferase Analysismentioning

confidence: 99%

A Comprehensive Multiomics Analysis Identified POLQ as a Promising Prognostic Biomarker in Pan-Cancer

Yang

Huang

et al. 2023

Preprint

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Background DNA polymerase (POLQ) is a unique A-family polymerase that is correlated with homologous recombination and plays a vital role in maintaining the stability of the genome. Tumor immune microenvironment (TIME) plays an important role in the occurrence and development of tumor. POLQ is associated with TIME and a poor prognosis. However, the roles of POLQ in human cancers are still unclear. Hence, studying POLQ maybe provide a new strategy for tumor-immune therapy. Methods The mRNA expression data and clinical information of cancer were downloaded from TCGA and GTEx. We explored the prognosis, mutation, copy number variation (CNV) and single nucleotide variations (SNV), microsatellite instability (MSI), tumor mutational burden (TMB), mismatch repair (MMR) gene mutation levels and DNA methyltransferase expression, immune infiltration, enrichment analysis and pathway, and drug sensitivity analysis via Kaplan-Meier curves, cBioPortal, GSCA, TCGA, TIMER, The LinkedOmics database and Multiomics Data. Results POLQ expression was associated with adverse outcomes in uterine corpus endometrial carcinoma (UCEC), kidney renal papillary cell carcinoma (KIRP) and liver hepatocellular carcinoma (LIHC) patients. Additionally, our study revealed that genomic alteration of POLQ was associated with tumorigenesis in multiple tumors and POLQ was correlated with MSI, TMB, MMR gene mutation and DNA methyltransferase expression. POLQ expression was positively correlated with the infiltration of immune cells including B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells, especially in kidney renal clear cell carcinoma (KIRC), thyroid carcinoma (THCA). And POLQ expression was positively correlated with the immune score and immune checkpoint in KIRC and THCA. In particular, POLQ can increase the resistance to drug, especially to PAPR inhibitors. Conclusion POLQ could be a novel biomarker and a potential target for immune-related therapy in pan-cancer.

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Section: Tmb Msi Mmr Gene Mutation and Dna Methyltransferase Analysismentioning

confidence: 99%