The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers

Kim, Soyeon; Lee, Joo Won; Park, Young‐Seok

doi:10.3390/life10100228

Cited by 32 publications

(28 citation statements)

References 150 publications

(305 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The final step of wet-laboratory SM protocols is sequencing ( Garmaeva et al, 2019 ). Currently, the most widely used method due to low costs, high yield, and wide availability is sequencing by synthesis marketed by Illumina (San Diego, CA, United States) ( Kim et al, 2020 ). Despite numerous advantages, Illumina sequencing platforms share common challenge related to phage PhiX174 (approximately 5.3 kb) control used for quality and calibration assessment ( Manley et al, 2016 ).…”

Section: Sources Of Contamination In Microbiome Studiesmentioning

confidence: 99%

Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives

2021

View full text Add to dashboard Cite

We describe the most common internal and external sources and types of contamination encountered in viral metagenomic studies and discuss their negative impact on sequencing results, particularly for low-biomass samples and clinical applications. We also propose some basic recommendations for reducing the background noise in viral shotgun metagenomic (SM) studies, which would limit the bias introduced by various classes of contaminants. Regardless of the specific viral SM protocol, contamination cannot be totally avoided; in particular, the issue of reagent contamination should always be addressed with high priority. There is an urgent need for the development and validation of standards for viral metagenomic studies especially if viral SM protocols will be more widely applied in diagnostics.

show abstract

Section: Sources Of Contamination In Microbiome Studiesmentioning

confidence: 99%

Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives

2021

View full text Add to dashboard Cite

show abstract

“…By targeting mRNA, miRNA was involved in the regulation of various cellular processes such as cell proliferation, apoptosis and signal transduction, and played an important role in the development of tumors 29 . The abnormal expression of miRNA in OSCC caused the degradation or translation inhibition of the regulated mRNA, and then played the role of tumor suppressor gene or oncogene 30 . Therefore, the establishment of the miRNA-mRNA regulatory network was particularly important for the study of the pathogenesis of OSCC.…”

Section: Discussionmentioning

confidence: 99%

Construction of the miRNA-mRNA regulatory network and analysis of hub genes in oral squamous cell carcinoma

Cui¹,

Song²,

Chen³

et al. 2022

Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub

View full text Add to dashboard Cite

Background. Oral squamous cell carcinoma (OSCC) severely affects the quality of life and the 5-year survival rate is low. Exploring the potential miRNA-mRNA regulatory network and analyzing hub genes and clinical data can provide a theoretical basis for further elucidating the pathogenesis of OSCC. Methods. The miRNA expression datasets of GSE113956 and GSE124566 and mRNA expression datasets of GSE31056, GSE37991 and GSE13601 were obtained from the Gene Expression Omnibus databases. The differentially expressed miRNAs (DEMs) and mRNAs (DEGs) were screened using GEO2R. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by DAVID database. The PPI network was established through STRING database and the hub genes were preliminarily screened out by Cytoscape software. After identifying the hub genes in the TCGA database, we predicted the potential DEM transcription factors, constructed a miRNA-mRNA regulatory network, and analyzed the relationship between the hub genes and clinical data. Results. A total of 28 DEMs and 764 DEGs were screened out, which were composed of 285 up-regulated genes and 479 down-regulated genes. Enrichment analysis showed that up-regulation of DEGs were mainly enriched in extracellular matrix organization and cancer-related pathway, while down-regulation of DEGs were mainly enriched in muscular system process and adrenaline signal transduction. After preliminary screening by PPI network and identification in TCGA, the up-regulated FN1, COL1A1, COL1A2, AURKA, CCNB1, CCNA2, SPP1, CDC6, and down-regulated ACTN2, TTN, IGF1, CAV3, MYL2, DMD, LDB3, CSRP3, ACTA1, PPARG were identified as hub genes. The miRNA-mRNA regulation network showed that hsa-miR-513b was the DEM with the most regulation, and COL1A1 was the DEG with the most regulation. In addition, CDC6, AURKA, CCNB1 and CCNA2 were related to overall survival and tumor differentiation. Conclusions. The regulatory relationship of hsa-miR-513b/ CDC6, CCNB1, CCNA2 and the regulatory relationship of hsa-miR-342-5p /AURKA were not only verified in the miRNA-mRNA regulatory network but also related to overall survival and tumor differentiation. These results indicated that they participated in the cellular regulatory process, and provided a molecular mechanism model for the study of pathogenesis.

show abstract

“…NGS has been demonstrated to be a powerful tool that enables to detect very low allele frequency variants. Detecting somatic mutations by NGS is a critical part of cancer research and diagnostics ( 31 – 33 ). Sequencing depth is required since mutations need to be observed on a sufficient number of reads to pass predetermined variant calling threshold ( 21 ).…”

Section: Discussionmentioning

confidence: 99%

Next Generation Sequencing for Detecting Somatic FAS Mutations in Patients With Autoimmune Lymphoproliferative Syndrome

et al. 2021

View full text Add to dashboard Cite

Autoimmune lymphoproliferative syndrome (ALPS) is a primary immune regulatory disorder clinically defined by chronic and benign lymphoproliferation, autoimmunity and an increased risk of lymphoma due to a genetic defect in the FAS-FASL apoptotic pathway. Genetic defects associated with ALPS are germinal and somatic mutations in FAS gene, in addition to germinal mutations in FASLG, FADD, CASP8 and CASP10 genes. The accumulation of CD3+TCRαβ+CD4-CD8- double negative T-cells (DNT) is a hallmark of the disease and 20-25% of ALPS patients show heterozygous somatic mutations restricted to DNT in the FAS gene (ALPS-sFAS patients). Nowadays, somatic mutations in the FAS gene are detected through Sanger sequencing in isolated DNT. In this study, we report an ALPS-sFAS patient fulfilling clinical and laboratory ALPS criteria, who was diagnosed through NGS with a targeted gene panel using DNA from whole blood. Data analysis was carried out with Torrent Suite Software and variant detection was performed by both germinal and somatic variant caller plugin. The somatic variant caller correctly detected other six ALPS-sFAS patients previously diagnosed in the authors’ laboratories. In summary, this approach allows the detection of both germline and somatic mutations related to ALPS by NGS, avoiding the isolation of DNT as the first step. The reads of the somatic variants could be detected even in patients with DNT in the cut off limit. Thus, custom-designed NGS panel testing may be a faster and more reliable method for the diagnosis of new ALPS patients, including those with somatic FAS mutations (ALPS-sFAS).

show abstract

The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers

Cited by 32 publications

References 150 publications

Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives

Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives

Construction of the miRNA-mRNA regulatory network and analysis of hub genes in oral squamous cell carcinoma

Next Generation Sequencing for Detecting Somatic FAS Mutations in Patients With Autoimmune Lymphoproliferative Syndrome

Contact Info

Product

Resources

About