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The application of second-generation sequencing in congenital pulmonary airway malformations

ABSTRACT: Objective: To investigate the differential expression of genes in whole transcripts of congenital pulmonary airway malformation (CPAM) using second-generation sequencing (also known as next-generation sequencing, NGS) technology. Methods: Children with CPAM were strictly screened after setting the criteria, and grouped by taking CPAM parietal tissue and CPAM lesion tissue respectively, and RNA-Seq libraries were established separately using second-generation sequencing technology, followed by differential expression analysis and GO (gene ontology) functional enrichment analysis, KEGG pathway analysis and GSEA (Gene Set Enrichment Analysis) analysis. Results: Five cases were screened from 36 children with CPAM, and high-throughput sequencing was performed to obtain 10 whole transcripts of samples with acceptable sequence quality and balanced gene coverage. One aberrantly expressed sample was found by analysis of principal components, which was excluded and then subjected to differential expression analysis, and 860 up-regulated genes and 203 down-regulated genes. GO functional enrichment analysis of differentially expressed genes demonstrates the functional class and cellular localization of target genes. Conclusion: The whole transcript of CPAM shows obvious gene up- and down-regulation, differentially expressed genes are located in specific cells and belong to different functional categories, and NGS can provide an effective means to study the transcriptional regulation of CPAM from the overall transcriptional level.

ORGANISM(S): Homo sapiens

PROVIDER: GSE190620 | GEO | 2022/12/07

REPOSITORIES: GEO

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Project description:OBJECTIVE: To investigate the differentially expressed genes related to the chemosensitivity of laryngeal squamous cell carcinoma ï¼LSCCï¼by microarrays arrays. METHODS: 1. A total number of 11 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (7 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis 2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened. RESULTS: 1. Analyzed by microarrays, there were 1554 genes significantly related to the sensitivity to chemotherapy; Among these 1554genes, 777 showed a higher expression in the tissue from patients who are sensitive to chemotherapy , while 785 presented the contrasting pattern. CONCLUSIONS: The research revealed a gene expression signature of chemosensitivity in laryngeal squamous cell carcinoma by microarrays arrays. The result will contribute to the understanding of the molecular basis of laryngeal squamous cell carcinoma and help to improve diagnosis and treatment. 1. A total number of 11 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (7 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis 2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened.

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The application of second-generation sequencing in congenital pulmonary airway malformations

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