Project description:Mutation analysis of 77 frequently mutated genes in NSCLC in plasma DNA and corresponding PBMCs of NSCLC patients under ICI using the AVENIO Expanded Kit.
Project description:The AVENIO ctDNA Expanded Kit is a next-generation sequencing (NGS) liquid biopsy assay with a 77 gene panel (192 kb) containing genes in U.S. National Comprehensive Cancer Network (NCCN) Guidelines and emerging cancer biomarkers. This pan-cancer assay was applied to 48 plasma samples from patients with breast, colorectal and non-small cell lung cancer. After sequencing 150bp paired-end, reads were aligned to the hg38 genome with the AVENIO Oncology Analysis Software (version 2.0). These files are the deduplicated alignments generated by the analysis software used for subsequent variant, indel and CNV calling.
Project description:Ongoing progress in high-throughput next-generation sequencing (NGS) has enabled clinicians to comprehensively characterize the genomic landscape of tumors, guide treatment decisions, and facilitate clinical trial enrollment. The role of liquid NGS in anaplastic thyroid carcinoma (ATC) remains unclear, particularly in cases where tissue NGS is not feasible or yields inadequate results. Among these, 26 patients had adequate tissue for commercially available tissue NGS (ACTOnco®+, 440 genes), 15 had access to a commercially available liquid NGS platform (ACTMonitor®+, 50 genes), and 13 patients underwent both tissue and liquid NGS. The genetic alterations observed in ATC exhibited a high degree of heterogeneity, involving several pathways, including RAS/RAF/MEK/ERK, PI3K/AKT/mTOR, cell cycle regulation, other receptor tyrosine kinases, DNA damage response, DNA mismatch repair (MMR, 34.6%, including MLH1, MSH6, MSH2, and PMS1), and chromatin remodeling. The most frequently mutated genes in tissue NGS were TP53 (17/26, 65.4%) and BRAF (8/26, 30.8%). Among the 13 pairs analyzed on both platforms, the concordance rates were 84.6% and 69.2% for BRAF and TP53, respectively. Among two patients without sufficient tissue for NGS, liquid NGS provided additional information on genetic alterations. NGS platforms, whether applied to tissue or liquid samples, can empower clinicians to identify targetable oncogenic events in ATC. Liquid biopsy provides supplementary information when the tissue is insufficient for NGS.
Project description:MeRIP-Seq data aligned to the genome (GRCh38) for cells with IDH1-Mut or IDH1-WT genotypes. Aligned data (BAM) are separated into input RNA and m6A immunoprecipitated RNA for each cell sample.
Project description:Targeted next-generation sequencing (NGS) of 93 frequently mutated genes in breast cancer using the QIAseq Human Breast Cancer Targeted Panel (QIAGEN), which uses digital sequencing by incorporating unique molecular barcodes (UMI).