Comprehensive Genomic Profiling with TSO 500

Genomic DNA extraction and library preparation with TruSight™ Oncology 500 (TSO 500) Library Preparation Kit (Illumina, San Diego, CA, United States) were performed following protocols described previously (Li et al., 2021 (link)). The library was sequenced on the Illumina NextSeq 550Dx platform with the paired-end run of 150 base pairs. The quality of sequencing data was verified by TSO 500 Docker pipeline. The process of SNVs and Indels mutation calling, TMB measuring, and reads filtering were performed following the description in the previous study (Li et al., 2021 (link)). Germline variants could be filtered out using an in-house built database, and all parameters were set according to the previous workflow (He et al., 2021 (link)).

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Guo N., Chen Y., Jing Z., Liu S., Su J., Li R., Duan X., Chen Z., Chen P., Yin R., Li S, & Tang J. (2022). Molecular Features in Lymphatic Metastases Reflect the Metastasis Mechanism of Lymph Nodes With Non-Small-Cell Lung Cancers. Frontiers in Bioengineering and Biotechnology, 10, 909388.

Publication 2022

TruSight™ Oncology 500 (TSO 500) Library Preparation Kit NextSeq 550Dx platform

Genomic Germline variants Indels mutation Library Oncology

Corresponding Organization : Binzhou University

Other organizations : Chinese Academy of Sciences, Computer Network Information Center

Top 5 similar protocols

Variable analysis

independent variables

Genomic DNA extraction and library preparation with TruSight™ Oncology 500 (TSO 500) Library Preparation Kit (Illumina, San Diego, CA, United States)

dependent variables

SNVs and Indels mutation calling
TMB measuring
Reads filtering

control variables

The quality of sequencing data was verified by TSO 500 Docker pipeline
Germline variants could be filtered out using an in-house built database
All parameters were set according to the previous workflow (He et al., 2021)

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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