Comprehensive Molecular Profiling of FFPE and Liquid Biopsies
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Corresponding Organization :
Other organizations : Sun Yat-sen University, Sun Yat-sen University Cancer Center, Second Affiliated Hospital of Zhejiang University, Betta Pharmaceuticals (China)
Variable analysis
- Tissue collection at baseline
- Blood sample collection at baseline and C1D31
- DNA extraction from FFPE tissues using QIAamp DNA FFPE Tissue Kit
- Plasma and white blood cells DNA extraction using QIAamp Circulating Nucleic Acid Kit and Hipure Blood&Tissue DNA Kit
- DNA capture using SureSelect XT-HS Target Enrichment System with a 212-gene panel
- Sequencing using Illumina HiSeq-X10 platform with mean sequencing depths of approximately 20,000 times for blood samples and 4,000 times for tissue samples
- Filtering out clonal hematopoiesis variants and germline mutations by pairing samples and white blood cells
- Single-nucleotide variation and insert-deletion variant detection using MuTect2
- Gene fusion detection using LUMPY (version 0.2.13)
- Copy number variation detection using CNVkit software (v0.9.5)
- Calculation of mutation load and ALK mutation abundance
- QIAamp DNA FFPE Tissue Kit (Qiagen, Hilden, Germany) for DNA extraction from FFPE tissues
- QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany) and Hipure Blood&Tissue DNA Kit (Magen Biotechnology, Guangzhou, China) for plasma and white blood cells DNA extraction
- SureSelect XT-HS Target Enrichment System (Agilent Technologies, Santa Clara, CA, USA) with a 212-gene panel for DNA capture
- Illumina HiSeq-X10 platform (Illumina, San Diego, CA, USA) for sequencing
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