Sample preparation, library construction, targeted capture, next-generation sequencing, and bioinformatic analyses of tumor and normal samples were performed as previously described (23 , 37 (link)). Briefly, DNA was extracted from matched FFPE or frozen tumor tissue and buffy coat samples using the Qiagen DNA FFPE Tissue Kit or Qiagen DNA Blood Mini Kit (Qiagen GmbH). Genomic DNA from tumor and normal samples was fragmented and used for Illumina TruSeq library construction (Illumina) as previously described (23 , 37 (link)). Targeted regions of interest were captured using Agilent SureSelect in-solution capture reagents and a custom targeted panel for genes of interest according to the manufacturer’s instructions (Agilent). Paired-end sequencing, resulting in 150 bases from each end of the fragment for targeted libraries, was performed using the Illumina MiSeq (Illumina).
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Targeted Sequencing of Tumor Samples
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Corresponding Organization : Sidney Kimmel Comprehensive Cancer Center
Other organizations : Aarhus University Hospital, University of California, San Diego, University of Amsterdam, Academic Medical Center, Amsterdam UMC Location VUmc, The Netherlands Cancer Institute, Hvidovre Hospital
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Variable analysis
independent variables
- Sample preparation
- Library construction
- Targeted capture
- Next-generation sequencing
- Bioinformatic analyses
- Genomic DNA from tumor and normal samples
- Matched FFPE or frozen tumor tissue and buffy coat samples
- Qiagen DNA FFPE Tissue Kit or Qiagen DNA Blood Mini Kit (Qiagen GmbH)
- Illumina TruSeq library construction (Illumina)
- Agilent SureSelect in-solution capture reagents and a custom targeted panel for genes of interest
- Paired-end sequencing using the Illumina MiSeq (Illumina)
- Positive control: Not explicitly mentioned
- Negative control: Not explicitly mentioned
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