The purpose of the project is to determine how effective liquid biopsies can be in detecting metastases by detecting variants found in the DNA in plasma
Liver 1 (met) Liver 2A (met) Liver 5 (met) Plasma
Lymph Node (met) Omental (met) Ovary (met) Plasma
2 Liver mets 2 Breast primaries Normal Liver instead of buffy
Axillary (met) 2 Breast primaries Plasma
Heart (met) Left Kidney (met) Right Kidney (met) 2 Liver mets 2 Omental mets Plasma Uses patient 9 buffy as normal
- Indels removed
- Intron and intergenic variants removed
- All Phred-scale quality measures > 20 (99.9% accuracy)
- Plasma calls must have MAF > 0.01
- Tumor calls must have MAF > 0.05
- All Mutect2 calls must also be similarly called by Varscan or Freebayes