jwellsbio / variant_analysis

variant_analysis

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

Samples

Samples include:

Patient 10:

Liver 1 (met) Liver 2A (met) Liver 5 (met) Plasma

Patient 9:

Lymph Node (met) Omental (met) Ovary (met) Plasma

Patient 2

2 Liver mets 2 Breast primaries Normal Liver instead of buffy

Patient 8

Axillary (met) 2 Breast primaries Plasma

Patient 9A

Heart (met) Left Kidney (met) Right Kidney (met) 2 Liver mets 2 Omental mets Plasma Uses patient 9 buffy as normal

Filters used on variant calls

• 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