Scott Bratman (Princess Margaret Cancer Centre, Canada)
“Circulating Tumor DNA: Detection and Applications in Curable Cancers”
Can liquid biopsy replace it’s sue biopsy?
EGFR-mutant NSCLC: ctDNA analysis is standard for guiding EGFR
How about applied to cancers that are curable
CtDNA < 1% total cell DNA
Nat Rev Wan… Rosenfield et al. Nat Rev Cancer 2017
Rasta I and Bratman, Radiotherapy Oncol 2017: utilizing ctDNA for curable cancers: where is potential for clinical utility
1 minima residual disease (MRD): rise stratification after treatment
Molecular MRD analysis is
CtDNA for MRD in locally-advanced cervix anger
1. Serial HPV ctDNA
2. CtDNA for MRD in locally-advanced Corvus cancer. Han/Leung… Bratman et al JCO poster in press
3. CtDNA for MRD in locally-advanced cervix cancer
4. End-of-CRT ct DNA leverages ar strongly prognostic
Sensitivity of ctDNA for MRD in not perfect, Factors affecting sensitivity for MRD. Nat Biotecnology 2016 Newman et al
1. Blood/plasma volume me
2. DNA extraction rate
3. Fragment recovery rate
4. Number of reporters
5. Proportion of patients
6. Background error rate
Cancer Personalied profiling by dep Seq (CAPP-seq) Nat MEdicine 2014
approaches for greater sensitivity (more tumor marker s to increase signal)
Cancer discovery 2017
Decrease noises (error suppression) Nat Biotecnology 2016 Newman et al
Part II [NPC and EBV DNA detection]
Lo, Lin, and 2017 NEJM Chan et al
EBV qPCR: MRD sensitivity
Insufficient sensivity (46%) in Lin et al NEJM 2004 and JNCI 2002 Chan et al (33? 38%)
Hypothesis: EBV-seq is more sensitive
Nat REv Genetic 2011
Analytic sensitivity
QPCR detection limit = 1-10 EBV GE
DdPCR detection limit = 10EBV GE
EBV-seq detection limit =0.01 EBV GE
20ng DNA is sufficient
VirusFinder 2.0 (80 viral genomes including 12 EBV genomes
EBV-seq performed on baseline plasma rom 12 patients
4 x 10&7 paired-end reads
Over-sequence (via tag) —> 40 millions reads is too high cut 100 fold to 4 x 10^5 paired-end reads
Cancer control cohorts
Expand cohor 2 (EBV qPCR-undetectable) -19 patients
Add in cohort 4 (healthy control)
4 x 10^5 paired-end reads
1. EBV ctDNA is shorther than autosomal cfDNA
2. cfDNA from non-NPC is shorter than EBV ctDNA
EBV-seq has great analyiscal sensitivity than the BamHI W qPCR assay
High sensitivity for detecting EBV DNA in pretreatment plasma