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Coordinación científica:
Dr. Rafael López López
Complejo Hospitalario Universitario de Santiago de
Compostela
Organizado por: Sede:
San Francisco Hotel Monumento
Campillo de San Francisco, 3 - Santiago de
Compostela
Genomic profiles employed in liquid
biopsy
Emiliano Calvo, MD PhD
Oncología Médica
START Madrid, CIOCC
Hospital HM Madrid Norte Sanchinarro
Agenda
• Challenges of solid and liquid biopsies
• PCR-based vs. NGS-based ctDNA liquid biopsies
• How to choose the best platform
– Tumor type (target vs drug)
– Expected Mutation Allele Fraction
– Indication
• How we do it
Agenda
• Challenges of solid and liquid biopsies
• PCR-based vs. NGS-based ctDNA liquid biopsies
• How to choose the best platform
– Tumor type (target vs drug)
– Expected Mutation Allele Fraction
– Indication
• How we do it
Issues of Precision Medicine: When the tissue is not contributive
• Tumor heterogeneity
– Metachronic
– Synchronic
• Primary vs. Metastatic
What’s the target?
Issues of Precision Medicine: tumor heterogeneity
Gerlinger M et al, NEJM 2012; 366: 883-892
Issues of Precision Medicine: tumor heterogeneity
Precision Medicine: ctDNA vs. tissue biopsy
The challenge of plasma
cfDNA
Number of accessible copies of tumor genome
are often low, dilute and degraded www.sysmex-inostics.com
The challenge of plasma
cfDNA
• Highly fragmented, typically 50–200bp range (165bp peak)
believed to be a mix of DNA shed from tumor via apoptosis and
necrosis
• Short half-life: ~30min (until stabilized)
• Low abundance: highly variable, but generally low
nanograms per ml plasma constituting <0.1–50% of total
plasma DNA
• Number of tumor molecules in plasma decrease with
successful treatment
• Normal DNA contamination is a major issue
Agenda
• Challenges of solid and liquid biopsies
• PCR-based vs. NGS-based ctDNA liquid biopsies
• How to choose the best platform
– Tumor type (target vs drug)
– Expected Mutation Allele Fraction
– Indication
• How we do it
Comparison of methods of
liquid biopsy
Zhang et al. Cell Physiol Biochem 2017;41:755-768
Plasma cfDNA
sequencing
cruk.cam.ac.uk/research-groups/rosenfeld-group
• Due to challenges with cfDNA, assays for
detection must be highly sensitive and specific
• Assays can be single gene, panel of genes or
whole genome
Not all liquid biopsies are
created equal
Not all liquid biopsies are
created equal
Oxnard et al. 2016 J Clinical Oncology
Comparison of methods of
ctDNA
Normano et al, ESMO 2017
Agenda
• Challenges of solid and liquid biopsies
• PCR-based vs. NGS-based ctDNA liquid biopsies
• How to choose the best platform
– Tumor type (target vs drug)
– Expected Mutation Allele Fraction
– Indication
• How we do it
IDEAL BIOMARKER:
– Proof of target
– Proof of concept
– Proof of activity
– Proof of efficacy
(Biomarker with no therapeutic relevance and clinical benefit for patients... Only good for publications!)
Precision Medicine: a target-drug tango
Precision Medicine: a target-drug tango
Precision Medicine: a target-drug tango
Precision Medicine: a target-drug tango
Precision Medicine: a target-drug tango
NCCN Guideline
Genomic Targets
Eleven somatic genomic targets in seven cancer types
Reported methods for
cfDNA sequencing
Reported methods for
cfDNA sequencing
This is just a partial list…
… And will evolve rapidly!
Common cancers with
ctDNA detection: NSCLC
Cancer (Basel). 2017 Nov; 9(11): 154
Agenda
• Challenges of solid and liquid biopsies
• PCR-based vs. NGS-based ctDNA liquid biopsies
• How to choose the best platform
– Tumor type (target vs drug)
– Expected Mutation Allele Fraction
– Indication
• How we do it
Common cancers with
ctDNA detection
Bettegwoda et al, Sci Transl 2014
ctDNA is more frequently
found in advanced disease
ctDNA assays: One size
does not fit all
Agenda
• Challenges of solid and liquid biopsies
• PCR-based vs. NGS-based ctDNA liquid biopsies
• How to choose the best platform
– Tumor type (target vs drug)
– Expected Mutation Allele Fraction
– Indication
• How we do it
Clinical application should
inform choice of assay
Applications ctDNA
detection
MOLECULAR PROFILING
DETECTING MINIMAL RESIDUAL DISEASE
MONITOR RESPONSE
TO TREATMENT
EARLY DIAGNOSIS OF CANCER
ctDNA assays: One size
does not fit all
PCR-based
NGS-based
Clinical application should
inform choice of assay
Monitoring of EGFR mutations with specific assays
Agenda
• Challenges of solid and liquid biopsies
• PCR-based vs. NGS-based ctDNA liquid biopsies
• How to choose the best platform
– Tumor type (target vs drug)
– Expected Mutation Allele Fraction
– Indication
• How we do it
Precision Medicine at CIOCC
SOLID BIOPSY • Oncomine • Foundation One
LIQUID BIOPSY • Biocartis (single genes; BRAF, KRAS, NRAS) • OncoTrace (40 genes; it can be “personalized”) • Guardant 360 (73 genes) • Foundation ACT (62 genes, highly sensitive, specific and
validated)
OncoTrace
Guardant360
Foundation ACT
*Copy number ≥ 8 in genes with at least 4 targets; † Orthogonal methods: FoundationOne®, Digital Droplet PCR and break-point
PCR; ** From date Foundation Medicine receives a sample that meets requirements; MAF: mutant allele fraction.
Stephens, P.J., et al. (2016) Annual ESMO congress Poster 1159PD.
Foundation ACT
A LIQUID BIOPSY Assay for Circulating Tumor DNA, interrogating all known
classes of genomic alteration across 62 genes. Provides validated, blood-based profiling when tissue biopsy may not be
feasible
• TMB is an immerging biomarker for immunotherapy response can be assessed accurately with a CGP assay targeting ~1.1 Mb (as with FoundationOne®)1
• There is a significant need for diagnostic approaches enabling analysis of TMB in patients without tumor tissue available2
• Foundation medicine is developing and analytically validating a blood-
based assay that determines blood TMB with high accuracy and
precision at a low detection limit2
• Average values across both bTMB cutoffs (established against an
orthogonally validated TMB platform)2
• Positive predictive agreement: 95%
• Negative predictive agreement: 100%
• Positive predictive value: 100%
• Average precision: 96%, coefficient of variation = 17%
• Limit of detection: 1% of tumor content in ≥ 20 ng of cell-free DNA
Foundation ACT: Measurement of blood-based tumor mutational burden
Use of liquid biopsy in immunotherapy
Conclusions
High sensitivity cfDNA profiling techniques have the potential to reveal mutations not evident in standard tumor biopsies due to disease heterogeneity
Multiple assays exist in the academic and commercial setting for the detection of genomic aberrations in cfDNA
Methodologies and sensitivities are rapidly evolving, and performance may be variable across different assays (and genes!)
Various approaches to mutation detection are available (hotspotting, NGS, panels, etc) and should be matched with the intended application or indication