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