El papel de la biopsia líquida en el diagnóstico y seguimiento del cáncer

Emilio Alba

UGCI Oncología Médica. Hospital Universitario Regional y Virgen de la Victoria

Departamento de Medicina. Universidad de Málaga. IBIMASANAC 2017

Bettegowda, C., et al Sci. Trans. Med., (2014) vol 6

SANAC 2017

LOAD

Detection of cancers in high-risk population/early diagnosis

Monitoring for minimal residual disease

PROFILE

Detection of response/resistance to therapy

Choice of targeted agent

CONCLUSIONS

TOPICS

SANAC 2017

LOAD

Detection of cancers in high-risk population/early diagnosis

Monitoring for minimal residual disease

PROFILE

Detection of response/resistance to therapy

Choice of targeted agent

CONCLUSIONS

TOPICS

SANAC 2017

Selected Studies of ctDNA detection

Analytic PlatformMolecular

AlterationPatients Tumor Stage Sensitivity

Digital PCR(Beaver 2014)

SNV (PIK3CA) 14 Breast I-II 93%

BEAMing(Bettegowda 2014)

SNV (structural

variants)

7 Bladder Localized 57%

19 Breast Localized 53%

40 CCR Localized 78%

14 Gastric-E Localized 57%

9 Ovarian Localized 89%

121 Pancreatic Localized 50%

SCODA(Kidess 2015)

SNV (Kras, BRAF,

PIK3CA, EGFR)10 CCR I-II 60%

Beaver JA, Clin Cancer Res 2014

Bettegowda C, Sci Transl Med 2014

Kidess E, Oncotarget 2015

SANAC 2017

LOAD

Detection of cancers in high-risk population/early diagnosis

Monitoring for minimal residual disease

PROFILE

Detection of response/resistance to therapy

Choice of targeted agent

CONCLUSIONS

TOPICS

SANAC 2017

CTCs in Localized Disease

Tumor Patients Method Results

Prostate(Khurana 2013)

12 Cell Search Inconclusive

CRC(Tsai 2016)

95 CMx Platform > 5CTC = ↓ DFS

CRC(Bork 2015)

239 Cell Search ≥ 1 CTC = ↓ DFS, OS

Khurana KK, 2013

Tsai WS, Sci Rep 2016

Bork U, Br J Caancer 2015

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Presence of CTCs and clinical outcome in early breast cancer

Banys-Paluchowski M. Front Oncol 2016

SANAC 2017

Presence of persistent CTCs and outcome in early breast cancer

Banys-Paluchowski M. Front Oncol 2016

SANAC 2017

ctDNA as Diagnostic Tool

Correlation

BiopsyNGS: 10 gens more frecuently mutated(Illumina/BEAMING)

BloodctDNA

Mx: BIRADS 4a - 5

SANAC 2017

What’s Spotlight 59

• Targeted amplification / library preparation

– Amplicon panel; 277 amplicons across 59 genes– Sample tracking ID panel (104 amplicons)– Sequencing adaptors / barcodes (Illumina)

• Analysis: ERASE-Seq cloud bioinformatic solution

– Complete; from fastq to vcf generation– HIPAA compliant (encrypted data transfer, storage)

No restriction of search space (full panel)

The workflow enables calling variants down to 0.1% AF with over < 0.3 FP calls per 10kBSANAC 2017

Detection of Residual Disease after Surgery (ctDNA)

Method Tumor Patients Results

Chromosomal

Rearrangement(Olsson 2015)

Breast 20ctDNA : Recurrence 0 / 6

ctDNA + : Recurrence 13/14

NGS(Tie 2016)

CRC 178ctDNA + : Recurrence 11 / 14

ctDNA : Recurrence 16/164

Digital PCR(Garcia Murillas 2015)

Breast 37 ctDNA + v : HR: 25.1

Olsson E, EMBO Mol Med 2015

Tie J, Sci Transl Med 2016

García Murillas J, Sci Transl Med 2015

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Monitoring ctDNA

Olsson E EMBO Mol Med 2015

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En pacientes con el tumor primario intervenido (n=14) observamos una disminución del % de MAF al compararlo con los pacientes que no han sido intervenidos (n=10). Vemos un aumento en la media del % de MAF del 4,37 en los pacientes sin cirugía del tumor primario

Las diferencias de % de MAF dependiente de la presencia del tumor primario, aunque no sean estadísticamente significativas, podría deberse a que éste acumula un volumen mutacional mayor que las metástasis o que, al no estar presente el tumor primario, hubiera un déficit de células que vertieran ctDNA al torrente sanguíneo. SANAC 2017

Analizando los resultados de un paciente con mutación en KRAS, exón 2, Cd12 en diferentes procesos clínicos, podemos observar en las gráficas que en la intervención del primario hay una disminución del % del MAF presente antes de ella. Cuando comienza el tratamiento, baja el % de MAF hasta el límite donde la técnica determina como wildtype.

KRAS-2, cd12MAF: 1,71%

BEAMing-1: 01/06/2016 pre-Cx

WTMAF: 0,006%

BEAMing-3: 22/08/2016

En curso de ¨Xelox adyuvante”BEAMing-2: 20/06/2016 post-Cx

KRAS-2, cd12

MAF: 0,198%

Cx primario y hepática: 02/06/2016Tumor primario: KRAS-2, cd12

El BEAMing podría ser una excelente técnica para monitorizar la enfermedad, ya que a través de la sangre obtendríamos una representación de lo que ocurre en ese momento concreto de la evolución tumoral o de la respuesta del paciente al tratamiento.

SANAC 2017

Ciriello G Nat Genetics 2014

Most frequent mutated and methylated genes

SANAC 2017

LOAD

Detection of cancers in high-risk population/early diagnosis

Monitoring for minimal residual disease

PROFILE

Detection of response/resistance to therapy

Choice of targeted agent

CONCLUSIONS

TOPICS

SANAC 2017

Lanman et al. 2015 PLOS One

Tissue NGS vs. Plasma Cell-Free NGS on 165 Paired Samples from Five Centers

SENSITIVITY

SPECIFICITY

DIAGNOSTIC ACCURACY

Cell-free DNA vs. Tissue NGS

85.0% (78.9%-89.7%)

99.6% (99.4%-99.7%)

99.3% (99.1%-99.4%)

Tissue vs. Cell-free DNA NGSSENSITIVITY

SPECIFICITY

DIAGNOSTIC ACCURACY

80.7% (74.4%-85.8%)

99.7% (99.5%-99.8%)

99.3% (99.1%-99.4%)

Cell-free DNA sensitivity may be limited when tumor DNA is not shed into circulation. Tissue DNA sensitivity may be limited because samples fail to capture tumor heterogeneity. All sequencing (both tissue and cfDNA) on Illumina HiSeq 2500.

0 25 50 75 100I I I I I

0 25 50 75 100I I I I I

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Concordancia tejido/plasma en CCR diseminado

Concordancia global 25/28 89,2%

Concordancia nativos 9/12 75%

Concordancia mutados 16/16 100%

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Lebofsky R Mol Oncol 2014

Concordance tissue/blood in a clinical trial

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Baselga J, et al. SABCS 2015. Abstract S6-01.

BELLE-2: Efficacy by PIK3CA Mutation in ctDNA

PIK3CA mutation analysis in ctDNA by BEAMing method (N = 587 pts) Buparlisib + fulvestrant extended PFS in pts with PIK3CA mutations vs fulvestrant alone

Median PFS, Mos(95% CI)

Buparlisib + Fulvestrant

Placebo + Fulvestrant

HR (95% CI)

P Value

ctDNA PIK3CA mutant(n = 200)*

7.0 (5.0-10.0) 3.2 (2.0-5.1) 0.56 (0.39-0.80) < .001

ctDNA PIK3CA non-mutant(n = 387)†

6.8 (4.7-8.5) 6.8 (4.7-8.6) 1.05 (0.82-1.34) .642

*n = 87 buparlisib + fulvestrant; n = 113 placebo + fulvestrant.†n = 199 buparlisib + fulvestrant; n = 188 placebo + fulvestrant.

ORR higher with buparlisib + fulvestrant in pts with PIK3CA mutations vs fulvestrant alone (18.4 % vs 3.5%) but similar in pts with non-mutant PIK3CA (11.6% vs 10.6%)

SANAC 2017

Karachaliou et al. 2015 EURTAC trial JAMA Oncology

Erlotinib

Carboplatin with docetaxel or gemcitabine

A - EGFR L858R or exon 19 Del Measured in Tissue (N = 86)Median PFS (95% CI):

Erlotinib arm 10.4 mos (8.4 – 12.9)Chemotx arm 5.1 mos (4.5 – 5.8)

B - EGFR L858R or exon 19 Del Measured in Plasma (N = 49)Median PFS 995% CI) by qPCR or TaqMan:

Erlotinib arm 12.3 mos (8.4 – 14.7)Chemotx arm 5.5 mos (4.5 – 6.7)

Whether measured in tissue or blood, EGFR L858R and ex19 deletions responded to erlotinib. This is intuitive since the mutations in the blood come from the tissue.

SANAC 2017

Kim et al. 2016 ASCO Abstract J Clinical Oncology 34;15_suppl

Gastric Cancer (N = 78)

NSCLC(N = 72)

ctDNA matched Therapies (n) 10 17

Therapeutic Targets

ERBB2 amplification (6)PIK3CA mutation (2)FGFR2 amplification (1)MET amplification (1)

EGFR mutation (8)EGFR T790M mutation (8)EML4-ALK fusion (1)

Results 1 PD, 1 CR, 5 PR, 3 SD 1 PD, 1 SD, 15 PR

Response Rate (PR+CR) 60% 88%

Disease Control Rate (PR+CR+SD) 90% 94%SANAC 2017

LOAD

Detection of cancers in high-risk population/early diagnosis

Monitoring for minimal residual disease

PROFILE

Detection of response/resistance to therapy

Choice of targeted agent

CONCLUSIONS

TOPICS

SANAC 2017

Kim et al. 2016 ASCO Abstract J Clinical Oncology 34;15_suppl

EGFR T790M Mutations Respond to Osimertinib When Measured in Plasma (ddPCR)

There was no difference in PFS between plasma-detected and tissue-detected EGFR T790M, the median response duration was 9.7 months (95% CI, 8.3 to 11.6) in the osimertinib group and 4.1 months (95% CI, 3.0 to 5.6) in the platinum–pemetrexed group.SANAC 2017

Proyecto de utilidad clínica de la biopsia líquida no invasiva (Guardant 360) en pacientes con NSCLC no escamosos en estadios avanzados

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9 Pacientes había recibido tto previo con Qt. 5 no

Resultados:

De los 13 resultados disponibles, 2 pacientes (15,88%) se están tratando en base a resultados: 1 EGFR mutado (L858R) y 1 FGFR + SANAC 2017

FACTS CTCs ARE PROGNOSTIC MARKERS IN EARLY AND METASTATIC DISEASE CTCs AND ctDNA DETECT MRD HIGH CONCORDANCE TISSUE/BLOOD PREDICTIVE FACTORS FOR SOME ANTITARGET THERAPY

PROMISES ctDNA AS SCREENING TOOL CTCs AND ctDNA AS SURROGATE MARKERS OF ALL TUMOR

POPULATIONS (heterogeneity) CLINICAL UTILITY OF EARLY DIAGNOSIS OF MRD CLINICAL UTILITY AS PREDICTIVE FACTORS

CONCLUSIONS

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