BIOPSIA LÍQUIDA y nuevas NGS EN CÁNCER DE PULMON€¦ · NGS 1-0.002% A large number of mutation...
Transcript of BIOPSIA LÍQUIDA y nuevas NGS EN CÁNCER DE PULMON€¦ · NGS 1-0.002% A large number of mutation...
BIOPSIA LÍQUIDA y nuevas NGS EN CÁNCER DE PULMON
Prof. Mariano Provencio
Servicio Oncología Médica
LiquidBiopsyLabPdH (@LiquidBiopsyLab)
ctDNA
Crowley, E. et al. (2013) Nat. Rev. Clin. Oncol.
Technical challenges
• The fraction of ptDNA in total plasma is often small
• The quality of plasma is highly dependent on how it is processed
• Assaying for rare mutation detection is akin to looking for needles in haystack
Where is the mutant Pablo?
Where is the mutant Pablo?
• ctDNA shows superior sensitivity in detecting various cancers compared with circulating tumour cells (CTCs)
Detection of disease and its recurrence
Liquid biopsy may provide clinical benefit
• Detection of residual disease with liquid biopsy may enable personalised therapies earlier in
disease progression
• Serial liquid biopsies can be used to monitor disease progression and detect early recurrence
Provencio M , et al . Oncotarget. 2017 Aug 7;8(36):60291-60298. Provencio M , et al . Oncotarget. 2017 Nov 16;9(1):488-494
• ctDNA is a fraction of a fraction of the plasma1 and increases with disease progression2
Detection of ctDNA requires highly sensitive techniques
Tumor-derived nucleic acids and their detection
• The amount of ctDNA released into the blood is
dependent on several factors
Tumor grade,
histology and
vascularity1,2,3
Physiological
clearance and
degradation4,5,6
Rate of release
and cell
status3,4
Time of blood
draw and
therapy1,7,8
1. Hinrichsen, T., et al. (2016) J Lab Med. 40:313-22; 2. Bettegowda C, et al. (2014) Sci Transl Med. 6:224ra24; 3. Diaz, L.A., &
Bardelli, A. (2016) J Clin Oncol. 32:579-86; 4. Siravegna, G., et al. (2017) Nat Rev Clin Oncol. advance online publication; 5. Forte,
V.A., et al. (2016) Cancer Biol Med. 13:19–40; 6. Leung, F., et al. (2016) Clin Chem. 62:1054–60; 7. Diehl, M., et al. (2008) Nat
Med. 14:985-90; 8. Tie, J., et al. (2015) Ann Oncol. 26:1715–22.
0
100
80
60
40
20
Fre
qu
en
cy o
f cases w
ith
dete
cta
ble
ctD
NA
(%
)
Stage I (n = 49)
Stage 2 (n = 133)
Stage 3 (n = 51)
Stage 4 (n = 136)
Adapted from Bettegowda C, et al 20142
Technology
Vendrell JA et al.Circulating Cell Free Tumor DNA Detection as a Routine
Tool forLung Cancer Patient Management. Int J Mol Sci. 2017;18(2)
Diaz LA . J Clin Oncol. 2014 Feb 20;32(6):579-86.
Diaz LA . J Clin Oncol. 2014 Feb 20;32(6):579-86.
PRINCIPLE Sensitivity (MAF) Adventage Limitations
dPCR 1-0.01%
Ease of use
Robustness
Inexpensive
Only a limited
number of mutations
can be testedLimited
NGS 1-0.002%
A large
number of
mutation
can be
tested at a
time Expensive
EGFR
KRAS Unknown
A growing number of
potentially targetable cancer-related
genes are being identified
Increasing numbers
of targeted therapies are
becoming available
2004
Clinically relevant driver mutations identified in patients with lung adenocarcinoma*
*Patients referred for genomic
testing between January 2014
and March 2016 Sourced from Jordan et al. 20178
© 2017 American Association for Cancer Research
KRAS
EGFR
Unknown
2004 2016
EGFR exon 20
EGFR T790M
EGFR WT amp
EGFR sensitising
No mutations
Other drivers
PTEN loss
CDKN2A loss
BRAF non-V600E
NF1 loss
FGFR1/2
NRAS
PIK3CA
MAP2K1
ERBB2 mut
TSC1/2 loss
BRCA1/2 loss
ERBB2 amp
MET amp
MET splice
BRAF V600E
RET fusion
ROS1 fusion
ALK fusion
A growing number of potentially targetable cancer-related genes are being identified
Paciente Gen Proteína NGS (%) dPCR (%)
ARS-ALK ALK p.Gly1269Ala 0,87 0,42
AMLO-ALK ALK p.Gly1269Ala 2,99 2,81
NGS vs dPCR
Pearson´s r=0,987;p<0,0001
AF=2,81%
AF=2,99%
4 pacientes translocados:
Provencio et al submitted.
Shaw AT, et al. Resensitization to crizotinib by the lorlatinib ALK resistance mutation L1198F. N Engl J Med. 2016;374(1):54–61
Katayama R, Lovly CM, Shaw AT. Therapeutic targeting of anaplastic lymphoma kinase in lung cancer: a paradigm for precision cancer medicine. Clin Cancer Res. 2015;21:2227–35.
Friboulet L et al. The ALK inhibitor ceritinib overcomes crizotinib resistance in non-small cell lung cancer. Cancer Discov. 2014;4:662–73.
MOLECULAR PROFILING IN ALK (+) PATIENTS
Diaz LA . J Clin Oncol. 2014 Feb 20;32(6):579-86.
PRINCIPLE Sensitivity (MAF) Adventage Limitations
dPCR 1-0.01%
Ease of use
Robustness
Inexpensive
Only a limited
number of mutations
can be testedLimited
NGS 1-0.002%
A large
number of
mutation
can be
tested at a
time Expensive
Commercial NGS liquid biopsy test
Guardant 360 (Guardant Health)
FoundationOne@liquiq (Foundation
Medicine)
AVENIO ctDNA Targeted Kit, ctDNA Expanded
Kit and ctDNA Surveillance Kit (Roche
Diagnostics)
Oncomine Lung cfDNA Assay (Thermo Fisher
Scientific
NEOliquid (New Oncology)
Reveal ctDNA 28 Kit (ArcherDX)
OptiSeq™ Pan-Cancer Panel (DiaCarta)
PlasmaSELECT™-R 64 (PGDx)
Signatera™ RUO (Natera)
75.6% of oncologists reported using NGS tests in the past 12 months to guide treatment decisions
“More than 50% of oncologists in our study reported that NGS test results were difficult to interpret either often or sometimes. In addition, 25% indicated that they referred patients to other providers for NGS testing..”
* F1 CDx bait-set available Ex-US from 01 October 2018; † From date of receipt. FFPE: formalin-fixed, paraffin-embedded; HC: hybrid capture; MSI: microsatellite instability; NGS: next-generation sequencing; TMB: tumour mutational
burden; . 1. Foundation Medicine. (2018) FoundationACT Technical Specifications. Accessed Jun 2018 from
https://assets.ctfassets.net/vhribv12lmne/3SPYAcbGdqAeMsOqMyKUog/3b10e8355a717f658c82d7544503df9f/FACT_TechnicalInformation_09_RD.pdf;
2. Foundation Medicine. (2018) FoundationACT Sample patient report; 3. Foundation Medicine. (2017) FoundationACT Webpage summary. Accessed Oct 2017 from https://www.foundationmedicine.com/genomic-testing/foundation-act; 4.
Foundation Medicine. FoundationOne Liquid Technical Specifications to be published Sept 2018; 5. Foundation Medicine. (2017) FoundationOne Technical Specifications. Accessed Oct 2017 from
https://assets.ctfassets.net/vhribv12lmne/6YRrchSINOeSu48YwuesoY/0c3651c8421fa3647ccede76de9dce61/MKT-0054-02_F1_TechSpecs_digital.pdf; 6. Foundation Medicine. (2017) FoundationOne Webpage summary. Accessed Oct
2017 from https://www.foundationmedicine.com/genomic-testing/foundation-one; 7. Frampton, G.M., et al. 2013. Nat Biotechnol 31:1023-31; 8. Foundation Medicine. (2017) FoundationOneHeme Technical Specifications. Accessed Oct 2017
from https://assets.ctfassets.net/vhribv12lmne/zBxaQC12cScqgsEk8seMO/abf6133874f1e5929403f66d90c3b900/F1H_TechnicalInformation_06_digital.pdf; Foundation Medicine. (2018) FoundationOneCDx Technical Specifications.
Accessed Jun 2018 from https://assets.ctfassets.net/vhribv12lmne/4ZHUEfEiI8iOCk2Q6saGcU/671b313cb6bb85bfe861f83e31c9716d/F1CDx_TechInfo_09-03.pdf;
9. Foundation Medicine. (2017) FoundationOneHeme Webpage summary. Accessed Oct 2017 from https://www.foundationmedicine.com/genomic-testing/foundation-one-heme;
10. He, J., et al. 2016. Blood 127:3004-14.
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FoundationOne® Liquid complements the Foundation
Medicine portfolio
FoundationOne®Liquid 1-4 Foundation®One 5-7 FoundationOne®Heme 8-10
Target patient population Solid tumours Solid tumours Haematologic malignancies & Sarcomas
Specimen type Peripheral blood FFPE tissue FFPE tissue Bone marrow aspirate Peripheral blood
Genes assayed 70 324* 406 265 (via RNA)
Genes with complete exon coverage 35 324* 406
All 4 classes of genomic alterations Yes Yes Yes
TMB No Yes Yes
MSI Yes Yes Yes
Method HC-based NGS HC-based NGS HC-based NGS
Turnaround time† < 14 days 14 days or less 14 days
* Only use authorised Specimen Collection and Shipping Boxes and refer to regional team guidance on specimen preparation and logistics. 1. Foundation Medicine.
(2017) Specimen instructions. Accessed Jun 2018 from
https://assets.ctfassets.net/vhribv12lmne/1gXe0jfhP6U60yQC2CwmIQ/66046b354aa6a26a235fd59a24464e9c/FACT_SpecimenInstructionsMA_01-05_HH_1_.pdf; 2.
Foundation Medicine. (2018) FoundationACT Technical Specifications. Accessed Jun 2018 from
https://assets.ctfassets.net/vhribv12lmne/3SPYAcbGdqAeMsOqMyKUog/3b10e8355a717f658c82d7544503df9f/FACT_TechnicalInformation_09_RD.pdf.
Provide 2 tubes of peripheral whole blood using the
Foundation One® Liquid Specimen Collection and
Shipping Box* 1
From 11 to 14 days turnaround from
sample receipt at the Foundation Medicine
laboratories2
Comprehensive report provided2
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• For genes covered by both tissue and liquid assays, a total of 68 reportable genomic alterations were detected in 33 tissue samples:
– 75.0% (51 / 68) were also detected in temporally matched cfDNA, which includes 83.0% (44 / 53) of short variant mutations, 38.5% (5 / 13) of CNAs and 100% (2 / 2) rearrangements
• 75.0% (51 / 68) of genomic alterations detected in cfDNA were also detected in tissue
• Overall, of the 33 cases with a genomic alteration in
tissue, 87.9% (29 / 33) had at least one concordant genomic alteration in cfDNA
cfDNA: cell-free DNA; CNA: copy number amplification; ctDNA: circulating tumour DNA; NSCLC: non-small-cell
lung cancer.
Clark, T.A., et al. (2018) J Mol Diagn
Validation data shows high concordance
Number of samples profiled
FoundationACT (ctDNA) FoundationOne (tissue)
283 23,619
128 12,535
67 12,653
63 2,424
NSCLC
Breast
CRC
Prostate
Frequency
(% FoundationOne samples)
0 20 40 60 80
0
20
40
60
80
Fre
quency
(%
F
oundationA
CT
sam
ple
s)
KRAS
ALK-rearrangement
r = 0.98
TP53
TP53
TP53 TP53
KRAS
EGFR PIK3CA
PIK3CA
BRAF
ESR1 KRAS
ctDNA was in 80% of samples detected ctDNA in 86% in these cases
* F1 CDx bait-set available Ex-US from 01 October 2018; † From date of receipt. FFPE: formalin-fixed, paraffin-embedded; HC: hybrid capture; MSI: microsatellite instability; NGS: next-generation sequencing; TMB: tumour mutational
burden; . 1. Foundation Medicine. (2018) FoundationACT Technical Specifications. Accessed Jun 2018 from
https://assets.ctfassets.net/vhribv12lmne/3SPYAcbGdqAeMsOqMyKUog/3b10e8355a717f658c82d7544503df9f/FACT_TechnicalInformation_09_RD.pdf;
2. Foundation Medicine. (2018) FoundationACT Sample patient report; 3. Foundation Medicine. (2017) FoundationACT Webpage summary. Accessed Oct 2017 from https://www.foundationmedicine.com/genomic-testing/foundation-act; 4.
Foundation Medicine. FoundationOne Liquid Technical Specifications to be published Sept 2018; 5. Foundation Medicine. (2017) FoundationOne Technical Specifications. Accessed Oct 2017 from
https://assets.ctfassets.net/vhribv12lmne/6YRrchSINOeSu48YwuesoY/0c3651c8421fa3647ccede76de9dce61/MKT-0054-02_F1_TechSpecs_digital.pdf; 6. Foundation Medicine. (2017) FoundationOne Webpage summary. Accessed Oct
2017 from https://www.foundationmedicine.com/genomic-testing/foundation-one; 7. Frampton, G.M., et al. 2013. Nat Biotechnol 31:1023-31; 8. Foundation Medicine. (2017) FoundationOneHeme Technical Specifications. Accessed Oct 2017
from https://assets.ctfassets.net/vhribv12lmne/zBxaQC12cScqgsEk8seMO/abf6133874f1e5929403f66d90c3b900/F1H_TechnicalInformation_06_digital.pdf; Foundation Medicine. (2018) FoundationOneCDx Technical Specifications.
Accessed Jun 2018 from https://assets.ctfassets.net/vhribv12lmne/4ZHUEfEiI8iOCk2Q6saGcU/671b313cb6bb85bfe861f83e31c9716d/F1CDx_TechInfo_09-03.pdf;
9. Foundation Medicine. (2017) FoundationOneHeme Webpage summary. Accessed Oct 2017 from https://www.foundationmedicine.com/genomic-testing/foundation-one-heme;
10. He, J., et al. 2016. Blood 127:3004-14.
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FoundationOne® Liquid complements the Foundation
Medicine portfolio
FoundationOne®Liquid 1-4 Foundation®One 5-7 FoundationOne®Heme 8-10
Target patient population Solid tumours Solid tumours Haematologic malignancies & Sarcomas
Specimen type Peripheral blood FFPE tissue FFPE tissue Bone marrow aspirate Peripheral blood
Genes assayed 70 324* 406 265 (via RNA)
Genes with complete exon coverage 35 324* 406
All 4 classes of genomic alterations Yes Yes Yes
TMB No Yes Yes
MSI Yes Yes Yes
Method HC-based NGS HC-based NGS HC-based NGS
Turnaround time† < 14 days 14 days or less 14 days
Brand name FoundationACT® FoundationOne® Liquid FoundationOne® Liquid
Version 1.0 2.0 3.0
Commercial launch date* May 2016 September 2018 2020**
Genes 62 70 > 70
Microsatellite instability - Yes Yes
Tumour mutational burden - - Yes
Companion diagnostic - - Yes
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First-generation liquid biopsy test, FoundationACT, available until August 2018
Second-generation liquid biopsy test, FoundationOne Liquid, available from September 2018
* Timelines for studies may vary – refer to study protocol for more details ** Opportunity to launch earlier depending on filing timelines
Primary objective
BEP: biomarker evaluable population; bTMB: blood tumour mutational burden; cfDNA: cell-free DNA; CI: confidence interval;
HR: hazard ratio; NSCLC: non-small cell lung cancer; OS: overall survival; PD-L1: programmed death-ligand 1; PFS:
progression-free survival; SNV: single nucleotide variant; TMB: tumour mutational burden. Gandara., D., et al. (2017) Ann
Oncol 28 (suppl. 5): v460-96. 27
Retrospective clinical validation of the FMI bTMB
assay
Clinical efficacy of atezolizumab vs docetaxel in bTMB
subgroups
0 0,2 0,4 0,6 0,8 1
BEP+
≥ 10
≥ 16
≥ 20
OAK POPLAR
bTMB subgroup P
FS
HR
95% CI of *(0.68, 1.20) and **(0.73, 1.04)
* **
To test and validate a novel blood-based assay to
measure bTMB and to evaluate its association with
atezolizumab efficacy in patients with NSCLC
Methods
bTMB assay interrogates single nucleotide variants
(SNVs) in 394 genes from cfDNA in plasma and reports
score based on number of high-confidence SNVs
identified
Biomarker evaluable population (BEP) grouped by
bTMB cut points based on minimum number of SNVs:
• POPLAR – 211 patients
• OAK – 583 patients
Results
• POPLAR: Improved progression-free (PFS) and overall survival (OS)
hazard ratios with atezolizumab observed in the TMB ≥ 16 subgroup
• OAK: PFS benefit with atezolizumab vs docetaxel observed in the
TMB ≥ 10 subgroup
• TMB in blood did not correlate with PD-L1 expression
Two studies show that bTMB is associated with enriched clinical benefit with atezolizumab
Rizvi NA et al. Science. 2015;348:124-8.
Assessing TMB in liquid biopsies
Source of bias. Clonal haematopoiesis
• CHIP is defined by the presence of somatic mutation in blood or BM but without other diagnostic criteria for a haematological malignancy.
• More frequent in aged patients, patients with solid tumours • More likely to be detected with deeper sequencing approaches. • May account for false positive ctDNA sequencing results.
KR
AS
G1
2D
Hu Y et al. False-Positive Plasma Genotyping Due to Clonal Hematopoiesis.Clin Cancer Res. 2018 Mar 22.
Charles Swanton et al. Journal of Clinical Oncology 36, no.
15_suppl (May 20 2018) 12003-12003.
CHIP prevalence by age and type of Tumor
Ptashkin RN et al JAMA Oncol. 2018 Jun
5.
CHIP is Prevalent in some cancer related genes
M et al. Nat Med 2014;20:1472-
1478.
Ptashkin RN et al JAMA Oncol. 2018 Jun
5.
• Biomarker testing through ctDNA sequencing by NGS is possible.
• However, there are some concerns about false due to CHIP.
• The impact of CHIP in TMB assessment using LB has not been thoroughly evaluated
• New pipelines designed to effectively filter out germline mutations as well as mutations derived from clonal hemaotopoiesis are needed
Conclusions