11. FoundationOne CDx
FoundationOne CDx™ (F1CDx™) is a next
generation sequencing based in vitro diagnostic
device for detection of substitutions, insertion
and deletion alterations (indels), and copy
number alterations (CNAs) in 324 genes and
select gene rearrangements, as well as genomic
signatures including microsatellite instability
(MSI) and tumor mutational burden (TMB) using
DNA isolated from formalin-fixed paraffin
embedded (FFPE) tumor tissue specimens.
https://assets.ctfassets.net/vhribv12lmne/6Rt6csmCPuaguuqmgi2iY8/e3a9b0456ed71a55d2e4480374695d95/FoundationOne_CDx.pdf
12. FoundationOne CDx
FoundationOne CDx™ (F1CDx™) is a next
generation sequencing based in vitro diagnostic
device for detection of substitutions, insertion
and deletion alterations (indels), and copy
number alterations (CNAs) in 324 genes and
select gene rearrangements, as well as genomic
signatures including microsatellite instability
(MSI) and tumor mutational burden (TMB) using
DNA isolated from formalin-fixed paraffin
embedded (FFPE) tumor tissue specimens.
https://assets.ctfassets.net/vhribv12lmne/6Rt6csmCPuaguuqmgi2iY8/e3a9b0456ed71a55d2e4480374695d95/FoundationOne_CDx.pdf
13. Sample
Adequate sample Clinical CGP can be
successfully performed for solid tumour samples
(generally formalin fixed, paraffin embedded
material), bone marrow, and blood, although
many other tissue samples such as FNAs can
be analysed. In general, a sample
approximately 15 mm2 with a minimal depth of
40 mm is adequate for CGP.
Ross JS. Pathology, 2016
14. Sample
Adequate sample Clinical CGP can be
successfully performed for solid tumour samples
(generally formalin fixed, paraffin embedded
material), bone marrow, and blood, although
many other tissue samples such as FNAs can
be analysed. In general, a sample
approximately 15 mm2 with a minimal
depth of 40 mm is adequate for CGP.
Ross JS. Pathology, 2016
15. Sample
For assays that measure gene copy number,
tumour nuclei should account for at least 20% of
the total nuclei present. When tumour nuclei are
less than 20%, the risk of missing a copy
number gain or homozygous loss increases
dramatically
Ross JS. Pathology, 2016
16. Sample
Contamination with non-cancerous tissue or
high levels of necrosis can affect detection
sensitivity, although macro-dissection can often
be used to enrich the sequenced sample for
tumour nuclei.
Ross JS. Pathology, 2016
17. Detecting alteration
Point mutations that selectively alter enzyme
activity or induce early protein termination,
genomic rearrangements that disrupt genes or
create novel oncogenic molecules, copy number
gains or losses that dramatically change
transcript levels, and small insertions and
deletions (indels) with various effects depending
on the gene and alteration location
Ross JS. Pathology, 2016
18. Bio-informatics
Although managing a clinical CGP assay
requires technical expertise across many
domains, the computational bioinformatics
expertise required for high-quality analysis and
interpretation is key
Ross JS. Pathology, 2016
19. Actionable genomic alterations
The term ‘actionable’ describes a sequencing
result that can direct a specific action by a
treating oncologist
Ross JS. Pathology, 2016
37. Oncomine
Based on robust Ion AmpliSeq™
technology, the assay requires only
10 ng of DNA or RNA per pool,
enabling analysis of even small and
challenging FFPE samples
53. Oligodendrogliomas
1p/19q co-deletion IDH1/2 mutation Median survival
+ + 8.2 years
- + 6.3 years
+ - 1.5 years
L, Knoff DS, Schultz N, et al. Clinical multiplexed exome sequencing distinguishes adult oligodendroglial neoplasms from astrocytic and mixed lineage
IDH1/2 mutations are CRITICAL to prognosis in Oligodendrogliomas.
Comprehensive Genomic Profiling is superior to IHC by 20%.
Ramiksoon LA. Curr Treat Options Oncol, 2018
54. Glioblastoma
Chromosome 7
amplifiaction
CDKN2A/B homozygous
deletion
EGFR amplification
PTEN-loss
TP53 mutation PDGFRA amplification Hemizygous NF1 loss
Common, but not actionable, mutations in GBM
BRAF mutation
Uncommon, but actionable, mutations in GBM
Dabrafenib +
Trametinib
Ramiksoon LA. Curr Treat Options Oncol, 2018
68. Ali SM. The Oncologist, 2017
NSCLC
Comprehensive genomic profiling detected
canonical ALK rearrangements and ALK
rearrangements with noncanonical fusion
partners in a subset of patients with NSCLC with
previously negative ALK FISH results. In this
series, such patients had durable responses to
ALK inhibitors, comparable to historical
response rates for ALK FISH-positive cases.
The Oncologist 2016;21:762–770
77. CRC
Rankin A. The Oncologist, 2017
Missed detection of KRAS non-G12/13
mutations by prior focused molecular testing
78. CRC
Rankin A. The Oncologist, 2017
1644 RAS/RAF wild type
by CGP
31% Genomic alteration associated with
resistance of anti EGFR therapy
PI3KCA PTEN EGFR Her2
79. CRC
Rankin A. The Oncologist, 2017
Quantitation of CRC cases with potential driver alterations and co-occurrence of KRAS
mutations. Breakdown of specific subtypes of RTK, MEK1, PIK3CA, and PTEN alteration
classes and overlap with RAS/RAF alterations.
83. Melanoma
Boussemart L. The Oncologist, 2019
385 BRAF mutations in melanoma detected
with CGP
Records of prior BRAF testing in 79 (21%)
11/57 (19%) V600+ were BRAF
negative with prior testing
16/20 (80%) non-V600 mutated
BRAF were negative with prior
testing
And 2/2 activating BRAF fusions
84. Ali SM. The Oncologist, 2017
Melanoma
CGP identifies diverse activating BRAF
alterations in a significant fraction of cases with
prior negative testing. Given the proven clinical
benefit of BRAF/ MEK inhibitors in BRAF-
mutated melanoma, CGP should be considered
for patients with metastatic melanoma,
particularly if other testing is negative.
The Oncologist 2019;24:1–7
92. Breast
Ross JS. Pathology, 2016
Prognostic assessment ie TP53 mutation
Predicting hormonal
therapy resistance
AKT1, AKT2, BCAR1, BCAR3, EGFR,
ERBB2, GRB7, SRC, TLE3 and TRERF1
Predicting resistance to
targeted therapy
ESR1 and ERBB2 mutations.
93. Breast
Ross JS. Pathology, 2016
Base substitution in ESR1 Tamoxifen resistance
ESR1 fusions and
rearrangements
AI resistance
Acquired ERBB2 mutation in
CDH1 mutated lobular ABC
100% ORR with Neratinib + Fulvestrant
in ERBB2/CDH1 co-mutated lobular BC
31% after prolonged anti HR therapy
94. Breast
Ross JS. Pathology, 2016
ERBB2 amplification Correlates with FISH
ERBB2 activating
mutations
Potential targets to anti-Her2 therapy
Acquired ERBB2 mutation in
Her2 amplified BC
Potential acquired resistance
mechanism for patients with HER2+ by
IHC
2.4%
Acquired PIK3CA/MET/PTEN
mutations in Her2 amplified
BC
Potential acquired resistance
mechanism for patients with HER2+ by
IHC
95. Breast
Ross JS. Pathology, 2016
BRCA1/2 mutations
Sensitivity to Olaparib or
Rucaparib
Mutations in other HR-
associated genes
May be targeted by PARP-inhibition
15%
TMB (>20 per megabase) May benefit from Anti-PD(L)1 therapy
5%
Rare, potentially actionable
mutations
EGFR1 amplification, SRC, ALK/EML4,
Ret-fusions
96. Breast
Ross JS. Pathology, 2016
Basal genomics Acquired mutations Implications
Lobular
CDH1/Pi3k pathway
mutations
Acquired ERRB2
(30-40%)
May benefit from the
addition anti Her2
therapy
Inflammatory breast
cancer
ERBB, MTOR, FGFR and
DNA repair pathways
Mucinous
FGFR1 and ERBB2
alterations
Secretory breast
cancer
ETV6-NTRK3 fusion
Entrectinib/Larotrecti
nib
Adenoid Cystic
Breast Cancer
MYB-NFIB
Similar to salivary
gland carcinomas
Triple-negative and
metaplastic BC
ERBB2 mutations, RTK pathway
mutations, and DNA repair
BRCAness pathways.
Different targets
103. Tumor agnostic
BRCA1/2 mutations
Sensitivity to Olaparib or
Rucaparib
Mutations in other HR-
associated genes
May be targeted by PARP-inhibition
MSI / POLE May benefit from Anti-PD(L)1 therapy
NTRK Larotrectinib/Entrectinib
105. SHIVA
AR over expression Abiraterone
MAPK (PTEN/AKT/RICTOR,
etc)
Everolimus
Her2 amplification Trastuzumab + Lapatinib
PDGFR Sorafenib
ER over expression Tamoxifen
Le Tourneau, Ann Oncol, 2016
106. SHIVA
Le Tourneau, Ann Oncol, 2016
MTA: Molecular
targeted agent
TPC: Treatment at
physicians choice
110. Le Tourneau, Ann Oncol, 2016
The cross-over analysis of the
SHIVA trial identified 37% of patients
who crossed over from TPC to MTA
with a PFSMTA/PFSTPC ratio
exceeding 1.3.
SHIVA
119. Payer issues
Insurance wants you out for two reasons:
1. You requested the test (US 4000-5000)
2. They fail to see the point in using an expensive drug, in an unproven setting…
121. When should you use it?
Consider using CGP in PS0/1 patients, in which ALL
established treatment options have been tried
With a “reasonable” expectation of getting a reliable
CGP test (not home-made)
Good (ie, not only PBS), insurance
International medical coverage
With a “reasonable” expectation of getting MTA
treatment, should it be advised
Today
Also, in PS0/1 patients, with non-curable RARE
tumors with no clear standard of care
122.
123. In the NEAR
future, we will
use CGPs for the
INITIAL
treatment in the
vast majority of
tumors.