molecular diagnosis of developmental tumors: opportunities ......department of oncology....
TRANSCRIPT
Molecular diagnosis of
developmental tumors:
Opportunities and challenges of NGS
Dra. Carmen de Torres
Department of Oncology. Developmental Tumor Biology Laboratory
Hospital Sant Joan de Déu, Barcelona
2
Adult cancer versus
developmental tumors
Marshall GM, et al. Nat Rev Cancer 2014
3
NGS: Somatic alterations in
developmental tumors
Lawrence MS, et al. Nature 2013
4
Pediatric and adult
high-grade gliomas
Jones and Baker, Nature Rev Cancer 2014
5
Diagnosis-Research
Diagnosis
• Somatic alterations
• Diagnosis
• Prognosis
• Minimal residual disease
• Therapeutic targets
• Germline predisposition to cancer
Research
- Neuroblastoma
- Sarcomas
- CNS tumors
- Retinoblastoma
- Leukemia
6
Somatic alterations: Diagnosis
SMALL ROUND BLUE
CELL TUMORS
➢ EWING’S SARCOMA/PNET
➢ RHABDOMYOSARCOMA, other
sarcomas
➢ NEUROBLASTOMA
➢ WILMS
➢ LEUKEMIA, LYMPHOMA
7
Somatic alterations: Diagnosis
• Translocation-associated sarcomas
- Chimeric transcription factors
- Chimeric tyrosine kinases
• Karyotypically complex sarcomas
Lineage
Prognosis
Driver alterations
Taylor BS, et al. Nat Rev Cancer 2011
8
Somatic alterations: Diagnosis
KIAA1549-BRAF
7q34
Forshew T, et al. J Pathol 2009
Dougherty MJ, et al. Neuro Oncol 2010
9
Somatic alterations: Diagnosis
Butrynski JE, et al. N Engl J Med 2010
10
Translocations: Methods
11
Translocations: Methods
Interphase fluorescent in situ hybridization (i-FISH)
?
12
Translocations: Methods
Pierron G, et al. Nat Genet 2012
13
Translocations: Methods
1: A673 (EWSR1-FLI1 type 1)
2: SK-ES-1 (EWSR1-FLI1 type 2)
3: A4573 (EWSR1-FLI1 type 3)
4: Biopsy
5: NTC
Messahel B, et al. Lancet Oncol 2005
RT-PCR and sequencing
TBP
EWSR1-FLI1
14
Translocations: Methods
RNA-seq
15
Somatic alterations: Prognosis
Huang M, et al. Cold Spring Harb
Perspect Med 2013
Brodeur GM. Nat Rev Cancer 2003
16
Somatic alterations: Prognosis
Northcott PA, et al. Nature 2012
Robinson G, et al. Nature 2012
17
Somatic alterations: Prognosis
18
- Precise staging
- Local-regional tumors with MRD
- Involvement of CNS
- Response to treatment
- Early detection of relapses
Minimal residual disease: clinical relevance
19
Minimal residual disease: methods
20
MRD: Neuroblastoma and retinoblastoma
y = -1.1773x + 5.9808R² = 0.9989
0
1
2
3
4
5
6
7
0 1 2 3 4 5
dC
T
Log Y79 dilution
CRX mRNA
y = 3.8747x - 3.0715R² = 0.9994
-4
-2
0
2
4
6
8
10
12
14
0 1 2 3 4 5
dC
T
Log SK-N-JD dilution
PHOX2B mRNA
21
Liquid biopsy
• BRAF V600E cfDNA
• CRX mRNA CSF
0
100
200
300
400
500
600
0 2 4 6 8N
um
be
r o
f co
pie
sWeeks on treatment
MRD: Langerhans cell
histiocytosis
22
MRD: ddPCR vs RT-qPCR
• Hayashi M, et al. Highly personalized detection of minimal Ewing sarcoma
disease burden from plasma tumor DNA. Cancer. 2016;122:3015-23 – tumor-
specific EWS-ETS breakpoints; animal models
• Cavalli M, et al. Comparative analysis between RQ-PCR and digital droplet
PCR of BCL2/IGH gene rearrangement in the peripheral blood and bone
marrow of early stage follicular lymphoma. Br J Haematol 2017;177(4):588-
596
23
MRD: NGS vs RT-qPCR
Ladetto M, et al. Next-generation sequencing and real-time
quantitative PCR for minimal residual disease detection in B-cell
disorders. Leukemia 2014;28:1299-307
- compared immunoglobulin heavy-chain-gene-based minimal
residual disease (MRD) detection by real-time quantitative PCR
(RQ-PCR) and next-generation sequencing (NGS)
- NGS showed at least the same level of sensitivity as
allele-specific oligonucleotides-PCR, without the need for patient-
specific reagents
24
Precision medicine
25
Somatic alterations: Therapeutic targets
4 weeks on dabrafenib
Courtesy O. Cruz
Pleomorphic xanthoastrocytoma
BRAF V600E
26
NGS: Somatic alterationsin developmental tumors
Nat Genet. 2014;46:457-61
Proc Natl Acad Sci U S
A. 2014;111:E5564-73
Cancer Discov. 2014;4:1326-41
27
Diffuse intrinsic pontinegliomas (DIPG)
Nat Genet. 2014;46(5):457-61
- Not curable
- First human
disease driven by a
histone mutation
- ACVR1
28
DIPG
Nat Genet. 2014;46(5):457-61
Two molecular and
clinical subgroups
• H3.3 (K27M or
G34V/R)
• H3.1 (K27M) and
ACVR1
H3.3 and H3.1 - Nat Genet. 2012;44(3):251-3
29
Complementary genomic approaches
highlight the PI3K/Mtor pathway as
common vulnerability in osteosarcoma
Proc Natl Acad Sci U S A. 2014 ;111:E5564-73.
30
NGS: Germline alterations in
developmental tumors
Bardai A, et al. N Engl J Med 2015
31
NGS: Diagnosis, prognosis and
therapeutic targets
Worst BC, et al. Eur J Cancer 2016
Next-generation personalised medicine for high-risk paediatric cancer
patients - The INFORM pilot study
32
33
First molecular tumor
board: selection of
case-specific best
options
Second molecular
tumor board: final
decision
34
Robinson et al. J Clin Oncol 2015
35
FGFR1
p.N577K - GOF
Missense
Pkinase_Tyr
Int J Mol Med. 2016 Jul;38(1):3-15
dcc.icgc.org
36
Nat Commun. 2015; 6: 7557
Germline and somatic / variants and CNVs
• Diagnosis, prognosis
• Therapeutic targets
• Germline predisposition
Pediatric solid tumor
panels
37
Variants and CNAs
Somatic and germline
Diagnosis, prognosis,
therapyInterpretation
Precisionmedicine for
pediatric solidtumors
38
Data
Interpretation
39
• Patient
• Sample
• Date of biopsy – clonal evolution
• Quality
• Liquid biopsy - metastasis - primary tumor
• Sequencing
• Panels / exome / genome
• Variants / Copy number alterations
• Quality
• Variant calling
NGS for therapy selection:
Challenges
40
NGS for therapy selection:
Challenges
• Interpretation of variants: LOF / GOF
• Treatment selection:
• Level of evidence
• Context – tumor dependent
• Avatar
• Multidisciplinary team
• Report: Context!
• TAT
41
Gen Variante Tumor Fármaco Evidencia Ensayos clínicos
Evidencia en el
mismo tipo de
tumor
-
Evidencia en
otros tumoresCCND2 p.W149* Pulmón Palbociclib Ensayo clínico I/II NCT02154490
PIK3R1 p.Y580C Endometrio, otros Inhibidores PI3K Preclínica, caso
42
Acknowledgements
HSJD lab team
HSJD clinical team
IMEGEN
N López-Bigas
CNAG
J Biegel
C Jones
Broad Institute
MSKCC
B Royer-Pokora
43
Muchas gracias
© 2015 IMEGEN – Información confidencial. Todos los derechos reservados.
Instituto de Medicina Genómica SL
Agustín Escardino 9,
Parc Científic de la Universitat de València
46980 Paterna (Valencia, España)
+34 963 212 340
Imegen.es
© 2015 IMEGEN – Información confidencial. Todos los derechos reservados.