molecular testing in tumor samples - AIOM€¦ · Form a presentation by Dr Anne-Claire...
Transcript of molecular testing in tumor samples - AIOM€¦ · Form a presentation by Dr Anne-Claire...
Implications of
BRCA1/2
molecular testing
in tumor samples
Dr Etienne ROULEAU
SITUATION
27/05/2019TITRE DU DIAPORAMA Général
BRCA1/2 up-to-2016
Genes BRCA1 et BRCA2
Breast and ovarian cancer predisposition
Few therapeutic applications…
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R Cancer
At 70
year-old
BRCA1 BRCA2
Breast Ovarian Breast
Controlat.
Breast Ovarian Breast
Controlat.
Mavaddat
& al. 2013
60%
(44-75)
59%
(43-76)
83%
(69-94)
55%
(41-70)
16.5%
(7.5-34)
62%
(44-79.5)
Form a presentation by Dr Anne-Claire HARDY-BESSARD
Rapport DPN, IMG, DPI et formes héréditaires de cancers
K breast, 31
year-old
K
breast,
44 year-
old
K prostate,
59 year-old
46 year-old 45 year-old 58 year-old
50 year-old89 year-old39 year-old89 year-old
63 year-old55 year-old
30 year-old 34 year-old 24 year-old
2 year-old
4 year-old
K ovary, 43
year-old
23
Leukemia
K
breast,
40
year-
old
BRCA1/2 testing in France
Germline testing in France – 16 labs
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2014 2015 2016
Total number of consultations dedicated to breast-ovarian syndrome
39 133 45 430 51 971
Among them, many consultations dedicated to isolated ovarian cancers
1 642 2 445 3 374
Regional average of the number of consultations per 100,000 inhabitants 55 63 72
Index case that has been genetically tested for breast-ovarian syndrome 11 688 14 700 17 821
Index cases identified as carriers of a mutation related to breast-ovarian syndrome 1 207 1 610 1 762
Proportion of carriers 10% 11% 10%
Screening timeline in weeks 33 34 24
Rapport d’activité de l’oncogénétique en France 2017, INCa.
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O’Connor, Molecular Cell, 2015
Tumour cells harbouring deleterious BRCA1/2mutations are highly sensitive to PARP inhibition1
Efficacy of PARP inhibitors is clinically proven in ovarian cancer2-4, breast5 and prostate cancer6…
Inactivation process1
> Germline/somatic mutation
> Loss of wild-type allele
> (methylation of BRCA1)
Contrary to germline testing, tumour testing has additional considerations
Somatic testing in France > 25 labs 1. Ashworth A. J Clin Oncol 2008;26:3785–3790
2. Tutt A et al. Lancet 2010;376:235–244
3. Kaufman B et al. J Clin Oncol 2015;33: 244–250
4. Ledermann J et al. Lancet Oncol 2014;15: 852–861
5. Tutt, A et al J Clin Oncol 2009
6.Mateo, J., et al NEJM 2015
6.
To a therapeutic impact
Acceleration in BRCA testing
December 2014 – january 2018 Olaparib AstraZenecaTreatment / maintenance of mutated BRCA ovarian cancer
Treatment of mutated BRCA breast cancer
December 2016 Rucaparib Clovis Treatment mutated BRCA ovarian cancer
March 2017 Niraparib Tesaro Maintenance in ovarian mutated BRCA
October 2018 Talazoparib Pfizer Treatment of mutated BRCA breast cancer
Committee for Medicinal Products for Human Use (CHMP)
Summary of opinion post authorisationMEA
FDA
FDA approval - Ashworth 2019 AACR
New indications
Extension of indications in 2018 for French labs
At least 2 - Pancreas / Breast / Prostate 11/22
Breast 5/22
No extension / on demand 5/22
Post mortem 1/22
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TEST CHALLENGING
Comparaison between blood and tumor
Blood – 99,2% concordant (Local / Central)
Tumor– 82,9% concordant (Local / Central)
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392 Case included
2 WT 1 UV 388 MT
392 cases includes
23 no sample 27 failure
(7%)
341
324 MT
12WT
5 UV
Supplement to: Moore K, Colombo N, Scambia G, et al. Maintenance
olaparib in patients with newly diagnosed advanced ovarian cancer.
N Engl J Med.
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cbioportal / 2016
20kb
Challenges to tumour testing
Heterogeneity of the material
> Limit of detection1,2
> Tumour samples are a mix of tumoral and normal cells3–5
> Tumour heterogeneity3–5
DNA degradation with fixation (FFPE – process from
operating theatre)6
> Adaptation of methods for detection
Low quantity of DNA extracted from sample6
> Choose methods with low DNA quantity
> Development of NGS
1. Ellison G et al. J Clin Pathol 2013;66:79–89
2. Lee HJ et al. Korean J Pathol 2013;47:52–60
3. de Bruin EC et al. Science 2014;346:2516
4. Gerlinger M et al. N Engl J Med 2012;366:883–892
5. Piotrowska Z et al. Cancer Discov 2015;5:713–722
6. Sah S et al. Genome Med 2013;5:77
DNA quality and quantity
Figure : Tapestation profiles of 3 DNA with the average size of
DNA A) usually profile 2kb, B) high quality C) Low quality
A)
B) C)
Quality impact
Size of the operative piece
Age of the block
Chemotherapy treatment
Various factors on the pre-analytical block
Co
nce
ntr
ation
ng
/µL
Cases n= 145
10% 4
20% 5
30% 4
2mm² 1
5mm² 1
Neoplastic cells
Surface
Genetiss 2018 – minimum requirement
survey of BRCA1/2 practices
Gustave Roussy – experience in DNA concentration
No requirement (9/22)
Germline testing (3/22)
Minimum cells (13/22)
Minimum surface
Minimum age
Performing the testing
BRCA1/2 = NGS screening
QUALITY STANDARD> Full coding sequence coverage
• 11/24 300X to more
• 12/24 give the result with the coverage if below to 300X
> Stability of the enrichment
> Sensitivity• 12/24 up to 5% - 11/24 up to 10%
> Ability to detect rearrangement or allelic drop-out
BIOINFORMATIC SOLUTION> Limit of detection: 10%
> Alterations• Insertion/deletion (>20 pb)
• Large rearrangements
Detection of large rearrangement
No 16
Bioinformatic analysis 6
Germline testing 1
MLPA 1
Genetiss 2018 – time to report
Less than 15 days 3
Less than 21 days 5
Less than 1 month 5
1 to 2 months 10
Genetiss 2018 – survey of BRCA1/2 practices
Performing the testing
Mainly amplicon and dedicated to BRCA1/2
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2017 2018
Ion Proton (Life Technologies) 0 1
Ion S5 system (Life Technologies) 4 4
MiniSeq (Illumina) 1 1
MiSeq (Illumina) 14 14
NextSeq (Illumina) 1 2
PGM IonTorrent (Life Technologies) 2 2
2017 2018
Multiplicom 10 13
Agilent Sureselect 2 2
Qiagen 2 1
Thermofisher 5 5
Fluidigm 0 1
Sophia Genetics 1 2
Genetiss 2018 – survey of BRCA1/2 practices
LARGE REARRANGEMENTS
Large rearrangements
Lack of Enrichment - Large Rearrangements
> Coverage failure
> Enrichment - medium size rearrangements
Elimination during bioinformatic alignment
Imperfect compensation:
> Bioinformatic algorithm
> MLPA27/05/2019 TITRE DU DIAPORAMA Général
BRCA1/2
BRCA1/2
BRCA1/2
RGT
SNP
WT
Detection of large rearrangements
A) Deletion of exon 2 BRCA1 with MLPA, B) Deletion of
exon 2 BRCA1 from NGS normalization, C)
Duplication of exons13-14-15 BRCA1 from NGS
normalization
Technique XT Sureselect Agilent® - panel de 12 gènes
A)
B)
C)
QUANTITATIVE VARIATIONS
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Loss of heterozygosity
Main mechanism of inactivation : LOH + mutation
100% BRCA1 and 76% BRCA21
81% BRCA1 and 72% BRCA22
Secondary mutation <1%; 1/1363
Quantitative variation1
> Heterogeneity of alterations
> LOH of the mutated allele will enrich in mutated allele
> Disease progression can increase the allelic frequency of tumour
mutations, favouring detection of the mutated allele
LOH, loss of heterozygosity
1. Kanchi KL et al. Nat Commun 2014;5:3156;
2. Cancer Genome Atlas Research Network. Nature 2011;474:609–615; 3. TGCA ovarian cancer -
bioportal
B
A
50% A
50% B100% B
n=21
Note any obvious LOH on the allelic frequency of the mutation. 5
It is not necessary to report the allele frequency on the reports 9
Others 7
Genetiss 2018 – survey of BRCA1/2 practices
Resistance mechanisms
Risk of reversion to ‘wild-type’ BRCA1,2
> Potentially following platinum-based chemotherapy or PARP inhibitor treatment
> Loss of the mutated allele
> New mutations and/or loss of mutated allele
> Following resistance to treatment original germline mutation may no longer be detectable in tumour samples
23 - -
1. Ashworth A. J Clin Oncol 2008;26:3785–3790
2. Sakai W et al. Nature 2008;451:1116–1120
Resistance by
synthetic lethality
TAA
No protein
STOP codon
TAA
Mutation inframeGermline mutation with
premature STOP codon Truncated protein
Functionally active
Resistances tracking
Quigley D, et al.
Analysis of Circulating Cell-Free DNA Identifies Multiclonal Heterogeneity of BRCA2 Reversion Mutations
Associated with Resistance to PARP Inhibitors. Cancer Discov. 2017 Sep;7(9):999-1005.
BRCA1/2 EQA
Gen&tiss experience
Some data presented here are preliminary results – thanks not to diffuse them
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Numéro
d'échantillonCellularité % BRCA1 BRCA2 EEQ Divers (hors EEQ)
18-O-16 90%
c.2601del
p.(Gln867fs) VAF: 75%
Délétion des exons 14 à 24*
WT GENOTYPETP53: c.358A>G p.(Lys120Glu)
VAF:75%
18-O-17 80% WT/NC***
c.8487+1G>A
p.(?)
VAF: 90%
/ NC***
GENOTYPETP53.c.1024del p.(Arg342Glyfs*3)
VAF:75%
18-O-18 90% WT WT GENOTYPE -
18-O-19 90% WT WT GENOTYPE
TP53: c.713G>C; p.(Cys238Ser)
RAD51C : c.577C>T; p.(Arg193*)
VAF:95%
18-O-20 90% WT WT GENOTYPE
TP53 c.713G>A p.(Cys238Tyr)
RAD51D:c.803G>A (p.(Trp268*)
VAF:95%
Echantillon
éducatif "OVAIRE
2018"
NA Délétion des exons 1 à 14 WT EDUCATIFTP53: c.818G>A;p.(Arg273His)
VAF:75%
Genotyping
2017 : 3 false negative – 2,7%
> 110 analysis
> 22 participants
2018 : 3 false negative / 4 false positive – 5,6%
> 125 analysis
> 25 participants
Other genes 2018
> 2018 – TP53 – 5 participants – no error
> RAD51C – 3 participants detected
> RAD51D – 1 participant detected
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Educative sample
2017
> BRCA1: 11/20 (55.0%) participants miss a class III variant
c.1303G>T; p.(Asp435Tyr) VAF 7%
> BRCA2: 10/20 (50.0%) participants miss a class V variant
c.8021dup; p.(Ile2675Aspfs*6) VAF 10%
2018
> Large rearrangement in BRCA1 : 5 / 21 (educational)
> Large rearrangement in BRCA1 : 2 / 25 (case 1)
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VALIDATION AND REPORTING
THE RESULTS
Variants identified in BRCA1/2
Inactivating mutations – more than 75% are STOP
mutations
UMD BRCA1/2 database 2013 – French population – germline mutations
N=683 variants in BRCA1; N=624 deleterious variants in BRCA2
7% splicing
2% RGT
89% STOP
3% missense
8% splicing
11% RGT
77% STOP
Variants interpretation
Many databases (clinvar to national)
Currently, the assessment of variants
is done only for high-risk families and
only for this level of risk
Process of variant assessment
> High-risk family and co-segregation
> Histological data
> Functional data (RNA, protein)
> Co-occurrence (no bi-allelic BRCA1, rare bi-
allelic BRCA2)
Classe 1
= NEUTRE
= POLYMORPHISM
Classe 5
= DELETERE
Questions on the report
Tumor BRCA1/2 mutated / no germline reported
- 10/24 proposal to a new germline test to check
- 14/24 proposal to oncogenetic consultancy
Tumor BRCA1/2 non mutated / no germline testing
- 17/24 proposal to an oncogenetic consultancy
- 12/24 proposal to a germline testing for large
rearrangement
Variants
Any variant (UV-3) must be reported on the report - 20/23
A variant can be rendered with a therapeutic application, but without
application for the family (class 4) - 13/23
Oncogenetic consultation systematically for any variant (3, 4, 5) - 17/23
Variant interpretation
Estimation of the impact of a variant: 3 dimensions
Absence of
cancer predisposition
Presence of
cancer predisposition
Absence of a
therapeutic effectPresence of a
therapeutic effect
SENSITIVITY
RESISTANCE
Interpretation of variants
Gen&tiss 2017 – Interpretation 10 variants in the BRCA1/2 genes assessment from 19 labs.
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BRCA1 BRCA1 BRCA1 BRCA1 BRCA1 BRCA2 BRCA2 BRCA2 BRCA2 BRCA2
c.5408G>C c. 5545G>T c.4485-1G>T c. 68_69delExon 20
duplicationc.10137T>A c.8725A>T c.9609C>G c.8167G>C Exon 3 deletion
p.(Gly1803Ala) p.(Glu1849*) splicing p.(Glu23Valfs*17) LRG p.(Tyr3379*) p.(Lys2909*) p.(Tyr3203*) p.(Asp2723His) LRG
Class PARP-Inhibitor Familial counselling V V V V V I V V V V
V-Causal Yes Yes 20 11 17 24 9 1 15 21 25 22
IV -Likely causal Yes No 1 2 0 0 3 0 2 1 0 1
IV -Likely causal Yes Yes 2 5 8 1 5 0 6 2 0 2
IV -Likely causal No No 0 2 0 0 0 0 0 0 0 0
III -Unclassified variant No No 2 3 0 0 8 10 2 1 0 0
I- Polymorphism/Neutral No No 0 2 0 0 0 14 0 0 0 0
Score 1,72 1,16 1,68 1,96 1,04 1,56 1,52 1,8 2 1,88
BRCA1 BRCA1 BRCA1 BRCA1 BRCA1 BRCA2 BRCA2 BRCA2 BRCA2 BRCA2
c.5408G>C c.562G>T c.4485-13
_4485-1delc.5221_5238del c.5117G>A c.10137T>A c.6842_6937del c.9609C>G c.8167G>C Exon 3 deletion
p.Gly1803Ala p.Glu188* splicing p.Val1741_His1746del p.Gly1706Glu p.Tyr3379* p.Glu2282_Gly2313del p.Tyr3203* p.Asp2723His LRG
Class PARP-Inhibitor Familial counselling V V IV III V I III V V V
V-Causal YES YES 16 15 3 1 4 3 3 18 18 14
IV -Likely causal YES YES 0 1 8 3 9 0 0 1 1 2
IV -Likely causal YES NO 1 3 4 2 6 0 1 0 0 1
IV -Likely causal NO NO 0 0 3 3 0 1 1 0 0 0
III -Unclassified variant NO NO 1 0 1 10 0 7 14 0 0 2
I- Polymorphism/Neutral NO NO 1 0 0 0 0 8 0 0 0 0
Score 1,74 1,79 1,79 1,21 1,21 1,21 1,47 1,95 1,95 1,63
Gen&tiss 2018 – Interpretation 10 variants in the BRCA1/2 genes assessment from 25 labs.
Interpretation of variants
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Gen&tiss – comparison between 2017 and 2018
BRCA1 BRCA2 BRCA2 BRCA2 BRCA2
c.5408G>C c.10137T>A c.9609C>G c.8167G>C Exon 3 deletion
p.(Gly1803Ala) p.(Tyr3379*) p.(Tyr3203*) p.(Asp2723His) LRG
2017 1,74 1,21 1,95 1,95 1,63
2018 1,72 1,56 1,80 2,00 1,88
N %
Better 9 50%
Worse 5 28%
Same 3 17%
Twice full score 1 6%
Only 1 participation 8
EXTENSION TO OTHER GENES
What is the best HRD panel !
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Présentation de Myriad Genetics
Beyond BRCA1/2
Panel HRD
Roy R, Chun J, Powell SN. BRCA1 and BRCA2: different roles in a common pathway of
genome protection. Nat Rev Cancer. 2011 Dec 23;12(1):68-78.
Che R, Zhang J, Nepal M, Han B, Fei P. Multifaceted Fanconi Anemia Signaling.Trends
Genet. 2018 Mar;34(3):171-183.
PARP
BRCA1BRCA2
Different panels
Thermofisher
Oncomine Comprehensive Assay v3
16 gènes impliqués dyear-old l’HRD
>30 gènes
TSO500, Illumina
Mutations and tissue
Cancer Genome Atlas Research Network Nature
474:609–615, 201
Heeke AL, Lynce F, Baker T, et al J Clin Oncol
35:1502, 2017 (suppl 15)
Prithard 2016
Norquist CCR2018
Girard, E et al. International Journal of Cancer
144, no. 8 (April 15, 2019): 1962–74.
Ovary
Prostate
Breast
Gènes Ovaire Sein Prostate
ATM
ATR
BARD1
BRCA1
BRCA2
BRIP1
BLM
CDK12
CHEK1
CHEK2
FAM175A
FANCA
FANCD2
FANCI
FANCL
FANCM
FANCC
MRE11A
NBN
PALB2
RAD50
RAD51
RAD51B
RAD51C
RAD51D
RAD52
ATRX
WHAT IS THE LEVEL OF
EVIDENCE ?
Limited clinical trials
Swisher EM et al. Rucaparib in relapsed, platinum-sensitive high-grade ovarian carcinoma (ARIEL2 Part 1):
an international, multicentre, open-label, phase 2 trial. Lancet Oncol. 2017 Jan;18(1):75-87.
Limited functional data
Swisher. Lancet Oncology
Volume: 18 Issue 1 (2017)
Rucaparib in relapsed,
platinum-sensitive high-grade
ovarian carcinoma (ARIEL2
Part 1): an international,
multicentre, open-label,
phase 2 trial.
Limited functional data
No concordant data
Abstract 2476: Preclinical
assessment of the PARP inhibitor
rucaparib in homologous
recombination deficient prostate
cancer models
Minh Nguyen, Andrew D. Simmons
and Thomas C. Harding
BARD1, CDK12, FANCA, PALB2,
RAD51, RAD51C, RAD51D, and
RAD54L increased rucaparib
efficacy ≥ 2-fold in at least 1 cell line
examined
RAD51C
RAD51D
Effect on confirmed ovarian cancer risk
Seconds in frequency after BRCA1/2 in ovarian cancer RAD51C: 0.4 to 2% - constitutional mutations 3% - somatic mutations 3% RAD51D: 0.3 to 1.1% - constitutional mutations 5% - somatic mutations 0%
Kondrashova O et al Secondary Somatic Mutations Restoring <i>RAD51C</i> and <i>RAD51D</i> Associated
with Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma. Cancer Discov.
2017 Sep;7(9):984-998
GREAT
12/21 labs want to move a large panel in 2019
Genomic BRCA and Extensive ovArian cancer Testing
> To date 66 declared centers / 23 associated platforms
> Ovarian cancer – prospective cohort
> Supporting the capture approach
> Basic panel : BRCA1/2 + RAD51C/D
> Largest panel possible
> No intervention – follow-up of variants for clinical outcomes
> Support by ARCAGY-GINECO
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CONCLUSION
Conclusion
Improve again the quality of tumour testing
> Large rearrangement / Limit of detection
> Reversion detection
Extend molecular testing to other biomarkers
> Beyond BRCA1/2 : difficulty of scarcity - clinical evidence =>
Collecting data
Improve the variant interpretation
Improve the report harmonization
diane-latrille.com
Thanks
Comité de pilotage
Jean-Christophe SABOURIN
Aude LAMY
Céline GARREC
Frederique PENAULT-LLORCA
Cécile AUBE
Anne CAYRE
Cédric LEMARECHAL
Laurent DOUCET
Clotilde DESCARPENTRIES
Isabelle QUINTIN-ROUE
Hélène BLONS
Jean-François EMILE
Jean-François COTE
Antoinette LEMOINE
Valérie DURANTON-TANNEUR
Yves DENOUX
Karen LEROY
Isabelle SOUBEYRAN
Véronique HADDAD
Paul HOFMAN
Florence PEDEUTOUR
Alexandre HARLE
Ludovic LACROIX
Alexander VALENT
Marc-Antoine BELAUD-ROTUREAU
Pierre-Jean LAMY
AFAQAP
Caroline Egele
Jean-Pierre Bellocq
Dominique Fetique
Gustave Roussy
Jean-Yves Scoazec
Isabelle Miran
Catherine Richon
Ludovic Lacroix
Sophie Cotteret
Birama Ndiaye
Biomedical Quality Assurance
Research unit of the University
of Leuven
Cleo Keppens
Kelly Dufraing
Els Dequeker
Lien Tembuyser
Veronique Tack
Departement of Pathology
of the Radboud University
Nijmegen Medical Centre
Marjolijn Ligtenberg
Han van Krieken
Institut National du Cancer
Frédérique Nowak
Etienne Lonchamp
Support financier :
UFR de Médecine Marseille
Genetics and Bioinformatics team
Christophe BEROUD
David SALGADO
Jean-Pierre DERIVES
UFR de Médecine - Nantes
Laboratoire de Biochimie
Marc DENIS
Projects
Variant interpretation
Report harmonization
Standardization - artificial sample
> Large rearrangement
> Low allelic frequency on different mutations
> Reversion cases
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