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BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
How to read results of an NGS analysis
Interpretation of a report focusing on mutations that can be germline
Kathleen ClaesCentre for Medical Genetics
Ghent University Hospital
A little bit of history
MORGANTI ET AL. CRIT REV ONCOL HEMATOL. 2019 JAN;133:171-182.2 /
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
Multi-gene panels for tumor genome analysis
tumor genome sequencing to identify: driver mutations predictive of
response to targeted therapies variants with potential diagnostic
and/or prognostic implications
But: germline variants may be identified with clinical implications for both the
patient and his or her family members
3 /
Genes in cancer panels which contain germlinemutations
4 /
Hematological tumorsANKRD26
CEBPACEBPADDX41ELANEETV6
GATA2GFI1PTEN
PTPN11RUNX1SAMD9
SAMD9LSRP72TP53WAS
APCATMBAP1
BARD1BMPR1ABRCA1BRCA2BRIP1CDH1CDK4
CDKN2ACHEK2CYLD
DICER1EPCAM
FHFLCN
GREM1HOXB13
LZTR1MAX
MEN1METMITFMLH1
MRE11AMSH2MSH6
MUTYHNBNNF1NF2
PALB2PMS2
POLD1POLE
PRKAR1APTCH1PTEN
RAD50RAD51CRAD51D
RB1RET
SDHAF2SDHBSDHCSDHD
SMAD4SMARCB1SPRED1STK11SUFU
TMEM127TP53TSC1TSC2VHLWT1
Solid tumors
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
Quantification of germline variants with therapeuticactionability – TCGA data: 10.389 cancers
THAVANESWARAN ET AL. NATURE REVIEWS ONCOLOGY 2019 FEB 20195 /
• Tier 1: variants for which at least one FDA- approved targeted agent is available
• Tier 2: variants with a similar level of evidence to those included in tier 1, albeit with no FDA- approved agent available
• Tier 3: variants with any available evidence of clinical benefit.
“Actionability” of the genes – French point of view
Class 1Screening and or prevention strategies available
Report findings to prescribing physician and the patient
Class 2Genes with significant risks
Detection/prevention possibilities but level of evidence too low to measure the real benefit of anintervention in asymptomatic setting (not yet sufficient evidence to develop guidelines)
Class 3Genes with moderate risk of cancer and/or prevention
Limited or nonexistent therapeutic possibilities
Not recommended to give information to the patients
PUJOL ET AL. EUR J HUM GENET. 2018 DEC;26(12):1732-1742.6 /
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
List of cancer genes
According to SFMMP classification
Only “IARC class 5” variants
7 / PUJOL ET AL. EUR J HUM GENET. 2018 DEC;26(12):1732-1742.
Variant classification at the germline level
8 /
Predictive testingPrenatal testingPGD
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
Comparison French and US guidelines
9 /
Class 1
Class 1
Class 2
Class 3
Actionable accordingto French guidelines
Actionable according toUS guidelines
PUJOL ET AL. EUR J HUM GENET. 2018 DEC;26(12):1732-1742
What if a (potentially) pathogenic germline variant is found?
Prior to request the test: inform the patient about potential to identify germlinevariants
Request germline testing for patients with potential germline mutation
Refer to clinical geneticist for genetic counseling
Impact:May offer an explanation for the disease in the patient (and relatives)May predict future (recurrence) risksPredictive testing to relatives can be offeredPreconceptual advice can be offered PGTIn case of hematological disorders: avoid to use asymptomatic carriers as donor for SCT
10 /
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
Multitier reporting of cancer gene variants
11 /
SPURDLE ET AL TOWARDS CONTROLLED TERMINOLOGY FOR REPORTING GERMLINE CANCER SUSCEPTIBILITY VARIANTS: AN ENIGMA REPORT. J MEDGENET. 2019 APR 8.
Experience in clinical practiceCase 1: Patient with multiple tumors
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
Personal history
Age 55: lobular breast cancer
Age 66: colorectal cancer
• IHC defect MLH1/PMS2
• MSI-high, hypermethylation MLH1
• No mutation in KRAS, NRAS, BRAF
Age 71: pancreatic cancer
• IHC defect MSH2/MSH6
• MSI-high, hypermethylation MLH1LIN ET AL. J BIOMED SCI. 2011 JUN 7;18:36
14 / YANTISS RK, SAMOWITZ WS. SURG PATHOL CLIN. 2012 DEC;5(4):821-42.
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
Personal history
Age 55: lobular breast cancer
Age 66: colorectal cancer
• IHC defect MLH1/PMS2
• MSI-high, hypermethylation MLH1
• No mutation in KRAS, NRAS, BRAF
Age 71: pancreatic cancer
• IHC defect MSH2/MSH6
• MSI-high, hypermethylation MLH1
Sequencing:
POLE c.1231G>A (p.(Val411Met)); VAF= 35% - pathogenic variant
POLE c.1471G>A (p.(Glu491Lys)); VAF= 45% - VUS
Familial anamnesis:
daughter breast cancer at age 42
some foci with loss of MSH2/MSH6
some foci with loss of MLH1/PMS2
germline
A model of replication repair deficiency
MODIFIED FROM URI TABORI ET AL. CLIN CANCER RES 2017;23:E32-E316 /
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
Experience in clinical practiceCase 2: “germline” is not always “germline”
Personal historybreast cancer at age 40, ER+, PR+
Familial anamnesisMaternal grandmother with breast cancer at age 45
Genetic test: HBOC panel – DNA extracted from blood: TP53 c.1024C>T, p.(Arg342Ter); VAF = 46%
Predictive test for 5 children and mother: negative???
18 /
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
VOETTEKST19 /
Blood
Buccal swab
Hypotheses:
- Post-zygotic somatic mosaicism?
- clonal hematopoiesis?= expansion of a hematopoietic clone containing a somatic driver mutation with a low allelic fraction, usually not more than 10% to 20%
chemotherapy-induced Weber-Lassalle et al. Hum Mut 2018:
AGO-TR1 trial: 26/523 patients (5.0%)
age-related
Genetic variation attributable to distinct biologicalprocesses
20 /
Post-zygotic somaticLineage restricted somatic
Somatic mutations related to cancerERIC Q. KONNICK AND COLIN C. PRITCHARD. GENOME MED. 2016; 8: 100.
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
patient with fallopian tube carcinoma who underwent multigene panel testing for cancer predisposition
TP53 c.733G>T (p.Gly245Cys) – VAF= 50% - interpreted as germline
1 year later: acute myelogenous leukemia: TP53 mutation absent in benign tissue but present in
leukemic cells.
sequencing of the fallopian tube tumor tissue revealed a different TP53 gene mutation, c.818G>T
(p.Arg273Leu)
abnormal result of genetic testing for hereditary cancer susceptibility should be carefully interpreted
when VAF ~ 50% but when the clinical presentation is atypical, when the patient is older, when the gene
in question is known to have potential germline and somatic mutations such as TP53
J Natl Compr Canc Netw 2018;16(5):461–466
VOETTEKST22 /
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
23 /
Take home messages
substantial burden of germline variants across a range of tumour histologiesinform the patient prior to request genetic tumor testing about potentially revealing data also relevant for relatives
germline alterations = ideal predictive biomarkers (due to clonal nature) demand for germline testing and its clinical interpretation will increase
complexity of the clinical interpretation of germline variants: variants might reach a threshold of being clinically relevant for therapy but not for risk management
clonal hematopoiesis: caution should be exerted in interpretation of NGS assays so that accurate therapeutic selection is realized for individual patients.
molecular tumor boards: ideal forum to discuss the management of challenging cases24 /
BGDO Digestive Oncology Course 2019 How to read results of an NGS analysisKathleen Claes
Functie
Afdeling of dienst
Universitair Ziekenhuis Gent
C. Heymanslaan 10 | B 9000 Gent
T +32 (0)9 332 21 11
E info@uzgent.be
www.uzgent.be
Volg ons op
KATHLEEN CLAESAssociate professor
Centrum voor medische genetica
Thank you!
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