How to read results of an NGS analysis - BGDO · 2019-05-29 · BGDO Digestive Oncology Course 2019...

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 /


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


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 /


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


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 /


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


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.


Personal history

Age 55: lobular breast cancer

Age 66: colorectal cancer

• IHC defect MLH1/PMS2


• No mutation in KRAS, NRAS, BRAF

Age 71: pancreatic cancer

• IHC defect MSH2/MSH6


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 /


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 /


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.


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 /


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 /


Functie

Afdeling of dienst

Universitair Ziekenhuis Gent

C. Heymanslaan 10 | B 9000 Gent

T +32 (0)9 332 21 11

E [email protected]

www.uzgent.be

Volg ons op

KATHLEEN CLAESAssociate professor

Centrum voor medische genetica

Thank you!

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How to read results of an NGS analysis - BGDO · 2019-05-29 · BGDO Digestive Oncology Course 2019...

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