New genetic cancer tests within gynecology Patrick Willems GENDIA Antwerp, Belgium

or Disclosure CEO and shareholder of GENDIA (private lab offering genetic tests) NO financial relationship with research bodies, medical or pharmaceutical companies, hospitals or government or

2. SOMATIC MUTATIONS IN CANCER New genetic tests 1. GERMLINE MUTATIONS NIPT STID WES / WGS CANCER RISK 2. SOMATIC MUTATIONS IN CANCER DNA profiling of tumors CT-DNA (liquid biopsy)

New genetic tests In procreation NIPT and STID

NIPT www.DOWNsyndromeNIPT.info NON – INVASIVE PRENATAL TESTING Testing of cff DNA (cell free fetal DNA) from maternal blood during pregnancy for trisomy 21, 18 and 13, and fetal sex www.DOWNsyndromeNIPT.info

NIPT NIPT currently is most common genetic test The most common genetic test : Approximately 1 million NIPTs per year worldwide Future Market value : 4 billion US / year (price : 300 – 500 Euro per test)

STID SCREENING TEST for INHERITED DISEASE With testing of common recessive diseases from parental blood before or during pregnancy If both parents are carrier of the same disease the fetus has a 25 % risk of being affected and prenatal testing (CVS/AC) can be offered www.STID-GENDIA.net

STID for Recessive disorders Gene Frequency Cystic Fibrosis CFTR 1/3000 Spinal muscular atrophy SMN1 1/5000 Deafness GJB2 1/2000 Fragile X FMR1 Thalassemia HBB 1/3000 (1/300) Many metabolic disorders 100 genes 1/200

New genetic tests for cancer CANCER RISK test DNA profiling test CT-DNA test

Genetics of cancer Majority of cancers are caused by somatic mutations only occuring in the tumor Minority of cancers is inherited due to germline mutations occuring in all cells (also germline) : Ovarian Cancer : 15 % Breast Cancer : 10 % Colon cancer : 5% Prostate cancer : low Lung cancer : very low

CANCER RISK test in BOC Germline DNA testing Classical BOC testing BRCA1/2 test 2 genes in patients Single mutations in family members Selected families Patients affected with BOC Young patients Multiplex families with multiple affected members Ovarian Ca

Germline DNA testing in BOC BOC testing of BRCA1/2 only identifies 50 % of mutations BOC testing of BRCA1/2 misses therapeutic targets Selected family testing only identifies 50 % of mutations

Germline DNA testing in BOC BOC testing of BRCA1/2 only identifies 50 % of mutations BOC testing of BRCA1/2 misses therapeutic targets Selected family testing only identifies 50 % of mutations

Germline mutations in BOC Breast cancer : 10 % is inherited BRCA1 and BRCA2 mutations : 5 % CHEK2, ATM, TP53, PALB2: 3-5 % Other mutations : ? Ovarian cancer : 15 % is inherited BRCA1 and BRCA2 mutations : 10 % HNPCC mutations : 1-2 % CHEK2,ATM,TP53,PALB2,BARD1,BRIP1,CDH1,EPCAM,MLH1, MSH2, MSH6,NBN,PMS2,PTEN,RAD51C,RAD51D,STK11 BRCA1/2

Germline DNA testing in BOC BOC testing of BRCA1/2 only identifies 50 % of mutations BOC testing of BRCA1/2 misses therapeutic targets Selected family testing only identifies 50 % of mutations

Germline DNA testing in BOC PARP inhibitors for tumors with deficient DNA repair : Deficient DNA repair due to mutations in BRCA1/2 Deficient DNA repair due to mutations in other genes : BARD1, BRIP1, PALB2, ATM, CHEK2, PTEN, RAD51C, RAD51D, NBN, TP53, EPCAM, MLH1, MSH2, MSH6, PMS2 ,

Germline DNA testing in BOC BOC testing of BRCA1/2 only identifies 50 % of mutations BOC testing of BRCA1/2 misses therapeutic targets Selected family testing only identifies 50 % of mutations

CGC-based genetic screening CGC (Clinical Genetics Center) Criteria : Patients affected with BOC Young patients Multiplex families Ovarian Ca

BOC testing for all women 50 % of women with BOC mutation do not fulfill CGC criteria Mary-Claire King advocates genetic screening of all adult women (JAMA vol 312, Sept 2014)

Breast cancer testing BRCA1/2 in selected patients with high risk PREVIOUSLY : BRCA1/2 in selected patients with high risk CURRENTLY : Screening of ALL BOC genes in ALL women

Cancer risk test Sequencing of 30 cancer genes : 19 genes involved in BOC : BRCA1, BRCA2, ATM, BARD1, BRIP1, CDH1, CHEK2, EPCAM,MLH1, MSH2, MSH6, NBN, PALB2, PMS2, PTEN, RAD51C, RAD51D, STK11, and TP53 + 11 genes involved in colon, uterine, pancreas, and skin cancer : APC, BAP1, BMPR1A, CDKN2A, CDK4, GREM1, MITF, MUTYH, POLD1, POLE, and SMAD4

What if I have a mutation ? Children have 50 % risk of inheriting the mutation If already BOC, personalised treatment eg with herceptin, PARP inhibitors If unaffected : increased risk for BOC Increased surveillance (MRI, Mammography, CA125, abdominal echography, CT-DNA liquid biopsy) Profylactic surgery : 51% bilateral mastectomy; 64% oophorectomy (Meijers H. The Lancet, june 2000)

2. SOMATIC MUTATIONS IN CANCER New genetic tests 1. GERMLINE MUTATIONS NIPT STID WES / WGS CANCER RISK 2. SOMATIC MUTATIONS IN CANCER DNA profiling of tumors CT-DNA (liquid biopsy)

DNA profiling of BOC tissue CURRENT TESTING of BOC tissue : Estrogen receptor (ER) : tamoxifen (anti-E), anastrozole (anti-Aromatase) Progesteron receptor (PR) : mifepristone HER2 : Herceptin FUTURE TESTING of BOC tissue : DNA repair genes : PARP inhibitors (Olaparib, Iniparib, Veliparib) Microsatellite instability (MSI): immunotherapy RNA signature to determine thr need of chemo Driver genes : targeted therapy with designer molecules

Frequency of oncogenic mutations in different cancers GENE Lung Colon Breast Ovary Melanoma Prostate Pancreas EGFR 30 50   3 TP53 34 45 23 46 12 14 36 KRAS 17 4 57 BRAF 1 11 7 2 PIK3CA 26 9 NRAS 18 CTNNB1 48 6 2-3 GNAS 16 FOXL2

Treatment of cancer Personalised treatment Surgery Radiation Chemotherapy Personalised treatment

Targeted treatment for cancer Personalised targeted treatment inhibits specific mutations that cause cancer These mutations are patient-specific Therapy is dependent upon the specific mutation Mutations can be detected by molecular studies of : . tumor material (biopsy) : FFPE, fresh or frozen . blood (liquid biopsy)

in plasma of healthy individuals (Mandel and Métais,1948) cell-free DNA testing Cell-free DNA (cfDNA) in plasma of healthy individuals (Mandel and Métais,1948)

cell-free DNA testing Cell-free DNA (cfDNA) in plasma of healthy individuals (Mandel and Métais,1948) cffDNA (NIPT) : Cell-free DNA from the fetus in the maternal circulation A proportion of cfDNA in pregnant women is fetus-derived (cffDNA) : Lo et al. (1997) Non-Invasive Prenatal testing (NIPT) : 2012 : start 2015 : > 1 million tests   Market : 4 billion USD ctDNA (liquid biopsy) Cell-free DNA from the cancer cells in the circulation Increased concentrations of cfDNA in the circulation of cancer patients : Leon et al. (1977) A proportion of cfDNA is tumor-derived : Stroun et al. (1987) Circulating tumor DNA (ctDNA) testing (liquid biopsy) : 2015 : start   Market : 40 billion USD

CT DNA test screens Circulating Tumor DNA from the cancer cells in blood (liquid biopsy)  

CT-DNA test on liquid biopsy GENE PROTEIN MUTATIONS EGFR Epidermal growth factor receptor 32 TP53 Tumor protein p53 9 KRAS Kirsten rat sarcoma viral oncogene 18 BRAF Braf murine sarcoma viral oncogene 6 PIK3CA Phosphatidylinositol 3-kinase, catalytic, alpha 14 NRAS Neuroblastoma ras viral oncogene 10 CTNNB1 Catenin, beta-1 4 GNAS Guanine nucleotide-binding protein, alpha 2 FOXL2 Forkhead transcription factor foxl2 1 1. DESCRIPTION : 96 mutations in 9 cancer genes 2. SAMPLE : blood in specific test kits with Streck tubes (GENDIA) 3. TURNAROUND TIME : 3 weeks 4. PRICE : 500-900 Euro

Advantages liquid biopsies No tissue biopsy needed No FFPE fixation Profiling the overall genotype of cancer primary cancer circulating cells metastases Better evaluation of : reaction to therapy development of resistance Also screening of patients without tumor but high cancer risk

Indications for CT DNA testing (liquid biopsy) Follow up of patients with cancer during treatment Screening of individuals at high risk for cancer BRCA, HNPCC carriers History of cancer Family history of cancer In the future : annual screening of all adults

From patient testing towards population screening Form testing of 1 gene in 1 % of the population suspected of a genetic disorder to : Whole genome testing (WGS) of the whole population to identify germline mutations 2. Annual screening for cancer DNA by liquid biopsy to identify somatic mutations