A CANCER GENETICIST S (2 ND ) BEST FRIEND IS THEIR PATHOLOGIST. Dr Alan Donaldson Consultant in Clinical Genetics St Michaels Hospital Bristol

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1 A CANCER GENETICIST S (2 ND ) BEST FRIEND IS THEIR PATHOLOGIST Dr Alan Donaldson Consultant in Clinical Genetics St Michaels Hospital Bristol

2 Topics to be covered How pathology contributes to genetic diagnosis in: Lynch syndrome. Genodermatosis. Kidney cancer. Breast / ovarian cancer. Genetic testing 100,000 genomes project

3 Lynch Syndrome. Hereditary non polyposis colorectal cancer HNPCC Autosomal Dominant disorder. Due to mutations in one of the mismatch repair genes. MSH2 50% MLH1 40% MSH6 ~7% PMS2 <5% (TACSD1) ~1-2% Accounts for 1-5% of all colon cancers.

4 Amsterdam Criteria Three or more family members, one of whom is a first degree relative of the other two, with HNPCC-related cancers*. Two successive affected generations. One or more of the HNPCC-related cancers diagnosed before age 50 years. Exclusion of (FAP). * Colon, endometrial, small intestine, hepatobiliary, urinary tract.

5 Lynch Syndrome Cancer risks Lynch (Pop.) Colon 50-80% (5%) Endometrial 25-60% (2.7%) Ovary 4-12% (2%) Gastric 6-13% (<1%) Urinary Tract <4% (<1%) Small Bowel 3-6% (<1%) Sebaceous Neop 1-9% (<1%)

6 DNA Mismatch repair defect DNA repair system DNA Mutation(s) Cancer Mutagen Replication error

7 Mismatch repair function MSH6 MSH2 MSH3 HmutS HmutS TTT TTTT TTT TTTTT TTTTTTTT TTTTTTTTTTTTTT PMS1 HmutL? MLH3 PMS2 MLH1

8 Immunohistochemical (IHC) staining of the mismatch repair proteins MLH1 PMS2 MSH2 MSH6

9 Advantages / disadvantages of IHC Advantages. Cheap. Tells you what gene is involved. Disadvantages. Preoperative chemotherpay may give a false positive result. Still need to extract DNA for Braf / hypermethylation.

10 Microsatellite instability (MSI) 1.

11 Normal tissue Tumour tissue Arrows indicated additional peaks and microsatellite instability.

12 Sporadic loss of MLH % of all colorectal cancers. Associated with DNA methylation. Associated with BrafV600E in colonic tumours, but not endometrial.

13 Advantages / disadvantages of MSI Advantages. Better sensitivity & Specificity than IHC. Able to detect BRAFV600E mutations. Disadvantages. More expensive than IHC. Doesn t tell you what gene is involved.

14 Why do tumour analysis? To identify 1-5% of individuals whose colon cancer may be due to Lynch syndrome, for DNA analysis. ~15% of colon cancers are MSI high. Generally have a better outcome. Poorer response to 5 Fluorouracil?

15 Which Lynch related tumours to test? Colon Endometrial Ovary X Gastric X Small bowel? Urinary tract? Bowel polyps?

16 Who is ordering these tests? Dermatology Oncology Gynaecology Surgery? Pathology? Reflex testing Genetics

17 Lynch Syndrome NICE guidelines

18 Genodermatoses. Muir Torre Birt Hogg Dube Hereditary leiomyomatosis & renal cell cancer (HLRCC) Pten Hamartoma syndrome

19 What is Muir-Torre? Combination of sebaceous neoplasms of the skin. sebaceous adenomas sebaceous carcinomas epitheliomas Keratoacanthomas & one or more internal malignancies. Is this the same as Lynch syndrome?

20 Roberts et al 2013, Journal of Genetic Counselling 90 sebaceous neoplasms tested for loss of IHC MMR proteins 51 (7%) showed abnormal IHC 40 non MTS 11 suspected MTS 14 tested 8 had mutations (MSH2 6, MSH6 2) Positive predictive value 24% 16/90 post renal transplant patients 14/16 had loss of IHC Conclusion: IHC has poor diagnostic utuility

21 Roberts et al 2014, Genetics in Medicine Variable Score: Age at sebaceous neoplasm diagnosis (years) 60 or older 0 Younger than 60 1 Total number of sebaceous neoplasms or more 2 Personal history of any Lynch-related cancer No 0 Yes 1 Family history of any Lynch-related cancer No 0 Yes don t test 2+ test

22 Muir Torre syndrome without MSI / Loss of IHC. MutYH associated polyposis (MAP) Recessive >15 colonic polyps Upper GI polyps Other cancers e.g thyroid ( 2 of Roberts patients found to have MAP)

23 STK11 GI track Hamartomatous polyps small & large bowel Colon cancer Small bowel cancer Pancreatic cancer Breast cancer Peutz Jeghers

24 Clear cell VHL SDHB, SDHC CDKN2B FLCN Papillary SDHB, SDHC Met (type1) Fumarase (type 2) Pten Kidney cancer hybrid oncocytic renal cell carcinoma / oncocytoma / chromophobe renal cell carcinoma FLCN

25 Pten Hamartoma syndrome (Cowden, Ruvalcaba- Myhre syndrome) Skin lesions Trichilemmomas Papillomatous lesions Mucosal lesions Macrocephaly Cancer Kidney Breast Thyroid Endometrial Colon Learning difficulties Diffuse esophageal glycogenic acanthosis

26 Folliculin (FLCN) mutations. Skin Fibrofolliculomas Trichodiscomas Kidney Kidney cysts Kidney cancer Lung Cysts Pneumothorax Colon cancer? Birt Hogg Dube

27 Hereditary leiomyomatosis & renal cell cancer (HLRCC) Fumarase mutations. Skin Leiomyomas Uterus Leiomyomas Kidney Kidney cysts Type 2 papillary renal cancer.

28 BRCA1 & 2 P53 Hereditary breast cancer Li fraumeni syndrome Breast cancer triple +ve Sarcomas Leukemia / lymphomas Brain tumours CDH1 Lobular breast cancer Diffuse gastric cancer Palb2 Breast cancer Pancreatic cancer Pten STK11

29 BRCA1 & 2 are involved in repairing double stranded breaks.

30 But so are a lot of other genes.

31 % BRCA related lifetime cancer risks. BRCA1 BRCA2 Breast. Up to 80 Up to 80 Male breast. ~6 Ovary. Up to 63 Up to 27 Prostate Colon. - Gastric. - Pancreas. 3-5

32 BRCA related tumour pathology. Breast cancer: Triple negative tumours BRCA1 & BRCA2 ER negative BRCA1 Her2 negative BRCA1 Lobular unlikely BRCA1. Ovarian Cancer: Non Mucinous, usually high grade serous. Not borderline.

33 PARP (Poly ADP ribose polymerase) inhibitors.

34 3.2 billion base pairs ~23,000 genes a typical [individual] genome differs from the reference human genome at 4.1 million to 5.0 million sites (Usually ) requires a blood sample from an affected individual for analysis Genetic testing

35 Next generation sequencing (NGS) Panels Clinical exomes Whole genomic sequencing (WGS)

36 Cancer panels Cancer gene panel menu of genes for analysis Patient Details (minimum requirement: full name and NHS number or other identifier on all pages) Surname: First Name(s): NHS No: OR Other unit number: Comments: Requesting Clinician Print: Signature: Surname: First Name(s): NHS No: OR Other unit number: Panel Required Additional phenotypes available Genes Carney complex Cyclindromatosis, trichoepithelioma DICER1-pleuropulmonary blastoma familial tumour predisposition syndrome PRKAR1A CYLD DICER1 Please select genes for next generation sequence and dosage analysis by: a) Check the box for panel(s) required - from inherited cancer, additional phenotypes, inherited haematological panels sections or b) Check a customised selection of genes from the full 155 gene list Please send this menu, with our referral form ( and sample to: Leeds Genetics Laboratory (molecular genetics), Ashley Wing, St James's University Hospital, Leeds LS9 7TF, UK If the laboratory already has a sample banked, this form alone is sufficient to activate analysis. a) Panel Required Inherited cancer panels: Genes + and * genes - See notes on page 3 Diffuse gastric cancer Hereditary multiple exostoses Inherited lung cancer Nevoid basal cell carcinoma syndrome Retinoblastoma Rubinstein-Taybi syndrome Tuberous sclerosis Wilms tumour CDH1 EXT1, EXT2 EGFR PTCH1, SUFU RB1 CREBBP TSC1, TSC2 BUB1B, CDC73, CDKN1C, CTR9, DIS3L2, GPC3, REST, WT1 Bowel Breast including ovary APC +, BMPR1A, EPCAM*, GREM1* (& SCG5*), MLH1, MSH2 +, MSH6, MUTYH, NTHL1, POLE, POLD1, PMS2, PTEN, SMAD4, STK11 BRCA1, BRCA2, CDH1, PALB2, PTEN, STK11, TP53 Panel(s) Required Inherited haematological disorders Genes Myelodysplastic syndromes/ Acute leukaemia ANKRD26 +, CBL, CEBPA, CSF3R, DDX41 +, ELANE, ETV6, GATA2, G6PC3, GFI1, HOXA11, HAX1, HRAS, NF1, NSD1, PTPN11, RUNX1, RBM8A, SRP72, TERC, TERT +, THPO, TP53, NBN, PAX5 Kidney FH, FLCN, MET, PTEN, SDHB, SDHC, SDHD, STK11, TMEM127, VHL Aplastic anaemia (including Nijmegan breakage & Schwachman-Diamond syndrome) Ataxia telangiectasia NBN, PRF1, SBDS, SRP72, TINF2, TERC, TERT + ATM Neurofibromatosis, schwannoma, meningioma, and café au lait BAP1, LZTR1, PTEN, NF1, NF2, SMARCB1, SMARCE1, SPRED1, SUFU Bloom syndrome BLM Pancreas Pituitary cancer, parathyroid, hypercalcaemia, adrenal adenoma/hyperplasia. Pheochromocytoma and paraganglioma BRCA2, CDK4, CDKN2A +, PALB2, STK11 AIP, CASR, CDC73, CDKN1B, MEN1, PDE8B, PDE11A, PRKAR1A, RET EGLN1, EGLN2, KIF1B, MAX, NF1, RET, SDHA, SDHAF2, SDHB, SDHC, SDHD, TMEM127, VHL Diamond-Blackfan anaemia Dyskeratosis congenita (including telomere biology disorders) Fanconi Anaemia Rothmund-Thomson Syndrome RPL11, RPL15, RPL26, RPL35A, RPL5, RPS10, RPS17, RPS19, RPS24, RPS26, RPS29, RPS7 DKC1, TERC, TERT +, TINF2, NHP2, NOP10, POT1 BRCA1, BRCA2, BRIP1, ERCC4, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, PALB2, RAD51C, SLX4 RECQL4 Skin cancer melanoma BAP1, BRCA2, CDK4, CDKN2A +, POT1, POLE, TERT + Uterus FH, MLH1, MSH2 +, MSH6, PMS2, PTEN, STK11 Severe congenital neutropenia Thrombocytopenia Thromobocythaemia CSF3R, ELANE, G6P3C, GFI1, HAX1, WAS ANKRD26 +, ETV6, HOXA11, RBM8A, RUNX1, WAS JAK2, THPO

37 Cancer panels Surname: First Name(s): NHS No: OR Other unit number: c) Complete gene 155 list : Custom Selection AIP AKT1 ALK ANKRD26 APC + ATM BAP1 BARD1 BLM BMPR1A BRCA1 BRCA2 BRIP1 BUB1B CASR CBL CDC73 CDH1 CDK4 CDKN1B CDKN1C CDKN2A + CEBPA CHEK2 CREBBP CSF3R CTRC CTR9 CYLD DDX41 + DICER1 DIS3L2 DKC1 EGFR EGLN1 EGLN2 ELANE EPCAM* ERCC4 ETV6 EXT1 EXT2 EZH2 FANCA FANCB FANCC FANCD2 FANCE FANCF FANCG FANCI FANCL FANCM FH FLCN G6PC3 GALNT12 GATA2 GFI1 GPC3 GREM1* (&SCG5) HAX1 HNF1A HOXA11 HOXB13 HRAS JAK2 KIF1B KIT LZTR1 MAX MEN1 MET MITF MLH1 MSH2 + MSH6 MUTYH NBN NDUFA13 NF1 NF2 NHP2 NOP10 NSD1 NTHL1 NUDT1 OGG1 PALB2 PAX5 PDE11A PDE8B PDGFRA PHOX2B PIK3CA PMS2 POLD1 POLE POT1 PRF1 PRKAR1A PTCH1 PTEN PTPN11 RAD51C RAD51D RB1 RBM8A RECQL4 REST RET RHBDF2 RPL11 RPL15 RPL26 RPL35A RPL5 RPS10 RPS17 RPS19 RPS24 RPS26 RPS29 RPS7 RUNX1 SBDS SDHA SDHAF2 SDHB SDHC SDHD SLX4 SMAD4 SMARCB1 SMARCE1 SOS1 SOS2 SPINK1 SPRED1 SRP72 STK11 SUFU TERC TERT + TGFBR1 THPO TINF2 TMEM127 TP53 TSC1 TSC2 VHL WAS WT1 WRN Notes: Genes listed in red have more limited evidence regarding a role in hereditary cancer. They represent moderate/low penetrant genes or risk factors where guidelines for clinical management may not be well characterized. Dosage analysis is performed for all genes using NGS coverage data, any changes detected are confirmed by an independent method where possible (e.g. MLPA) and details specified at reporting. *Genes where ONLY dosage assessment performed. + Genes where analysis includes regions outside the normal scope of the assay (i.e. normal scope = all coding exons +/- 20bp flanking intronic sequence; please contact the laboratory or refer to our website for details)

38 2 main arms Rare diseases 100,000 genomes project Common cancers Germline Tumour

39 WGA report cancer

40 WGA report cancer

41 WGA report cancer

42 WGA report cancer

43 Any questions?