This document summarizes several genetic syndromes associated with an increased risk of colorectal cancer, including Lynch syndrome, familial adenomatous polyposis (FAP), MYH-associated polyposis, Peutz-Jeghers syndrome, and juvenile polyposis syndrome. It describes the characteristic features, inheritance patterns, cancer risks, and genes involved for each syndrome. Technological advances in genetic sequencing methods are making the identification of causal gene mutations more efficient.

1. Factors influencing decisions genetic syndromes ESO-ESSO Masterclass Cascais, Portugal 2011 Professor Sir John Burn MD FRCP FRCPCH FRCOG FMedSci Institute of Human Genetics, Newcastle University, UK With thanks to Professor Marco Novelli UCL London for several teaching slides used in this presentation Institute of Human Genetics Newcastle University Centre for Life, Newcastle UK

4. Roche Genome Sequencer FLX First run: 1 week 124 Mb of E coli sequence analysed Using Sanger sequencing manually In 1990 Would have taken a lifetime

5. New Technology: Sequence Capture Elute Fragment and hybridize to NimbleGen capture array 454 Sequencing Analyze Exon or loci sequences www.nimblegen.com gDNA Exon 1 Exon 2 Exon 3 Exon 4 Exon 5

6. Examples – complex mutations BRCA1 exon 16 (2) c.4964_4982del19 p.Ser1655TyrfsX15 BRCA2 exon 10 (1) c.891_899del9ins10 Newgene Ltd BRCA 1&2 600 euros 4 weeks

9. The two hit hypothesis Predisposed tumour All cells second hit

10. Lynch syndrome Endometrial Carcinoma Bertha Ted 3 CRC 9 skin cancers Family from which DNA used to Demonstrate hMSH2 mutation by Kolodner’s group 1993: 1 st of the MISMATCH REPAIR GENE DEFECTS 14 years ago

11. MMR genes are caretaker genes. Think of computer spell checker

14. MSS MSS MSS MSI-H MSI-H BAT26 NR21 BAT25 NR24 MONO27 Normal pattern MSI testing with quasimonomorphic 5 marker panel: no need to test normal tissue Normal pattern

15. Deletion in upstream EPCAM gene removes MSH2 promoter leaving gene methylated Deletions Removing the Last Exon of TACSTD1 Constitute a Distinct Class of Mutations Predisposing to Lynch Syndrome Marietta E. Kovacs,1 Janos Papp,1 Zoltan Szentirmay,2 Szabolcs Otto,3 and Edith Olah Human Mutation 2009;30:197 TACSTD1 MSH2 5KB

16. Loss of MLH1/PMS2 expression MSH2 MSH6 PMS2 MLH1

18. Newcastle 2009 285 samples 214 both normal 2 MSI failed IHC normal 58 samples 5 IHC failed 6 wrong tissue 13 IHC normal 26 IHC abnormal 19 other IHC combinations 12 MSI-L 1 MSI-H,+BRAF 1 MLH1 1 7 PMS2 6* 9 MLH1/PMS2 7 3 MSH6 2** 6 MSH2/6 6 Gene MSI-H, -BRAF 14 MSI-S 1 MSI-L 1 MSI-H, +BRAF 1 MSI-H, -BRAF (MSH2/6 nata) *1 MSI failed ** 1 MSI-S

21. Bayes probability sporadic MSI H Lynch syndrome PRIOR 0.16 0.03 BRAF-ive 0.6 1 JOINT 0.096 0.03 “ posterior” NEW ODDS 0.096: 0.03 3.2 : 1 only a quarter have LS

24. FAP Simon Burn et al J Med Genet 1990 Exon 11 Exon 15 1 2 2 1 22 11 1 2 2 1 1 2 2 1

26. APC protein domains and FAP phenotype association with (truncating) germline mutation position Heptad repeats (dimerisation) EB1 and HDLG binding sites Armadillo repeats 15-amino acid repeats (  -catenin binding) 20-amino acid repeats (  -catenin binding, GSK3  phosphorylation Basic domain (Microtubule binding, tubulin polymerisation) 6 57 453 767 1020 1169 1262 2033 2200 2400 2560 2843 1395 2000 Desmoids SAMP1 NESR3 1580 AAPC 457 1444 CHRPE 1250 1464 severe FAP 1309 Classical FAP 168 1580 400 AAPC 78

27. Truncation of APC Courtesy Inke Nathke Why is FAP so highly penetrant? Accumulation Aneuploidy Transformation Cell migration Chromosome segregation Deregulation of  -catenin

36. Peutz-Jegher’s polyp

38. Juvenile Polyp