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The Human Genome
23 Pairs of Chromosomes
About 30,000 Genes
Sporadic
~75%
Familial (gene(s)) not
known 15-20%
~20-25%
HNPCC
~2-3%
FAP (<1%)MYH (<1%)
Practical Colorectal Cancer Genetics
100 new colorectal cancer patients
1 with FAP1 with FAP 2 with HNPCC2 with HNPCC 17 with FH 17 with FH of polyps of polyps or canceror cancer
80 with no 80 with no FH of polyps FH of polyps or canceror cancer
Exons 1-14 Exon 15
AAPC AAPC
Severe DesmoidsProfuse Colorectal Polyposis
1309
Adenomatous Polyposis Coli Gene (APC)
Wild Type
Truncated Mutant Proteins
19 yo with Colon Cancer
D17S250
N T N T N T
– + LOH
1 2 3
Tumor Testing for Microsatellite Instability
The Canadian Contribution -Family C
Hereditary Nonpolyposis Colorectal Cancer
Germline mutations in mismatch repair genes
MSH2, MLH1, PMS1, PMS2, MSH6
5’
5’
3’
3’
hMSH2
hMLH1
Promoter
Exon
Mutation
5’
5’
3’
3’
hMSH2
hMLH1
Promoter
Exon
DNA Mismatch Repair & MSI Colorectal Cancer
CancerA
CancerB
MLH1 MSH2
Courtesy: Aaron Pollett
3
Colon dx~50
Bowel dx 55 Colon dx 55 Colon dx ?
Colon dx ?
pancreas, prostate, liver
Endo. dx 31Rectal dx 34Cecum dx 51Transverse colon dx 52Duodenum dx 53
d. 64
d. 80
d. 55
d. 55
28
52
84
MSH2 MSH2
MSH2 Immunohistochemistry
Duodenal Adenoma Duodenal Cancer
Courtesy: Aaron Pollett
Kids with Colorectal Cancer
d.12Duodenal ca dx 11
MetsCAL spots
36
0.06250
34
0.06250
9CRC dx 8
+ 3 dysplastic polypsAux. freckling
6CAF spots
Plexiform neurofibroma (tongue)
d.70Gastric dx 60s d. childbirth
30 d.18-19 d.war
d.62d. Lung ca
55
d.90CRC dx 60s
73
7
Both sides: Afganistan
ATCG ATCG
ATCG
ACC
ATCGATCG
ACC
ACC
ACC
GCC
GCC
III - 1 III - 2
IV - 1
IV - 2
IV - 3
Inherited Colorectal Cancer - It’s ‘Easy’
Familial Adenomatous Polyposis (FAP) - APC
Gene
Hereditary Nonpolyposis
Colorectal Cancer (HNPCC) - mismatch
repair genes
What have we learned from Hereditary Colorectal Cancer Syndromes?
Germline Mutation Somatic MutationFamilial Adenomatous APC gene APC gene
Polyposis (FAP)
Hereditary Nonpolyposis Mismatch Repair Mismatch Repair
Colorectal Cancer (HNPCC) Genes Genes
Sporadic Colorectal Cancer …….. APC gene
Mismatch Repair
Genes
5’ 3’
hMLH1
Promoter
Exon
Hypermethylation
Hypermethylation of MLH1 Promoter as an Epigenetic Cause
of MLH1 Inactivation in
SPORADIC COLORECTAL CANCER
MSS vs MSI-H colorectal cancer
Survival by Stage
Gryfe et al, NEJM 342:69-77;2000
Hazard Ratio0.45 (0.30-0.68)P<0.001
Adjuvant 5FU and Colon Cancer Survival
N Engl J Med 345(15) 1091-1097, 2001
Chemotherapy and Mismatch Repair Deficiency
Meyers et al; 61:5193, 2001
HCT 116
HCT 116 + chromosome 3
National Cancer Institute of Canada 292
North Central Cancer Treatment Group Protocol 784852 66
Protocol 874651 34 Gastrointestinal Intergroup, NCI 143
Fondation Francaise de Cancerologie Digestive 35
Total 570
No. Cases
MULTISITE COLLABORATION
Colorectal Cancer Genetics & 5-FU
Ribic CM NEJM 2003
MSS
MSI
Hazard Ratio
0.69 (0.50-0.94) p=0.02
2.17 (0.84-5.55) p=0.10
What about….?CPT11
Oxaliplatin
Avastin
Erbitux
?
Palliative Rx NEJM 2000
Aduvant Rx NEJM 2004
Palliative Rx NEJM 2004
Genetic Basis of Colorectal Cancers with Microsatellite Instability
100 CRC
15 MSI-H
85 MSS (1 FAP)
2 HNPCC1 MLH1 germline mutation
1 MSH2 germline mutation
13 Sporadic 13 MLH1 promoter methylation
Attenuated Polyposis
Family N - Autosomal Recessive Colorectal Cancer?
multiple polyps multiple polyps multiple polyps
DNA Base Excision Repair
Slupska et al, J Bacteriol. 178, 3885, 1996
Exon 7 (codon 165) …GGGCTACTATT…
Exon 7 (codon 165) …GGGCTGCTATT…
tyrosine
cysteine
Exon 13 (codon 382) …ctcaGGTCTGC…
Exon 13 (codon 382)… ctcaGATCTGC…
glycine
aspartic acid
Functionally Important MYH Mutations
MYH Associated Polyposis (MAP)
Autosomal Recessive Colorectal Cancer
multiple polyps multiple polyps multiple polyps
Y165C G382D
Y165C G382D
Y165C G382D
Y165C G382D
How did it happen?
Pancreatic cancer: Causes
Environmental factors• Smoking• Alcohol• Coffee• Diet• Chemicals
Host factors
• Past medical history
• Pancreatitis
Genetic predisposition
Familial cancer syndromes
Familial Aggregation
of cases
Somatic Mutations in Pancreatic Cancer
Gene or Region Frequency of Alteration (% of tumors)
K-ras >90
p16 >95
p53 50 - 75
DPC4 55
Chromosome 19q/AKT2 10 - 20
Chromosome 6q/MYB 10
Chromosome 20q/AIB1 10
BRCA2 7 – 10
LKB1/STK11 4
MKK4 4
TGF-β R-I or R-II <5
RB1 <5
Kern S. Molecular genetic alterations in ductal pancreatic adenocarcinomas. Med Clin North Am 2000(84): 691-695.
Familial Cancer Syndromes
PANCREATICCANCER
Familial Melanoma
(p16)
Familial Breast-ovarian cancer
syndrome
(BRCA1, BRCA2)
HNPCC
(hMSH2, hMLH1 & other
mismatch repair genes)
Peutz-Jeghers, Li-Fraumeni etc.
(less common)
Melanoma + Pancreas Cancer
Breast/Ovarian Cancer + Pancreas Cancer
Lifetime Risk of Pancreas Cancer
General Population ~ 0.2-0.5 %
BRCA2, PJS, HNPCC,
p16, Familial Pancreatitis ~ 5-10 %
Familial Pancreas Cancer ~ 20-30%
High Risk Pancreas Cancer Screening Program
Who?
BRCA2, p16, Familial Pancreas Cancer, Peutz-Jeghers, FAP, Hereditary NonPolyposis Colorectal Cancer, Familial Pancreatitis
What?
Yearly MRI, Ultrasound, Blood collection/banking
What Joe General Surgeon should know
BRCA1/2, MMR genes, APC, MYH, RET, p16, VHL
Keep your eyes and ears open for new ones!
Microsatellite instability/18q LOH in colorectal cancer
Somatic genetics of Wilms, neuroblastoma
Molecular based therapies - eg Herceptin, Gleevec
Non-cancer genetic syndromes
Sporadic
~75%
Familial (gene(s)) not
known 15-20%
~20-25%
HNPCC
~2-3%
FAP (<1%)MYH (<1%)
Is it ALL genetic? If it is, how do we figure it out?
Allelic architecture and mapping strategy
Mag
nitu
de o
f ef
fect
Frequency in population
Family-based linkage studies
Association studies in populations
Unlikely to exist
Slide thanks to D. Altshuler
http://pgaedu.net/GtD_Presentations/snp_palmer.ppt
Predisposing mutation Disease
Common complex genetic diseases
Normal cell Cancerhigh penetrance
BRCA1, BRCA2, othersAPC, MMR genes, others
MutantVariant A Cancer
low penetrance
Predisposing mutation Disease
Common complex genetic diseases
Normal cell Cancerhigh penetrance
BRCA1, BRCA2, othersAPC, MMR genes, others
MutantVariant A Cancer
low penetrance
SNP Example: Subject 1: GCGCTTAG A TTCCAGGCGCTTAG A TTCCAG
Subject 2: GCGCTTAG G TTCCAGGCGCTTAG A TTCCAG
Predisposing mutation Disease
Common complex genetic diseases
Normal cell Cancerhigh penetrance
BRCA1, BRCA2, othersAPC, MMR genes, others
MutantVariant A
MutantVariant B
Cancerlow penetrance
Cancerlow penetrance
Predisposing mutation Disease
Common complex genetic diseases
Normal cell Cancerhigh penetrance
BRCA1, BRCA2, othersAPC, MMR genes, others
MutantVariant A
MutantVariant B
Cancerlow penetrance
+
Gene:gene interactions
Predisposing mutation Disease
Common complex genetic diseases
Normal cell Cancerhigh penetrance
BRCA1, BRCA2, othersAPC, MMR genes, others
MutantVariant A
MutantVariant B
Cancerlow penetrance
+
Gene:environment interactions
Genome Wide Association Studies
Definition
Study of genetic variation across the genome, designed to identify
genetic associations with observable traits (eg. blood
pressure), or the presence or absence of a disease (eg.
colorectal cancer)
Genome Wide Association Studies of Common Multigenic Diseases
Risk Variants in an individual
Asthma
Diabetes
Arthritis
Autism
Colon Cancer
Risch, Nature 2000
How many subjects do you need for a powerful GWAS?
http://pgaedu.net/GtD_Presentations/snp_palmer.ppt
THE ARCTIC PROJECTAssessment of Risk of Colo-Rectal Tumors in Canada
GWS Stage 1 Design:
•1200 Cases (Ontario)•1200 Controls (Ontario)• 1.4 billion genetic tests
Brent Zanke, Steve Gallinger, CeliaGreenwood, Michele Cotterchio, Tom Hudson
Progress to Date
Genotyping (1200 CRC and 1200 controls)
1536 SNPs from candidate genes
10K coding non synonymous SNPs.
100K Affymetrix gene chip SNP array. 500K Affymetrix gene chip SNP array. (In Analysis)
Validation
250 ng Genomic DNA
RE Digestion
Adaptor Ligation
Xba XbaXba
Fragmentationand Labeling
PCR: One Primer Amplification
Complexity Reduction
AA BB AB
Hyb & Wash
Affymetrix Centurion 100K+500K SNP chips
Multi-Stage Analysis of ~100,000 SNPs
Stage 1: Ontario1257 cases/1336 controls
99,632 SNPs
Stage 2: Seattle + Newfoundland
1139 cases/1055 controls
Stage 3: Scotland 975 cases/1002 controls
Stage 4: Scotland 1910 cases/1985 controls
Validation: EPIC & France2199 cases/2401 controls
1142 SNPs
76 SNPs
9 SNPs
2 SNPs
1 SNP confirmed
Outcome of Two Best SNPs
OR 95%CI p-value
rs10505477
Stages 1-4 1.18 1.12-1.25 1.41E-08
French/EPIC 1.16 1.07-1.26 5.05E-04
All cohorts 1-7 1.17 1.12-1.23 3.16E-11
rs719725
Stages 1-4 1.14 1.07-1.20 1.32E-05
French/EPIC 0.98 0.90-1.06 0.61
All cohorts 1-7 1.08 1.01-1.15 0.023
rs10505477 (8q24 locus)
8q24 locusAffymetrix Illumina