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New Era of Genetic Testing in Colon Cancer
Carol Burke, MD, FACG, FASGE, AGAF, FACP
Sanford R Weiss Center for Hereditary Colorectal Neoplasia
Department of Gastroenterology and Hepatology
Cleveland Clinic, Cleveland, Ohio
September 19, 2015
Overview
• Recognize clues suggestive of a genetic colorectal
cancer syndrome
• Understand the genetic testing process for hereditary
colorectal cancer syndromes
Pathways to CRC
Sporadic
CRC
FAP
Adenoma
MAP
CIN-MSS
MSI
Lynch
Syndrome
CIMP
Sessile
Serrated Polyp
MSI
MLH1 promotor methylation
BRAF mutation
Chromosomal Instability
Pino MS, et al. NEJM 2010;339;1277
CpG Island Methylation (CIMP)
Gene
Expression
Gene
Silencing
Turns off MLH1
Multi Target Stool DNA Testing vs FIT
• Assay: Methylation of BMP3 and NDRG4, KRAS mutations ,
B-actin and a fecal immunochemical test
P < 0.001
P = 0.002
%
P < 0.001
Imperiale T, 2014;370:1287
Microsatellite Instability
• Repeated nucleotide sequences called “microsatellites”
• DNA fidelity maintained by Mismatch Repair Proteins (MMR)
MLH1
PMS2
MSH2
MSH6
Boland CR, Gastroenterology 2010;138:2073
Mismatch Repair Protein Function
Nucleotide
mismatch
Normal MMR
T
T C AC
AGCTG
TCGAC
AGCTG
Microsatellite
Stable (MSS)
Microsatellite
Instability (MSI)
T
T C AC
TCTAC
Etiology:
AGCTG
1. MLH1 promoter methylation
2. Germline MMR mutationLynch Syndrome
AGATG
Defective MMR
8
Tumor MSI Testing
NR21
BAT25
Normal Tissue
Tumor Tissue
MSI-H: > 2/5 (30%) consensus MSI sequences
Mono27
Immunohistochemistry
MLH1
MSH2
Multi Society Task Force
Universal Testing of CRC for dMMR
Giardiello FM , Am J Gastro 2014;109:1159
11
Universal Tumor Testing for LS
• 1066 unselected tumors assessed for MSI/MMR
• 19.5% had MSI
– 11% (21 patients) diagnosed with LS
• Phenotype:
– 43% diagnosed > 50 years
– 22% did not Amsterdam II or revised Bethesda guidelines
Germline Testing Results In 21 Proband’s Relatives
Relationship
Tested
Positive
Negative
First degree
54
25
29
Second degree
22
10
12
> Third degree
41
17
24
Total
117
52
65
Hampel H et al. NEJM 2005;352;18
Typical Genetic Counseling Appointment
• Collect personal and family history
• Perform risk assessment (including breast cancer
risk models)
• Educate about genetic syndromes, management
options, genetic testing process
• Informed consent and coordination of genetic
testing
• Psychosocial support and counseling
Who Should Have Genetic Counseling
for Lynch Syndrome?
• Abnormal MSI/IHC testing
– (Unless MLH1 methylation is proven)
• Colon or endometrial cancer < 50
• > 2 Lynch Syndrome cancers in individual
• > 2 relatives with LS cancer, 1 < 50
• > 3 relatives with LS cancer at any age
Who Should Have Genetic Counseling for
other Colon Cancer Syndromes?
• > 10 colon adenomas
• Peutz-Jeghers Polyp
• Juvenile/Inflammatory Polyps
• Colon cancer < age 50
• Close relative diagnosed < age 50 or >2 close relatives
with colon cancer
Hereditary Colon Cancer Syndromes
Syndrome
Gene(s)
Features
Lynch
MLH1, MSH2,
MSH6, PMS2,
EPCAM
Colon, endometrial, ovarian, gastric, urinary tract,
small bowel cancers, brain tumors, sebaceous
neoplasms
Li Fraumeni
TP53
Childhood cancers, sarcoma, leukemia, brain
tumors, breast cancer, colon cancer
Familial
Adenomatous
Polyposis (FAP)
APC
Adenomas, colon cancer, thyroid cancer, osteomas
and soft tissue tumors, desmoid tumors
MYH-Associated
Polyposis (MAP)
MUTYH*
Adenomas, colon cancer, thyroid cancer
Peutz-Jeghers
STK11
Mucocutaneous melanin spots, hamartomas,
breast, GI, pancreatic, and rare gyn cancers
Cowden
PTEN
Hamartomas, derm lesions, macrocephaly, breast,
thyroid, and endometrial cancers
Juvenile
Polyposis
Syndrome
BMPR1A,
SMAD4
Hamartomas, colon cancer, some with SMAD4
have HHT
Traditional Cancer Risk Assessment and Genetic
Testing
HNPCC/Lynch
syndrome!
d. stroke d. uterine ca
80
61
57
59
colon ca
47
27
24
60
d. colon ca
47
62
colon ca
50
35
32
30
Traditional Genetic Testing
• Utilizes Sanger sequencing and large
rearrangement analysis
• Testing often limited to 1-2 syndromes based on
assessment of personal/family history
• Only testing for high-risk, well known syndrome
• Variant of uncertain significance rate is low
• Results take 2-3 weeks
Next Generation Sequencing
• Whole genome, or several genes
can be analyzed at once
• Allows for testing many genes
relatively inexpensively
• Used for panel genetic testing
– Cancer specific vs
– Pan cancer
Multi-Gene Panels
• Benefits
• Limitations
– Increased mutation
– Not all tests are
positive rate
– Identification of
conditions of low
clinical suspicion
equal
– Various levels of
gene coverage
– Cost effective
– Lower turn-aroundtime then reflex
testing
– Increased VUS rate
– Moderate-risk genes
– Longer turn-aroundtime than single
gene
Insurance Coverage & Cost
• Most labs offer insurance pre-authorization
• Many labs billing with same CPT codes as BRCA,
Lynch testing
• Costs range from $1500-$4400
What Are Testing Options?
• 10 panels (5-28 genes)
• 10 panels (7-29 genes)
– Build your own
• 7 panels (7-29 genes)
– Build your own
• 1 panel (25 genes)
• 2 panels (20-52 genes)
Example from Invitae
Myriad Genetics Lab myRisk Gene Panel
High Risk Genes
Breast Cancer
Colon Cancer
• BRCA1/BRCA2 (HBOC)
• CDH1 (Hereditary Diffuse
• APC (Familial
Gastric Cancer)
• PTEN (Cowden)
• STK11 (Peutz-Jeghers)
• TP53 (Li-Fraumeni)
Adenomatous Polyposis)
• BMPR1A/SMAD4 (Juvenile
Polyposis)
• MLH1/MSH2/MSH6/PMS2/
EPCAM (Lynch Syndrome)
• MYH (MYH-Associated
Polyposis)
High Risk Genes
• Significant risk of developing certain types of
cancer
• Considerable research and professional society
guidelines for screening and surgery
• Family members can be tested for the same
mutation
Moderate Risk Genes
• ATM (Ataxia Telangiectasia)
– Breast, pancreatic, colon
• CDKN2A (Familial Atypical Mole Malignant Melanoma)
– Pancreatic, melanoma
• CHEK2 (Li-Fraumeni Like Syndrome)
– Breast, prostate, colon
• PALB2 (Fanconi Anemia)
– Breast, pancreatic
Moderate Risk Genes
• 2- to 4-fold risk over the general population risk.
• Cancer risk is not as elevated as a mutation in a
high risk gene.
• Limited research and no professional society
screening or surgical recommendations
• Family history is often better for risk stratification
• Unclear if it is beneficial to test other family
members for these mutations
Potential Results from myRisk
• Positive
– High risk gene
– Moderate risk gene
– New moderate risk gene
• Negative
• Variant of uncertain significance
Incidental Finding Case 2
Caucasian/N. American
90
85
dx female ca 65
AJ
Irish
no info
d. 83
dx br ca 60s
n
55
d. young
accident
61
test ca
64
45
65
42
dx br ca
42
34
Lynch Syndrome PMS2
NCCN 2.201
Incidental Finding Case 3
Hungary
d. 54
Panc ca
Sicily
2
81
89
CRC 89
47
50
88
br ca 45
d. 64
55
d.55 b/l
br ca 44
BRCA -
26
29
p
61
51
d. 40
Panc ca
Hereditary Diffuse Gastric Cancer
• CDH1 mutations
• 39% breast cancer risk by age 80
• Diffuse gastric cancer
– 67% for men and 83% for women by age 80
– Average onset 38 years (range of 14-69 years)
– Options for intense screening or prophylactic
gastrectomy/mastectomy
Variants of Uncertain Significance: Our results
• 235 VUS in 171 patients (41.4%)
– majority in moderate risk genes (62.2%)
• VUS rate lower in those of European ancestry than
African, Asian, and Middle Eastern (p=0.001)
Important Insurance Updates
• Companies requiring pre-test genetic counseling:
– CareSource
– CCF Employee Health Plan
– Cigna
– Medical Mutual of Ohio
Conclusions
• Variety of “Genetic” tests to determine cause of hereditary
colon cancer syndromes
• Currently, test the tumor first in patients with CRC
– Germline testing for polyposis or when tumor not available
• Genetic testing in transformation:
• NGS lowering costs and driving panel based testing
– Not all panel tests are created equal
• Caution: panel testing “easy” to order but complicated to
interpret
• Get a lot of information we might not understand
• Find unanticipated mutations that highly impact patient care