Carol Burke, MD, FACG, FASGE, AGAF, FACPSanford R Weiss Center for Hereditary Colorectal NeoplasiaDepartment of Gastroenterology and HepatologyCleveland Clinic, Cleveland, OhioSeptember 19, 2015
New Era of Genetic Testing in Colon Cancer
Overview
• Recognize clues suggestive of a genetic colorectal cancer syndrome
• Understand the genetic testing process for hereditary colorectal cancer syndromes
Pathways to CRC
AdenomaAdenoma SessileSessile Serrated Polyp Serrated Polyp
Sporadic CRC
CIN-MSS CIMPCIN-MSS CIMP
MSI MSIMSI MSI
MLH1 promotor methylation BRAF mutation
Lynch Syndrome
FAP MAP
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
Imperiale T, 2014;370:1287
P < 0.001%
P < 0.001P = 0.002
Microsatellite Instability
• Repeated nucleotide sequences called “microsatellites”
• DNA fidelity maintained by Mismatch Repair Proteins (MMR)
Boland CR, Gastroenterology 2010;138:2073
MLH1 PMS2
MSH2 MSH6
Mismatch Repair Protein Function
Nucleotide
mismatch
Normal MMR
Defective MMR Etiology: 1.MLH1 promoter methylation2.Germline MMR mutation- Lynch Syndrome
TT CCTT AA CC
A G C T GA G C T G
T C G A T C G A CCA G C T GA G C T G
TT CCTT AA CC
A G C T GA G C T G A G A G AA T GT G
T C T C TT A C A C
Microsatellite Instability (MSI)
Microsatellite Stable (MSS)
8
Tumor MSI TestingNR21 BAT25 Mono27
Normal Tissue
Tumor Tissue
MSI-H: > 2/5 (30%) consensus MSI sequences
MLH1 MSH2
Immunohistochemistry
Multi Society Task Force Universal Testing of CRC for dMMR
11
Giardiello FM , Am J Gastro 2014;109:1159
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
Hampel H et al. NEJM 2005;352;18
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
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
• > 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
Who Should Have Genetic Counseling for other Colon Cancer Syndromes?
Hereditary Colon Cancer SyndromesSyndrome 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
HNPCC/Lynch syndrome!
colon ca 50
d. uterine ca 61
d. stroke 80
colon ca 47
57 6059 62
32 302427 35
d. colon ca 47
Traditional Cancer Risk Assessment and Genetic Testing
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–Increased mutation
positive rate
–Identification of conditions of low clinical suspicion
–Cost effective
–Lower turn-around-time then reflex testing
• Limitations–Not all tests are
equal
–Various levels of gene coverage
–Increased VUS rate
–Moderate-risk genes
–Longer turn-around-time 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
• BRCA1/BRCA2 (HBOC)
• CDH1 (Hereditary Diffuse Gastric Cancer)
• PTEN (Cowden)
• STK11 (Peutz-Jeghers)
• TP53 (Li-Fraumeni)
Colon Cancer
• APC (Familial 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
42dx br ca
42
45 34
64 6555 d. youngaccident
61 test ca
85dx female ca 65
90 d. 83dx br ca 60s
no info
Caucasian/N. American IrishAJ
n
Lynch Syndrome PMS2
NCCN 2.2014
2926
55 d.55 b/l br ca 44 BRCA -
47 50
8189CRC 89
88br ca 45
d. 64
Hungary Sicily
61 51
p
2
d. 40 Panc ca
d. 54 Panc ca
Incidental Finding Case 3
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