Hereditary Cancer Testing Panels Presented by Ambry Genetics Kelly Gonzalez, MS, CGC Senior Manager of Clinical Genomics
Overview • Current Testing and Next-generation (NGS) Methodologies • Overview of NGS Panels and Indications • Clinical Utility • Variants of Uncertain Significance
Why Cancer NGS Panels? • Efficient sequencing of targeted regions of cancer related genes • Many genes implicated in each cancer – Testing multiple genes simultaneously can be more time and cost effective • Aid in clinical diagnosis when clinical criteria are uncertain • There are currently no dx breast cancer panels for intermediate risk genes – Need for expanded screening of breast cancer-related genes besides BRCA1 and BRCA2 as many patients are negative for BRCA1 and BRCA2 mutations
Sequence Capture: Hybridization vs PCR Hybridization
Clinical use: Whole exome sequencing Limitations: 35% (30/82) dx after the age of 60
• Reported at 24% (62/282) – 7% of these are structural changes
• OvaNext gene mutations – Individually Rare, Collectively Common
ColoNext •Gene Sequencing for all 14 genes
•Deletion and Duplication Analysis Gene
Syndrome
Colon Cancer Risk
Polyposis
Other Associated Cancer
STK11
Peutz-Jegher
57-81%
Yes
breast; uterine; testicular; cervical; lung; pancreas
CHEK2
Hereditary Breast and Colon
increased (~10%)
PTEN
Cowden
increased
TP53
Li-Fraumeni
increased
MUTYH
MUTYH-Assoc Polyposis
35-53%
Yes
breast
APC
FAP
~99%
Yes
stomach; pancreas; thyroid; CNS; hepatoblastoma
HNPCC
60-80%
JPS
9-50%
breast; ovarian Yes
breast; thyroid, renal breast, Sarcoma, brain, adrenocortical, leukemia
MLH1 MSH2 MSH6
uterine; ovarian; stomach; bladder, brain, ureter, other
PMS2 EPCAM BMPR1A SMAD4
Yes
Stomach; other
Hereditary Susceptibility to CRC
Jasperson et al. Gastroenterology 2010
“Everybody in my family gets cancer.” Pancreatic ca dx 57
prostate dx 65
Stomach ca dx 41
breast dx 55
Colon ca dx 51
d. 40 Accident
Lung ca dx 80
64 y
2 polyps 39
Leukemia dx 11
Lobular breast ca dx 32; 2 polyps, 34y
“GI” ca dx 45
Ductal breast ca dx 42
CancerNext •Gene Sequencing for 22 genes
•Deletion and Duplication Analysis, plus additional 55 genes. Gene
Syndrome
Breast Cancer Risk Ovarian Cancer Risk Uterine Cancer Risk Colon Cancer Risk
BARD1
HBOC
Increased
Increased
BRIP1
HBOC
Increased
Increased
MRE11A
HBOC
Increased
Increased
NBN
HBOC
25-35%
Increased
RAD50
HBOC
25-48%
Increased
RAD51C
HBOC
Increased
Increased
ATM
Ataxia Telectangasia
~25-60%
PALB2
Her. Breast/Panc
~25-40% 39%
CDH1
Her. Diffuse Gastric Ca
STK11
Peutz-Jegher
0.3
CHEK2
Her. Breast/Colon
~25%
PTEN
Cowden
25-50%
TP53
Li-Fraumeni
50%-70%
MUTYH
MUTYH-Assoc Polyposis
20-25%
APC
FAP
Polyposis
Other Associated Cancer
Yes
biallelic: leukemia, lymphoma pancreatic gastric testicular, cervical, lung, pancreas
Increased Increased Increased
Increased
57-81% increased (~10%)
5-10%
Increased
Increased
Increased 35-53% ~99%
Yes
Yes Yes
MLH1 MSH2
HNPCC
9-12%
20-60%
thyroid; renal sarcoma; brain; adrenocortical; leukemia stomach; pancreas; thyroid; CNS; hepatoblastoma uterine; ovarian; stomach; bladder; brain; ureter; other
60-80%
MSH6 PMS2 EPCAM BMPR1A
SMAD4
JPS
9-50%
Yes
Stomach; other
Data Sharing • ISCA collaboration- sharing of CNVs identified by array (https://www.iscaconsortium.org/) • ClinVar collaboration- sharing of sequence variants and classification (http://www.ncbi.nlm.nih.gov/clinvar/) • Publication- retrospective review of our data, variant classification, and genotypephenotype • Continuing updates via webinar – 6 month update on VUS rate, insurance coverage
• Quality of this information depends on you too! – Clinical Info – new test requisition form – Pedigree
NCCN Guidelines Gene
Syndrome
Discussed in NCCN Guidelines?
APC MUTYH STK11 PTEN TP53 MLH1 MSH2 MSH6 PMS2 EPCAM BMPR1A SMAD4 CDH1 PALB2 ATM CHEK2 BARD1 BRIP1 MRE11A NBN RAD50 RAD51C
Familial adenomatous polyposis MUTYH-Associated polyposis Peutz-Jegher syndrome Cowden syndrome Li-Fraumeni syndrome
Y Y Y Y Y
Lynch Syndrome
Y
Juvenile Polyposis syndrome
Y
Hereditary Diffuse Gastric Cancer Hereditary Breast/Pancreatic Cancer Hereditary Breast Cancer Hereditary Breast/Colon/Other Cancer
Y Y
Hereditary Breast and/or Ovarian Cancer
http://www.nccn.org/professionals/physician_gls/f_guidelines.asp
Lifetime Breast Cancer Risk & NCCN • Lifetime Breast Cancer Risk of 20-25% – Threshold for designating women high risk for breast cancer, as stated in ACS Guidelines for breast screening with MRI as an adjunct to mammography (Saslow etal 2007)
– “A high risk of breast cancer also occurs with mutations in the TP53 gene (LiFraumeni syndrome) and the PTEN gene (Cowden and Bannayan-RileyRuvalcaba syndromes). – “…In cases in which insufficient evidence to recommend for or against MRI screening, decisions should be made on a case-by-case basis…” Publications cited by NCCN guidelines for above statements: Saslow etal Ca Cancer J Clin 2007;57:75-89. Murphy etal Cancer 2008;113:3116-3120.
Cost of Sequencing Over Time THEN: Human Genome Project: $3 billion and 13 years End of 2011: Sequencing centers and laboratories: ~$15K and ~15 days
Data from the National Human Genome Research Institute (NHGRI)
Slide created by Kelly Gonzalez, MS, CGC, Ambry Genetics
Traditional Sequencing
Evolution of the molecular laboratory
Laboratory Directors & Genetic Counselors
NextGen Sequencing
Laboratory Directors Genetic Counselors
Laboratory Technicians
Bioinformaticians Laboratory Technicians
Evolution of the genetics clinic
Panel tests / Complicated results
Single gene tests/ Positive or negative results
Panel tests / Complicated results Single gene tests/
Positive or negative results
Ambry’s Variant Classification Scheme • Mutation
Always included in results report with interpretation of result and description of gene
• Variant, suspected pathogenic • Variant, unknown significance • Variant, suspected benign
Always included in result report, with interpretation of result, description of gene, and supplementary data
• Polymorphisms
Reported only if requested
VUS Reported Data Example: PALB2 p.P864S c.2590C>T • •
First detected in 1/96 BRCA-negative highrisk breast cancer families and 0/96 controls Allele frequency data – 1000genomes • 0.23% overall (5/2188) • 1.12% British sub-cohort (2/178)
– NHLBI Exome Sequencing Project • 0.20% overall (21/10737) • 0.26% European American (EA) (18/7,020)
•
Genotype frequency data – NHLBI Exome Sequencing Project – T/C heterozygotes: 19/5359 (0.35%) – T/T homozygotes: 1/5359 (0.02%)
– Co-segregatation: not available – Co-occurrence: none Guenard F et al. Genet Test Mol Biomarkers. 2010 Aug;14(4):515-26.
Thank you! Any questions?
