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Hereditary Cancer Testing Panels
Elizabeth Chao, MD
Director of Translational Medicine
Jill Siegfried, RN, MS, CGC
Certified Genetic Counselor
Overview
• Introduction to Ambry
• Current Testing and Next-generation (NGS)
Methodologies
• Overview of NGS Panels and Indications
• Clinical Utility
• Variants of Uncertain Significance
• Insurance Coverage
Ambry’s Current Major Diagnostic Methods
• Applications:
– Sanger Sequencing for single gene analysis
– Pyrosequencing and NextGen Seq for targeted mutation
analysis
– Targeted enrichment and Next-gen sequencing for larger
gene panels and exome analysis
– MLPA for single gene deletion/duplication analysis
– CMA and SNP-CGH array for genome wide
deletion/duplication analysis and structural variant
detection
Mission & Values
Mission:
Providing quality genetic and genomic answers and
tools to our clients for the care and management
of patients worldwide.
Values:





Partnership
Quality
Client Care
Flexibility
On-Time Delivery
Ambry’s Cancer Menu
Familial Adenomatous Polyposis (FAP), Gardner Syndrome, Turcot Syndrome, Attenuated FAP (AFAP)
APC Amplified
APC
PTEN-Related Disorders (including Autism Spectrum Disorder), Cowden Syndrome, PTEN HamartomaTUmor Syndrome (PHTS), Bannayan-RileyRuvalcaba syndrome, Proteus syndrome, Autism / Autism spectrum disorder
PTEN-Related Disorders (including Autism Spectrum Disorder)
PTEN
PTEN-Related Disorders (including Autism Spectrum Disorder), Cowden Syndrome, PTEN HamartomaTUmor Syndrome (PHTS), Bannayan-RileyRuvalcaba syndrome, Proteus syndrome, Autism / Autism spectrum disorder
PTEN-Related Disorders (including Autism Spectrum Disorder)
PTEN
PALB2-Related Cancer, Breast cancer, Familial, Fanconi Anemia, PALB2-Related, Pancreatic cancer, Familial
PALB2-Related Cancer
PALB2
CHEK2-Related Cancer
PTEN-Related Disorders (including Autism Spectrum Disorder), Cowden Syndrome, PTEN HamartomaTUmor Syndrome (PHTS), Bannayan-RileyRuvalcaba syndrome, Proteus syndrome, Autism / Autism spectrum disorder
CHEK2-Related Cancer
CHEK2
PTEN-Related Disorders (including Autism Spectrum Disorder)
PTEN
Malignant Melanoma, Cutaneous Malignant Melanoma Syndrome, Familial Atypical Mole-Malignant Melanoma Syndrome (FAMMM)
Malignant Melanoma (CDKN2A/p16)
CDKN2A
Pleuropulmonary Blastoma (PPB) Family Tumor and Dysplasia syndrome, DICER1 Syndrome
Pleuropulmonary Blastoma (PPB) Family Tumor and Dysplasia Syndrome, DICER1 Syndrome
DICER1
Familial Adenomatous Polyposis (FAP), Gardner Syndrome, Turcot Syndrome, Attenuated FAP (AFAP)
APC Amplified
APC
Malignant Melanoma, Cutaneous Malignant Melanoma Syndrome, Familial Atypical Mole-Malignant Melanoma Syndrome (FAMMM)
Malignant Melanoma (CDKN2A/p16)
CDKN2A
Multiple Endocrine Neoplasia Type 2 (MEN2), MEN2A (Sipple Syndrome), MEN2B (Mucosal Neuroma Syndrome), Familial Medullary Thyroid
Carcinoma (FMTC)
Multiple Endocrine Neoplasia Type 2 (MEN2)
RET
PALB2-Related Cancer, Breast cancer, Familial, Fanconi Anemia, PALB2-Related, Pancreatic cancer, Familial
PALB2-Related Cancer
PALB2
Familial Adenomatous Polyposis (FAP), Gardner Syndrome, Turcot Syndrome, Attenuated FAP (AFAP)
APC Amplified
APC
Hereditary Diffuse Gastric Cancer
Juvenile Polyposis Syndrome (JPS), HHT, SMAD4-Related
Hereditary Diffuse Gastric Cancer
Juvenile Polyposis AMPLIFIED™
HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome
HNPCC / Lynch syndrome DNA Analysis
HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome
HNPCC / Lynch Syndrome Tumor Testing
Juvenile Polyposis Syndrome (JPS), HHT, SMAD4-Related
Li-Fraumeni Syndrome
Juvenile Polyposis AMPLIFIED™
Li-Fraumeni Syndrome (TP53 AMPLIFIED)
HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome
HNPCC / Lynch syndrome DNA Analysis
HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome
HNPCC / Lynch Syndrome Tumor Testing
CDH1
BMPR1A, SMAD4
EPCAM, MLH1, MSH2,
MSH6, PMS2
MLH1, MSH2, MSH6,
PMS2, BRAF
BMPR1A, SMAD4
TP53
EPCAM, MLH1, MSH2,
MSH6, PMS2
MLH1, MSH2, MSH6,
PMS2, BRAF
Malignant Melanoma, Cutaneous Malignant Melanoma Syndrome, Familial Atypical Mole-Malignant Melanoma Syndrome (FAMMM)
Malignant Melanoma (CDKN2A/p16)
CDKN2A
Multiple Endocrine Neoplasia Type 2 (MEN2)
RET
Multiple Endocrine Neoplasia Type 2 (MEN2)
RET
Multiple Endocrine Neoplasia Type 2 (MEN2), MEN2A (Sipple Syndrome), MEN2B (Mucosal Neuroma Syndrome), Familial Medullary Thyroid
Carcinoma (FMTC)
Multiple Endocrine Neoplasia Type 2 (MEN2), MEN2A (Sipple Syndrome), MEN2B (Mucosal Neuroma Syndrome), Familial Medullary Thyroid
Carcinoma (FMTC)
HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome
HNPCC / Lynch syndrome DNA Analysis
HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome
HNPCC / Lynch Syndrome Tumor Testing
Multiple Endocrine Neoplasia Type 1
Multiple Endocrine Neoplasia Type 2 (MEN2), MEN2A (Sipple Syndrome), MEN2B (Mucosal Neuroma Syndrome), Familial Medullary Thyroid
Carcinoma (FMTC)
MUTYH-associated polyposis (MAP)
Multiple Endocrine Neoplasia Type1 (MEN1)
EPCAM, MLH1, MSH2,
MSH6, PMS2
MLH1, MSH2, MSH6,
PMS2, BRAF
MEN1
Multiple Endocrine Neoplasia Type 2 (MEN2)
RET
MUTYH-associated Polypsis (MAP)
MUTYH
PALB2-Related Cancer, Breast cancer, Familial, Fanconi Anemia, PALB2-Related, Pancreatic cancer, Familial
PALB2-Related Cancer
PALB2
PALB2-Related Cancer, Breast cancer, Familial, Fanconi Anemia, PALB2-Related, Pancreatic cancer, Familial
PALB2-Related Cancer
PALB2
Pancreatitis, CTRC-related
Pancreatitis, PRSS1-Related
Pancreatitis, SPINK1-related
Peutz-Jeghers Syndrome
Pancreatitis, CTRC-Related
Pancreatitis, PRSS1-Related
Pancreatitis, SPINK1-Related
Peutz-Jeghers AMPLIFIED™
CTRC
PRSS1
Pleuropulmonary Blastoma (PPB) Family Tumor and Dysplasia syndrome, DICER1 Syndrome
Pleuropulmonary Blastoma (PPB) Family Tumor and Dysplasia Syndrome, DICER1 Syndrome
DICER1
PTEN-Related Disorders (including Autism Spectrum Disorder), Cowden Syndrome, PTEN HamartomaTUmor Syndrome (PHTS), Bannayan-RileyRuvalcaba syndrome, Proteus syndrome, Autism / Autism spectrum disorder
PTEN-Related Disorders (including Autism Spectrum Disorder)
PTEN
PTEN-Related Disorders (including Autism Spectrum Disorder), Cowden Syndrome, PTEN HamartomaTUmor Syndrome (PHTS), Bannayan-RileyRuvalcaba syndrome, Proteus syndrome, Autism / Autism spectrum disorder
PTEN-Related Disorders (including Autism Spectrum Disorder)
PTEN
PTEN-Related Disorders (including Autism Spectrum Disorder)
PTEN
Retinoblastoma
RB1
Familial Adenomatous Polyposis (FAP), Gardner Syndrome, Turcot Syndrome, Attenuated FAP (AFAP)
APC Amplified
APC
HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome
HNPCC / Lynch syndrome DNA Analysis
HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome
HNPCC / Lynch Syndrome Tumor Testing
Von Hippel-Lindau Disease
Von Hippel-Lindau Disease
PTEN-Related Disorders (including Autism Spectrum Disorder), Cowden Syndrome, PTEN HamartomaTUmor Syndrome (PHTS), Bannayan-RileyRuvalcaba syndrome, Proteus syndrome, Autism / Autism spectrum disorder
Retinoblastoma
STK11
EPCAM, MLH1, MSH2,
MSH6, PMS2
MLH1, MSH2, MSH6,
PMS2, BRAF
VHL
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 different clinical implications for hereditary versus
sporadic breast and colon cancer patients and their families.
Important to understand genetic contribution for treatment
and prevention
• 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
• Scalability
NEXT-GENERATION TECHNOLOGY
NextGen Sequencing
Illumina GAIIx, HiSeq2000, Miseq
•
Massive parallel sequencing---leap from capillary sequencing (96 well x 500 bp) to
250 GB of sequence in a run
•
Since 2007 at Ambry
•
Introduced a number of diagnostic panels (XLMR, Marfan, PCD panels, and today new
cancer panels) on GAIIx, and Exome sequencing on Hiseq2000
•
Decreased per basepair cost allows for large panel design at reasonable cost and turnaround-time
The Ambry RainDance Technologies NGS Panels
DNA iso from
blood or saliva
Report
RDT Enrichment
TruSeq Library Prep,
Illumina GAIIx Sequencing
AVA: Ambry Variant Analysis
Alignment & NextGene
Sequence Viewer
Sanger Verification
• All identified Variants
• All amplicons with low coverage
Deletion/Duplication Analysis
CancerArray™ Design
Target gene implicated in cancer
Exon-level coverage
Exon
Backbone region
1 probe per 20kb
Exon
Targeted Regions
5.1 probes per exon
Exon
PANEL OVERVIEWS AND
INDICATIONS
Very rare high-risk variants and rare
moderate-risk variants
Hollestelle et al. 2010
Next-gen Cancer Panels
Hereditary breast, ovarian, and colorectal cancer
•
•
•
•
BreastNext
OvaNext
ColoNext
CancerNext
•
Comprehensive
sequence and
deletion/ duplication
testing
BreastNext
•Gene sequencing for all 14 genes
•Deletion and Duplication Analysis
Gene
Syndrome
Breast Cancer Risk
Other Associated Cancer
BARD1
HBOC
Increased
Ovarian
BRIP1
HBOC
Increased
Ovarian
MRE11A
HBOC
Increased
Ovarian
NBN
HBOC
25-35%
Ovarian
RAD50
HBOC
25-48%
Ovarian
RAD51C
HBOC
Increased
Ovarian
ATM
Ataxia Telectangasia
~25-60%
Increased
PALB2
Hereditary Breast and Pancreatic
~25-40%
Breast Pancreas
STK11
Peutz-Jegher
30%
Colon Pancreas
CHEK2
Hereditary Breast and Colon
~25%
Ovarian
PTEN
Cowden
25-50%
Thyroid; endometrial; renal
TP53
Li-Fraumeni
50%
Sarcoma; brain; adrenocortical;
leukemia
CDH1
Hereditary Diffuse Gastric Cancer
39-52%
Gastric colon
MUTYH
MUTYH-Associated Polyposis
20-25%
Colon
All Breast Cancer Susceptibility Genes are Not Created Equal
Moderate to High Penetrance Alleles
CDH1
MRE11A
NBN
RAD50
BARD1
MUTYH
Meindl et al 2011
In the context of family history
ATM, BRIP1, CHEK2, PALB2 and others with 2x increased lifetime risk
“
Therefore, mutation testing of these
genes for such women may be as
clinically relevant as is mutation testing
for BRCA1 and BRCA2. We argue that
detection of mutations in these genes
may be of considerable clinical
consequence in terms of absolute
breast cancer risk (that is, penetrance)
for women with a strong family history
”
No Family History
Family History
•
•
70% of women have a lifetime risk below
10% (solid blue)
For women with a genetic mutation and
FHx, 70% have a lifetime risk above 60%
(dashed red)
Byrnes et al Br Cancer Res 2008
Moderate Penetrance Breast Cancer
Genes
• “Mutations in
CHEK2, ATM,
NBS1, RAD50,
BRIP1, and PALB2
are associated
with doubling of
breast cancer
risks”
Walsh et al. Cancer
Cell 2007
Byrnes et al Breast Cancer Research 2008
Meta-analysis of large case-control studies of
mild to moderate risks variants
• ATM
– O.R. 1.20- 4.56
• CHEK2
– O.R 1.52-3.10
• NBN (NBS1)
– O.R. 2.42
Zhang et al. Lancet Oncology 2011
PALB2 and Breast Cancer
•
•
•
Reported in 1-3% of BRCA1/2
negative families
Also in the FA-BRCA pathway
•
Estimate a 2-4 fold increase in breast cancer
risk
•
Biallelic mutations result in Fanconi anemia
type N (FANCN)
WECARE study (Tischkowitz et al. Hum Mut 2012)
– O.R. : 5.3 (1.8-13.2)
– n~500 cases and ~500 controls
• Also at increased risk for:
– Pancreatic Cancer
– Ovarian Cancer (Walsh et al PNAS 2011)
(Jones et al Science 2009)
NBN(NBS1) and Breast Cancer
•
•
•
•
Founder mutation in Slavic
populations of Central and
Eastern Europe, c.657del5
–
Seen in 90% of NBS cases
and 50% of
heterozygotes with
cancer
–
Frequency of this mutation is
1/100-1/200 but has been
reported as high as 1/30
Truncating Mutations
Missense mutations may
have decreased
penetrance, such as
p.R215W
Mutation prevalence is
inversely correlated with
age at diagnosis
Bogdanova et al. Int J Cancer 2008
Steffen et al. Int J Cancer 2006
MUTYH and Breast Cancer
Review of conflicting data
•
Excess rate of extracolonic malignancies has been reported in individuals with
MUTYH mutations (1,2)
– Suggested elevated risk of CRC, gastric, ovarian, bladder, skin, breast and endometrial
cancers
•
•
Follow-up showed no association of MUTYH and breast cancer risk (3,4)
Increased risk of breast cancer in familial cancer and polyposis families
– 18% of female MAP patients with breast cancer (5)
– 5-7% of familial colorectal and/or breast cancer families were heterozygotes (6)
•
1.9% of controls
• Rates were similar in predominantly CRC vs Breast families
•
•
Increased breast Cancer Risk in Sephardic Jews (7): O.R. 1.39-1.86
Trend towards association of MUTYH heterozygotes with sporadic breast cancer
but insufficient power to detect O.R<2 (8)
1.
2.
3.
4.
5.
6.
7.
8.
Win et al Fam Cancer 2010
Vogt et al Gastroenterology 2009
Zhang et al. CEPB 2006
Beiner et al Br Can Res Treat 2009
Nielsen et al. J Med Genet 2005
Wasielewski et al. Br Can Res Treat 2010
Rennert et al. Cancer 2011
Out et al. Br Can Res Treat 2012
OvaNext
•Gene sequencing for all 19 genes
•Deletion and Duplication Analysis
Gene
Syndrome
Breast Cancer Risk Ovarian 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
Hereditary Breast and Pancreatic
~25-40%
Uterine Cancer
Risk
increased
Other Associated Cancer
Pancreas
STK11
Peutz-Jegher
30%
Colon; Pancreas
CHEK2
Hereditary Breast and Colon
~25%
Colon
PTEN
Cowden
25-50%
TP53
Li-Fraumeni
50%-70%
CDH1
Hereditary Diffuse Gastric Cancer
0.39
Gastric; colon
MUTYH
MUTYH-Associated Polyposis
20-25%
Colon
Lynch
??
increased
5-10%
Thyroid; endometrial; renal
increased
Sarcoma; brain; adrenocortical; leukemia
MLH1
MSH2
MSH6
PMS2
EPCAM
9-12%
20-60%
colon; stomach; other
Atypical Phenotypes
Li-Fraumeni Syndrome
“Mutations not associated with “typical phenotypes”
are of particular interest. For example, the three
TP53 mutations occurred in patients without a
family history of Li–Fraumeni syndrome and the two
MSH6 mutations occurred in patients without a
family history of Lynch syndrome. As
comprehensive genetic testing is undertaken for
individuals not selected for established syndromic
phenotypes, a wider range of expressivity
associated with germ-line mutations of cancer
susceptibility genes will become increasingly
apparent.”
Walsh et al. PNAS 2011
Prevalence of Hereditary Ovarian
Cancer
(Walsh et al. PNAS 2011)
• Previously reported by
TCGA at 14%, only in
BRCA1or BRCA2
• Reported at 24% (62/282)
– 7% of these are structural
changes
• 25% of hereditary ovarian
cancer is related to a
mutation in one of
OvaNext genes
Hereditary Susceptibility to CRC
?
Jasperson et al. Gastroenterology 2010
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
CDH1
Hereditary Diffuse Gastric
Cancer
Increased
stomach; breast; colorectum
CHEK2
Hereditary Breast and Colon
increased (~10%)
breast; ovarian
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%
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
“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
CLINICAL UTILITY
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.
NCCN Example – PTEN (Cowden Syndrome)
Genetic/Familial High-Risk Assessment Version1.2011
• Breast Cancer Screening Guidelines:
– BSE beginning at age 18y
– CBE every 6-12 mo, age 25y or 5-10y before the earliest known breast
cancer
– Annual mammography & breast MRI starting 30-35, or 5-10 y b/f earliest
known ca in family (whichever comes first)
– Discuss option of risk reducing mastectomy and hysterectomy on case-bycase basis….
• Add’l recommendations for endometrial, thyroid,
colon, and dermatologic screenings
Cited breast cancer risk:
An estimated breast cancer risk of 25-50% with average age of 38-46 years at diagnosis.
Publications cited by NCCN Guidelines for above statements:
Starink etal Clin Genet 1986;29:222-233
Brownstein etal. Cancer 1978;41:2393-2398
Emerging Data & NCCN Guidelines
• CDH1 - Discussed in:
– Genetic/Familial High-Risk Assessment Version 1.2011
• Cites a cumulative risk for female lobular breast cancer by age 75
as high as 52%, and that mutations may be associated with lobular
breast cancer in the absence of diffuse gastric cancer.
– Gastric Cancer Version 2.2011
• “E-Cadherin mutations occur in approximately 25% of families
with….[HDGC]”
• “Consideration should be given to prophylactic gastrectomy in
young asymptomatic carriers….”
Publications cited by NCCN guidelines for above statements:
Kaurah etal JAMA.2007; 297:2360-2372.
Schrader etal Fam Cancer 2008;7:73-82.
Masciari etal J Med Genet 2007;44:726-731.
Fitzgerald RC, etal. Gut 2004;53:775-778.
Huntsman DG etal. N Engl J Med 2001;344:1904-1909.
Emerging Data & NCCN Guidelines
• PALB2 - Discussed in:
– Pancreatic Adenocarcinoma Version 2.2012
• “… and particular mutations in PALB2 and MSH2 have
been identified as possibly increasing pancreatic cancer
susceptibility.”
• “….Thus, gemcitabine plus cisplatin may be a good
choice in selected patients with disease characterized
by hereditary risk factors (eg BRCA or PALB2
mutations).”
Publications cited by NCCN guidelines for above statements:
Canto etal Clin Gastroenterol Hepatol 2006;4:766-781.
Lowery etal Oncologist 2011;16:1397-1402.
Historic Perspectives on HBOC
Identification of Genetic Risk for Breast-Ovarian Cancer
•
•
1866- Paul Broca provides a detailed scientific description of inherited breast-ovarian cancer.
Mid 1980s - Quest for genetic basis of hereditary breast and ovarian cancer
•
Dec 1990 - HBOC linked to chromsome 17q21 by Mary-Claire King & colleagues, UC Berkeley
– Mar 1994 – Breast Cancer Linkage Consortium (BCLC) outlines risks for cancer beyond
breast cancer for BRCA1
– Oct 1994 – The cloning of BRCA1 described
•
Dec 1995 – The cloning/discovery of BRCA2
– Aug 1999 – BCLC outlines risks for cancer beyond breast/ovarian cancer for BRCA2
•
Dec 1999 – Publication of evidence that BRCA1 and BRCA2 are involved in the DNA damage
response. “BRCA1, BRCA2 and their possible function in DNA damage response.” Kate-Jarai Z
etal. PMID: 10584867
Historic Perspectives on HBOC
Prophylactic surgical interventions for women with HBOC
• 1995
– Prophylactic Oopherectomy in inherited breast/ovarian cancer families. Struewing etal
JNCI PMID: 8573450 :
• Eg: Struewing etal JNCI PMID: 8573450 : Multi-center study to determine the incidence of
post-oophorectomy carcinomatosis and to quantify the effectiveness of preventive surgery
• Sept 1999
– Studies demonstrate that prophylactic oophorectomy reduces ovarian cancer risk, and
then specifically shows that prophylactic oophorectomy reduces both ovarian and breast
cancer risk in BRCA carriers. Rebbeck etal JNCI PMID: 10469748
• Jan 1999
– “Efficacy of bilateral prophylactic mastectomy in women with a family history of breast
cancer.” Hartman etal NEJM PMID: 9887158
• Study supports the suggestion that prophylactic mastectomy reduces risk of breast cancer.
However, it was retrospective and many women did not have genetic analysis performed
• Mar 2004
– Bilateral prophylactic mastectomy reduces breast cancer risk in BRCA1 and BRCA2
mutation carriers: the PROSE Study Group. Rebbeck etal JCO PMID: 14981104
–
Demonstrates that bilateral prophylactic mastectomy reduces the risk of breast
cancer in women with BRCA1/2 mutations (with or without prophylactic oopherectomy, by
approximately 95%, and 90%, respectively).
Historic Perspectives on HBOC
Chemoprevention
• July/Sept 1998 –
– Three papers describe three trials that investigate the role of Tamoxifen as a chemopreventive
agent for breast cancer.
•
•
Fisher etal PMID: 9747868, Powles etal PMID: 9672274, Veronesi etal PMID: 9672273
Fisher B et al. Tamoxifen for prevention of breast cancer: report of the National Surgical Adjuvant Breast and Bowel
Project P-1 study. J Natl Cancer Inst 1998;90:1371–88. [PubMed: 9747868]
• June 2004
– Analysis of 491 women with stage I or stage II breast cancer, for whom a BRCA1 or BRCA2
mutation had been identified in the family
– Estimate risk of contralateral breast cancer in BRCA1 and BRCA2 carriers after diagnosis
– Authors conclude, “The risk of contralateral breast cancer in women with a BRCA mutation is
approximately 40% at 10 years, and is reduced in women who take tamoxifen or who undergo
an oophorectomy.”
•
Metcalfe et al. Contralateral breast cancer in BRCA1 and BRCA2 mutation carriers. J Clin Oncol 2004;22:2328–35. PMID:
15197194
MRI surveillance – similar trajectory
Targeted chemotherapeutics - PARP inhibitors in Phase II clinical trials
VARIANTS OF UNKNOWN
SIGNIFICANCE
Panel Genes
Variant Rates for Genes Previously
Available for sequencing at Ambry
50%
45%
40%
35%
30%
25%
20%
15%
10%
5%
0%
Average chance of a variant by Gene ~5%
PALB2
▪
CDH1
▪
STK11
▪
CHEK2
▪
PTEN
▪
TP53
▪
MUTYH
▪
APC
▪
MLH1
▪
MSH2
▪
MSH6
▪
PMS2
▪
EPCAM
▪
BMPR1A
▪
SMAD4
▪
BARD1
BRIP1
MRE11A
NBN
RAD50
RAD51C
ATM
‘▪’ = sequencing available at
Ambry for ~1-3 years
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
Family Studies Program
• Complimentary VUS analysis for informative relatives
• Available to the families of probands with a VUS
identified at Ambry
• Ultimate goal is variant re-classification
– Provide clinically-relevant information to our probands
• Family VUS testing generates co-segregation data
– Does the VUS track with disease?
– Can provide powerful evidence to support benign or pathogenic role
– Family studies data will be subsequently included in supplementary
materials for that particular variant
Enrolling in Family Studies Program
• Submit a detailed pedigree & application for family
studies
– Supplement to clinical information on Test Requisiton form
– http://ambrygen.com/sites/default/files/pdfs/cancer%20forms/CancerTestReqForm1.pdf
– http://ambrygen.com/sites/default/files/pdfs/forms/Cancer_Family-Studies-form.pdf
– Reviewed by genetic counselor/medical director
• Ambry GCs/MDs with clinician to select informative
relatives for cosegregation analysis
– Complimentary for approved relatives
• Results reported back to ordering physician
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.
Insurance Coverage/Pre-Verification
• Billing Options
– Institution Billing
– 3rd party payor (Insurance) Billing
• Medicare and many state Medicaid plans are accepted
• Extensive pre-verification department to assist
• Pre-verification available before sample submission or at the time
of sample submission
– Patient Direct Payment
• Payment Plan Options available
Thank you!
Any questions?