Hereditary Cancer Testing Panels
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Transcript of Hereditary Cancer Testing Panels
Hereditary Cancer Testing Panels
Elizabeth Chao, MDDirector of Translational Medicine
Jill Siegfried, RN, MS, CGCCertified 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-Riley-Ruvalcaba 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-Riley-Ruvalcaba 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 CHEK2-Related Cancer CHEK2 PTEN-Related Disorders (including Autism Spectrum Disorder), Cowden Syndrome, PTEN HamartomaTUmor Syndrome (PHTS), Bannayan-Riley-Ruvalcaba syndrome, Proteus syndrome, Autism / Autism spectrum disorder 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 Hereditary Diffuse Gastric Cancer CDH1 Juvenile Polyposis Syndrome (JPS), HHT, SMAD4-Related Juvenile Polyposis AMPLIFIED™ BMPR1A, SMAD4 HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome HNPCC / Lynch syndrome DNA Analysis EPCAM, MLH1, MSH2,
MSH6, PMS2 HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome HNPCC / Lynch Syndrome Tumor Testing MLH1, MSH2, MSH6,
PMS2, BRAF Juvenile Polyposis Syndrome (JPS), HHT, SMAD4-Related Juvenile Polyposis AMPLIFIED™ BMPR1A, SMAD4 Li-Fraumeni Syndrome Li-Fraumeni Syndrome (TP53 AMPLIFIED) TP53 HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome HNPCC / Lynch syndrome DNA Analysis EPCAM, MLH1, MSH2,
MSH6, PMS2 HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome HNPCC / Lynch Syndrome Tumor Testing 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), MEN2A (Sipple Syndrome), MEN2B (Mucosal Neuroma Syndrome), Familial Medullary Thyroid Carcinoma (FMTC) 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) RET
HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome HNPCC / Lynch syndrome DNA Analysis EPCAM, MLH1, MSH2, MSH6, PMS2
HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome HNPCC / Lynch Syndrome Tumor Testing MLH1, MSH2, MSH6, PMS2, BRAF
Multiple Endocrine Neoplasia Type 1 Multiple Endocrine Neoplasia Type1 (MEN1) MEN1 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 MUTYH-associated polyposis (MAP) 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, CTRC-Related CTRC Pancreatitis, PRSS1-Related Pancreatitis, PRSS1-Related PRSS1 Pancreatitis, SPINK1-related Pancreatitis, SPINK1-Related Peutz-Jeghers Syndrome Peutz-Jeghers AMPLIFIED™ STK11 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-Riley-Ruvalcaba 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-Riley-Ruvalcaba 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-Riley-Ruvalcaba syndrome, Proteus syndrome, Autism / Autism spectrum disorder PTEN-Related Disorders (including Autism Spectrum Disorder) PTEN
Retinoblastoma 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 EPCAM, MLH1, MSH2, MSH6, PMS2
HNPCC (Hereditary Non-Polyposis Colon Cancer), Lynch Syndrome, Muir-Torre Syndrome, Turcot Syndrome HNPCC / Lynch Syndrome Tumor Testing MLH1, MSH2, MSH6, PMS2, BRAF
Von Hippel-Lindau Disease Von Hippel-Lindau Disease 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 SequencingIllumina 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 turn-around-time
• All identified Variants• All amplicons with low coverage
The Ambry RainDance Technologies NGS Panels
RDT EnrichmentTruSeq Library Prep,
Illumina GAIIx Sequencing
Alignment & NextGene Sequence Viewer
Sanger Verification
DNA iso from blood or saliva
AVA: Ambry Variant AnalysisReport
Deletion/Duplication AnalysisCancerArray™ Design
Targeted RegionsBackbone region1 probe per 20kb
Target gene implicated in cancerExon-level coverage
5.1 probes per exon
ExonExon Exon
PANEL OVERVIEWS AND INDICATIONS
Very rare high-risk variants and rare moderate-risk variants
Hollestelle et al. 2010
Next-gen Cancer PanelsHereditary 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 OvarianBRIP1 HBOC Increased Ovarian
MRE11A HBOC Increased OvarianNBN HBOC 25-35% Ovarian
RAD50 HBOC 25-48% OvarianRAD51C 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 EqualModerate to High Penetrance Alleles
Meindl et al 2011
CDH1MRE11ANBNRAD50BARD1MUTYH
In the context of family historyATM, BRIP1, CHEK2, PALB2 and others with 2x increased lifetime risk
• 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
No Family HistoryFamily History“
”
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
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 (Jones et al Science 2009)
– Ovarian Cancer (Walsh et al PNAS 2011)
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 CancerReview 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. Win et al Fam Cancer 20102. Vogt et al Gastroenterology 20093. Zhang et al. CEPB 20064. Beiner et al Br Can Res Treat 20095. Nielsen et al. J Med Genet 20056. Wasielewski et al. Br Can Res Treat 20107. Rennert et al. Cancer 20118. 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
Uterine Cancer Risk Other Associated Cancer
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% increased PancreasSTK11 Peutz-Jegher 30% Colon; PancreasCHEK2 Hereditary Breast and Colon ~25% ColonPTEN Cowden 25-50% 5-10% Thyroid; endometrial; renalTP53 Li-Fraumeni 50%-70% increased increased Sarcoma; brain; adrenocortical; leukemiaCDH1 Hereditary Diffuse Gastric
Cancer 0.39 Gastric; colonMUTYH MUTYH-Associated Polyposis 20-25% ColonMLH1
Lynch ?? 9-12% 20-60% colon; stomach; other
MSH2MSH6PMS2
EPCAM
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 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 Yes breast; thyroid, renal
TP53 Li-Fraumeni increased breast; sarcoma; brain; adrenocortical; leukemia
MUTYH MUTYH-Assoc Polyposis 35-53% Yes breast
APC FAP ~99% Yes stomach; pancreas; thyroid; CNS; hepatoblastoma
MLH1
HNPCC 60-80% uterine; ovarian; stomach; bladder; brain; ureter; other
MSH2MSH6PMS2
EPCAMBMPR1A
JPS 9-50% Yes stomach; otherSMAD4
• Gene Sequencing for all 14 genes
• Deletion and Duplication Analysis
“Everybody in my family gets cancer.”
Ductal breast ca dx 42
prostate dx 65 Lung ca dx 80
breast dx 55Stomach ca dx 41
Pancreatic ca dx 57
d. 40 Accident2 polyps 39
64 y
Leukemia dx 11
Colon ca dx 51
Lobular breast ca dx 32;2 polyps, 34y
“GI” ca dx 45
Gene Syndrome Breast Cancer Risk
Ovarian Cancer Risk
Uterine Cancer Risk
Colon Cancer Risk
Polyposis
Other Associated Cancer
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% biallelic: leukemia, lymphoma
PALB2 Her. Breast/Panc ~25-40% Increased pancreaticCDH1 Her. Diffuse Gastric Ca 39% gastricSTK11 Peutz-Jegher 0.3 Increased 57-81% Yes
testicular, cervical, lung, pancreas
CHEK2 Her. Breast/Colon ~25% Increased increased (~10%) PTEN Cowden 25-50% 5-10% Increased Yes thyroid; renalTP53 Li-Fraumeni 50%-70% Increased Increased Increased sarcoma; brain;
adrenocortical; leukemiaMUTYH MUTYH-Assoc Polyposis 20-25% 35-53% Yes
APC FAP ~99% Yesstomach; pancreas; thyroid;
CNS; hepatoblastoma MLH1
HNPCC
9-12% 20-60% 60-80%
uterine; ovarian; stomach; bladder; brain; ureter; other
MSH2 MSH6 PMS2
EPCAM BMPR1A JPS 9-50% Yes Stomach; otherSMAD4
CancerNext• Gene Sequencing for 22 genes
• Deletion and Duplication Analysis, plus additional 55 genes.
CLINICAL UTILITY
NCCN GuidelinesGene Syndrome Discussed in NCCN
Guidelines?APC Familial adenomatous polyposis Y
MUTYH MUTYH-Associated polyposis YSTK11 Peutz-Jegher syndrome YPTEN Cowden syndrome YTP53 Li-Fraumeni syndrome YMLH1
Lynch Syndrome YMSH2MSH6PMS2
EPCAMBMPR1A Juvenile Polyposis syndrome YSMAD4CDH1 Hereditary Diffuse Gastric Cancer YPALB2 Hereditary Breast/Pancreatic Cancer YATM Hereditary Breast Cancer
CHEK2 Hereditary Breast/Colon/Other Cancer BARD1
Hereditary Breast and/or Ovarian Cancer
BRIP1MRE11A
NBNRAD50
RAD51C
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 (Li-Fraumeni syndrome) and the PTEN gene (Cowden and Bannayan-Riley-Ruvalcaba 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-by-
case 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 HBOCProphylactic 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 HBOCChemoprevention• 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
Variant Rates for Genes Previously Available for sequencing at Ambry
Average chance of a variant by Gene ~5%
Panel GenesPALB2 ▪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
0%
5%
10%
15%
20%
25%
30%
35%
40%
45%
50%
Ambry’s Variant Classification Scheme
• Mutation
• Variant, suspected pathogenic• Variant, unknown significance• Variant, suspected benign
• Polymorphisms
Always included in result report, with interpretation of result, description of gene, and supplementary data
Reported only if requested
Always included in results report with interpretation of result and description of gene
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
• Complementary for pre-approved relatives
VUS Reported Data Example: PALB2 p.P864S c.2590C>T
• First detected in 1/96 BRCA-negative high-risk 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?