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


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



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



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




Retinoblastoma Retinoblastoma RB1 Familial Adenomatous Polyposis (FAP), Gardner Syndrome, Turcot Syndrome, Attenuated FAP (AFAP) APC Amplified APC



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

http://www.illumina.com/landing/IlmnMkt.aspx?ilmnid=0092011004006

• 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 SyndromeBreast Cancer

RiskOther 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

PALB2Hereditary Breast and

Pancreatic ~25-40% Breast Pancreas

STK11 Peutz-Jegher 30% Colon Pancreas

CHEK2Hereditary Breast and

Colon ~25% Ovarian

PTEN Cowden 25-50% Thyroid; endometrial; renal

TP53 Li-Fraumeni 50%Sarcoma; brain; adrenocortical;

leukemia

CDH1Hereditary Diffuse Gastric

Cancer 39-52% Gastric colon

MUTYHMUTYH-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



RiskOvarian Cancer

RiskUterine

Cancer RiskOther 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%

PALB2Hereditary Breast and

Pancreatic ~25-40% increased Pancreas

STK11 Peutz-Jegher 30% Colon; Pancreas

CHEK2 Hereditary Breast and Colon ~25% Colon

PTEN Cowden 25-50% 5-10% Thyroid; endometrial; renal

TP53 Li-Fraumeni 50%-70% increased increased Sarcoma; brain; adrenocortical; leukemia

CDH1Hereditary Diffuse Gastric

Cancer 0.39 Gastric; colon

MUTYH MUTYH-Associated Polyposis 20-25% Colon

MLH1

Lynch ?? 9-12% 20-60% colon; stomach; other

MSH2

MSH6

PMS2

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 SyndromeColon Cancer

RiskPolyposis Other Associated Cancer

STK11 Peutz-Jegher 57-81% Yes breast, uterine; testicular; cervical; lung; pancreas

CDH1Hereditary Diffuse

Gastric Cancer Increased stomach; breast; colorectum

CHEK2Hereditary 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% Yesstomach; pancreas; thyroid; CNS;

hepatoblastoma

MLH1

HNPCC 60-80%uterine; ovarian; stomach; bladder; brain;

ureter; other

MSH2

MSH6

PMS2

EPCAM

BMPR1AJPS 9-50% Yes stomach; other

SMAD4

• Gene Sequencing for all 14 genes


“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 Accident

2 polyps 39

64 y

Leukemia dx 11

Colon ca dx 51

Lobular breast ca dx 32;

2 polyps, 34y

“GI” ca dx 45


RiskOvarian

Cancer RiskUterine Cancer

RiskColon Cancer

RiskPolypos

isOther Associated

CancerBARD1 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,

lymphomaPALB2 Her. Breast/Panc ~25-40% Increased pancreaticCDH1 Her. Diffuse Gastric Ca 39% gastric

STK11 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; renal

TP53 Li-Fraumeni 50%-70% Increased Increased Increasedsarcoma; brain;

adrenocortical; leukemiaMUTYH MUTYH-Assoc Polyposis 20-25% 35-53% Yes

APC FAP ~99%Yes

stomach; 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

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

http://ambrygen.com/sites/default/files/pdfs/cancer%20forms/CancerTestReqForm1.pdf

http://ambrygen.com/sites/default/files/pdfs/forms/Cancer_Family-Studies-form.pdf

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?

hereditary cancer testing panels

Documents

gardner syndrome

turcot syndrome

cowden syndrome

proteus syndrome

ruvalcaba syndrome

dysplasia syndrome

men2a sipple syndrome

men2b mucosal neuroma