45_Section_L _Exhibit_L-9_Sample_Long_Assessment.pdf

TQMC HT9402-15-R-0005 Section L, Exhibit L-9

Section L, Exhibit L-9 Sample Long Assessment, Evolving Practices, Devices, Medicines, Treatments and Procedures

BRCA1 and BRCA2 Gene Testing for Hereditary Breast Cancer (Long Health Technology Assessment)

June 5, 2012

Section L, Exhibit L-9 Sample Long Assessment, Evolving Practices, Devices, Medicines, Treatments and

TABLE OF CONTENTS

Purpose of Technology 6

Executive Summary 6 Key Questions 7 Response to Key Questions 7 Evidence-Based Conclusions 10 Other Considerations 10 Policy Guidance 10

Medical Background 11

Policy Context 13

Description 13

Evaluation of the Clinical Research Evidence 14 Search Strategy and Study Selection Criteria 14 Literature Review 14

Guidelines/Regulatory Status/Coverage Policies 23 Published Formal Technology Assessments 23 Published Reports of National Organizations 23 Regulatory Status 25 Coverage Policies 25

Related Issues 31 Cost 31 Economic Evaluations 31 Social, Legal, or Ethical Issues 31 Future Research 31

References 32

Appendixes 40 Appendix I. Literature Search Strategy Appendix II. Overview of Evidence-Grading Methodology Appendix III. Evidence Tables

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PURPOSE OF THE TECHNOLOGY

Testing of the breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) genes, which is available commercially as BRACAnalysis® and the BRACAnalysis® Rearrangement Test (BART) (Myriad Genetic Laboratories Inc.), is used to identify individuals who have a hereditary predisposition to breast and ovarian cancer. BRCA1/2 gene testing involves direct sequence analysis of coding regions and splice junctions, and potentially testing for large genomic rearrangements in variant-negative patients. Compared with the general population, individuals carrying a pathogenic variant in either the BRCA1 or BRCA2 gene have a significantly increased risk for breast and ovarian cancer, and are more likely to develop other types of malignancies, such as pancreatic and prostate cancer.

EXECUTIVE SUMMARY

It is estimated that approximately 3% to 5% of breast cancer cases are the result of inherited variants in the breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) genes. While pathogenic variants in these genes are relatively uncommon in most populations, occurring in 1 in 300 to 1 in 800 individuals, the effects of these variants are significant. The inheritance of a deleterious BRCA1 or BRCA2 gene variant is associated with a significantly increased risk for breast and ovarian cancer. The estimated lifetime risk of breast cancer may be up to 84% for BRCA1/2 carriers, while the estimated lifetime risk of ovarian cancer could be as high as 62%. BRCA1 carriers also have an increased chance of developing pancreatic, uterine, cervical, or early-onset prostate cancer, while BRCA2 carriers have an increased risk for pancreatic cancer, stomach cancer, melanoma, or early-onset prostate cancer.

The risk for male breast cancer is also elevated, particularly among men with BRCA2 gene variants.

For most individuals, BRCA1/2 gene testing involves a comprehensive analysis of the BRCA1 and BRCA2 genes, including testing for large genomic rearrangements in patients with a negative sequence analysis. However, targeted testing for a specific variant is generally sufficient in cases where a family member has previously tested positive for a variant known to be deleterious. For those of Ashkenazi Jewish descent, testing for the three most common variants in this population is typically performed prior to sequence analysis and rearrangement testing.

Depending on the patient’s personal and family history, she may receive a positive test result, a negative test result, or an uninformative or unclear test result, including the identification of a variant of unknown significance (VUS). To minimize the chance of an uninformative test result, it is recommended that an affected family member be tested before any unaffected family members seek predisposition testing. A variety of tools (e.g. the Couch model, the BRCAPro computer program, the Myriad Prevalence Tables [Myriad Genetic Laboratories Inc.], and the Manchester Scoring System) have been developed to determine the chance a deleterious variant will be detected in a given patient and to identify those most appropriate for testing.

For individuals who are found to carry a pathogenic BRCA1 or BRCA2 gene variant, options for disease surveillance and cancer prevention are available. For women, surveillance programs may involve regular self-examination and clinical breast examinations, annual mammograms, magnetic resonance imaging (MRI) of the breast, and screening for ovarian cancer using transvaginal ultrasounds and cancer antigen 125 (CA-125) measurements.

Prophylactic mastectomy and bilateral salpingo-oophorectomy are also available to minimize the chance of future breast and ovarian cancers. In addition, patients may be candidates for chemoprevention using tamoxifen. For carrier men, monitoring includes self-examination and clinical breast examinations, mammography if breast tissue

Section L, Exhibit L-9 Sample Long Assessment, Evolving Practices, Devices, Medicines, Treatments and is present, and screening for prostate cancer by digital rectal examination and prostate-specific antigen (PSA) testing.

Key Questions

The TRICARE MANAGEMENT AUTHORITY (TMA) has requested that this report address the following questions:

Does the published, peer-reviewed medical literature support a conclusion that the laboratory developed tests for BRCA1/2 are proven safe and effective? What patients should be offered BRCA1 and BRCA2 testing?

Therefore, this report addresses the following key questions:

1. What is the analytical validity of the methods used in BRCA1 and BRCA2 gene testing?

2. What is the clinical validity of BRCA1 and BRCA2 gene testing?

3. What are main limitations of BRCA1 and BRCA2 gene testing?

4. Is there demonstrated clinical utility for BRCA1 and BRCA2 gene testing in the diagnostic evaluation of breast cancer patients, or for risk estimation or medical management in asymptomatic individuals?

5. What are the most appropriate patient populations for BRCA1 and BRCA2 gene testing?

Response to Key Questions

Evidence for this report was obtained from a search of the MEDLINE and Embase databases spanning January 2007 to April 2012. After a preliminary review of the initial 641 references, 113 articles were evaluated in detail, and 37 articles (Appendix III, Tables 1-5) were considered in this assessment. The articles included in this assessment examined various aspects of the analytical validity, clinical validity, and/or clinical utility of BRCA1 and BRCA2 gene testing for breast cancer.

Analytical Validity

Due to patent restrictions, very little information is available regarding the analytical validity of BRCA1 and BRCA2 sequence analysis and rearrangement testing. The laboratory that offers BRCA1/2 gene testing on a clinical basis reports a sensitivity and specificity of > 99% for both tests, although published data demonstrating this performance is not available. A single quality assessment study evaluating the performance of BRCA1/2 gene testing in as many as 50 laboratories per year over 3 years, reported a false-negative rate of 3%, but this included other methodologies in addition to direct sequence analysis.

Clinical Validity

Recent studies indicate that the diagnostic yield of BRCA1/2 gene testing varies depending on the population being tested. The majority of recent studies found that between 14.5% and 33% of individuals considered high risk for hereditary breast and ovarian cancer carried deleterious variants in the BRCA1 or BRCA2 gene. The prevalence of large genomic rearrangements specifically was up to 5.9% in high-risk patient populations. For males with breast cancer, the prevalence of clinically relevant BRCA1 and BRCA2 gene variants was approximately 9%, although a smaller study, which did not meet the criteria for consideration in this assessment, found that 37% of

Section L, Exhibit L-9 Sample Long Assessment, Evolving Practices, Devices, Medicines, Treatments and male breast cancer patients (many of whom had a significant family history) were BRCA1/2 carriers. For high-risk women with triple negative breast cancer, the frequency of pathogenic BRCA1 variants ranged from 20.1% to 41.4%. For women with carcinoma in situ, the data suggest that the prevalence of pathogenic BRCA1 or BRCA2 gene variants is approximately 5.9%, although it may be higher for women diagnosed before age 50 or who have a significant family history of breast or ovarian cancer.

The risk of cancer for individuals found to carry deleterious variants in BRCA1 or BRCA2 is variable and likely depends on a patient’s personal and family histories, and on the specific variant he/she carries. Recent studies report that the risk of breast cancer to age 70 was up to 68% for BRCA1 carriers and up to 75% for BRCA2 carriers.

The risk of ovarian cancer to age 70 was up to 60% for BRCA1 carriers and up to 30% for BRCA2 carriers. For male BRCA2 carriers, the risk of breast cancer to age 70 was 7.1%. A single study evaluating the risk of cancer in an individual with a VUS found that the risk of cancer for the female first-degree relatives of a VUS carrier was lower than for those of someone with a known deleterious BRCA1/2 gene variant (16.2% versus 40.2%) and was not significantly different than the risk for the relatives of noncarriers.

Test Limitations

One of the main limitations of BRCA1/2 gene testing is the identification of VUS. In recent studies, such variants were found in 4.4% to 8% of patients with a high risk of hereditary breast and ovarian cancer based on personal and/or family history. VUS may eventually be reclassified as deleterious or benign; however, some remain unclassified despite the use of multiple methods to assess potential pathogenicity.

Clinical Utility

The majority of recent studies regarding the medical management options for BRCA1/2 carriers indicate that up to 27% of women with a clinically relevant variant elect to have a risk-reducing mastectomy, up to 55% elect to have a risk-reducing salpingo-oophorectomy, and up to 17% use chemoprevention to reduce their risk of breast cancer.

More than 80% of women who choose not to have mastectomy undergo regular surveillance with mammograms with or without breast MRI, while approximately half of BRCA1/2 carriers with intact ovaries are screened for ovarian cancer with transvaginal ultrasound and/or CA-125 levels. Although less common, some women with uninformative test results or variants of unknown clinical significance elect to have prophylactic surgery to reduce their risk (up to 10.3% for mastectomy and up to 20.6% for salpingo-oophorectomy). Factors that appear to play a role in a woman’s choice of management options include age, how recently she was diagnosed, family history, and concerns with fertility, sexuality, appearance, and early menopause. Recent studies assessing the medical management of male BRCA1/2 carriers were not identified.

For those that opt for prophylactic surgery, the risk of breast and/or ovarian cancer is significantly reduced. The majority of studies evaluating the effect of risk-reducing mastectomy among BRCA1/2 carriers show that < 1% of women were diagnosed with breast cancer after the procedure. Up to 1.1% of carriers who had risk-reducing salpingo-oophorectomy were diagnosed with primary peritoneal cancer after the procedure, and up to 1.3% were diagnosed with cancer of the fallopian tubes. In addition to reducing the risk of ovarian cancer, prophylactic salpingo-oophorectomy decreases the risk for breast cancer in BRCA1/2 carriers, and has been shown to reduce both ovarian cancer-specific and breast cancer-specific mortality.

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For women who choose not to have prophylactic surgery, recent data indicate that screening with MRI may be more beneficial than screening with mammography and clinical breast examinations alone. The incidence of advanced stage breast cancer was significantly decreased for those screened with MRI (hazard ratio [HR] 0.030;

P=0.02), compared with those who were not screened. In addition, the average size of the tumors detected by MRI (0.9 centimeters [cm]) was significantly smaller than for mammography and clinical breast examination (1.8 cm; P<0.001 for the difference).

The use of tamoxifen for chemoprevention is another option for those who elect not to have mastectomy.

Tamoxifen has previously been shown to reduce the risk of breast cancer in BRCA1/2 carriers. A recent study of more than 2000 women with breast cancer reported a reduction in contralateral breast cancer among BRCA1/2 carriers who received tamoxifen (n=27); however, the reduction in risk was not statistically significant, likely due to the small number of treated carriers. Additional studies evaluating the use of tamoxifen in women with clinically significant BRCA1/2 gene variants, including those who have no previous history of cancer, may further clarify the effect of this treatment on breast cancer risk.

Considering the treatment of BRCA1/2 carriers with breast cancer, recent data suggest that patients with clinically relevant BRCA1 or BRCA2 gene variants may be more likely to respond to certain chemotherapy regimens, such as those containing anthracycline, compared with noncarriers. However, the evidence is based on a small number of patients and needs to be replicated in large, prospective clinical trials.

Appropriate Candidates for BRCA1 and BRCA2 Gene Testing

Numerous studies that examined BRCA1/2 gene testing in a variety of patient populations found that genetic testing may be appropriate for patients with breast cancer diagnosed at an early age (before age 45); epithelial ovarian cancer at any age; multiple primary tumors (i.e., bilateral breast cancer or both breast and ovarian cancer); triple negative breast cancer (especially in the context of an early diagnosis or a relevant family history);

or male breast cancer. In addition, individuals with or without a personal history of cancer, who have a significant family history of BRCA1/2-related malignancies, such as breast, ovarian, and pancreatic, are strong candidates for BRCA1/2 gene testing, particularly when affected family members are first-degree relatives and one or more are diagnosed before age 50.

Quality of Evidence

A moderate level of fair- to good-quality evidence supports the clinical validity and clinical utility of BRCA1/2 gene testing. This evidence confirms a significantly increased risk for breast and ovarian cancer among BRCA1/2 carriers and shows that there are variety of effective options for reducing this risk or detecting early-stage malignancies, all of which are used by some proportion of BRCA1/2 carriers. The published evidence regarding the analytical validity of BRCA1/2 gene testing is extremely limited, although direct sequence analysis is generally considered the reference standard against which all other methods are compared. In addition, testing is performed in a laboratory with current Clinical Laboratory Improvement Amendments certification.

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Evidence-Based Conclusions

The available evidence suggests that BRCA1/2 gene testing provides valuable information for individuals considered at high risk for hereditary breast and ovarian cancer, based on personal and/or family history.

Specifically, the analysis may be beneficial in providing a more accurate cancer risk assessment, allowing for primary cancer prevention through prophylactic surgery, and allowing for more aggressive cancer screening or chemoprevention for carriers who elect not to have surgery.

Other Considerations

Current policies for five major payers indicate that BRCA1/2 gene testing is likely to be covered for individuals considered at high risk for hereditary breast and ovarian cancer. While the testing criteria outlined by each policy may vary, they generally follow the recommendations set forth by the National Comprehensive Cancer Network (NCCN). Recommendations provided by multiple national medical associations, such as the American Society of Clinical Oncology (ASCO) and the American College of Obstetricians and Gynecologists (ACOGB), are generally consistent with payer policies and the NCCN recommendations.

Policy Guidance

The current, peer-reviewed medical literature indicates that BRCA1/2 gene testing is beneficial for individuals with a personal and/or family history consistent with hereditary breast and ovarian cancer. The literature also demonstrates that BRCA1/2 gene testing may influence medical management and has the potential to improve patient outcomes. As such, policy modifications identifying patient selection criteria may be warranted.

The guidelines and recommendations provided by the NCCN are likely to limit testing to the most appropriate patient populations. These include individuals with early-onset breast cancer, epithelial ovarian cancer, multiple primary tumors (i.e., bilateral breast cancer or breast or ovarian cancer in the same individual), male breast cancer, or an ethnic background associated with a high prevalence of BRCA1/2 variants, as well as affected or unaffected individuals with a strong family history of BRCA1/2-related malignancies. A coverage policy based on NCCN guidelines would be reasonable.

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MEDICAL BACKGROUND

Heritable forms of breast cancer are estimated to account for 5% to 10% of all breast cancer cases, with approximately 3% to 5% resulting from deleterious variants in the breast cancer gene 1 (BRCA1) and breast cancer gene 2 (BRCA2) (ACOG, 2009; NCCN, 2012). Among individuals in the general population, it is estimated that 1 in 300 to 1 in 800 carry a deleterious variant involving either BRCA1 or BRCA2. In specific ethnic groups, the prevalence of BRCA1/2 variants may be much higher, such as 1 in 40 for individuals of Ashkenazi Jewish descent (Berliner and Fay, 2007; ACOG, 2009).

BRCA1 (located on chromosome 17 at band q21) and BRCA2 (located on chromosome 13 at band q12.3) are considered tumor suppressor genes; their protein products are believed to function in the DNA repair process (Berliner and Fay, 2007). The inheritance of one pathogenic BRCA1 or BRCA2 allele leads to a significantly increased risk for breast and ovarian cancers. Estimates of penetrance vary by study, with a lifetime risk of breast cancer ranging from 45% to 84% and a lifetime risk of ovarian cancer ranging from 11% to 62% (Petrucelli et al., 2010; NCCN, 2012). Breast cancers diagnosed in BRCA1 carriers are often high-grade infiltrating ductal carcinomas that are triple negative (i.e., negative for estrogen receptor [ER], progesterone receptor [PR], and human epidermal growth factor receptor 2 [HER2]) (Palma et al., 2006; Petrucelli et al., 2010). In contrast, breast cancers diagnosed in BRCA2 carriers are frequently medium-grade ductal carcinomas that are ER-positive. Ovarian cancers diagnosed in BRCA1/2 carriers are typically epithelial carcinomas (serous or endometrioid) (ACOG, 2009; Petrucelli et al., 2010). In addition to breast and ovarian cancer, primary peritoneal and fallopian tube cancers are considered part of the cancer spectrum in women with clinically relevant BRCA1/2 gene variants (Palma et al., 2006; ACOG, 2009).

BRCA1 and BRCA2 gene variants have also been associated with an increased risk for other malignancies, including pancreatic, uterine, and cervical cancer for women with BRCA1 gene variants and pancreatic cancer, stomach cancer, and melanoma for women with BRCA2 gene variants (Petrucelli et al., 2010; NCCN, 2012). Men harboring deleterious BRCA1 gene variants may have an increased risk of breast cancer, pancreatic cancer, and early-onset prostate cancer; however, the chance of developing one of these malignancies appears to be higher for men with BRCA2 gene variants (NCCN, 2012).

BRCA1/2 gene testing may take on several forms. For most individuals, testing involves direct sequence analysis of the BRCA1 and BRCA2 coding regions and intron-exon junctions, and testing for large genomic rearrangements in those who are negative for a sequence variant (Daly et al., 2010; Myriad Genetic Laboratories Inc., 2012a; Myriad Genetic Laboratories Inc., 2012b). For individuals from families transmitting a known pathogenic BRCA1 or BRCA2 gene variant, testing specifically for the familial variant is typically sufficient (ACOG, 2009). For those of Ashkenazi Jewish descent, testing for three specific variants common in this population (c.68_69delAG [commonly referred to as 187delAG] and c.5266dupC [commonly referred to as 5385insC] in BRCA1 and c.5947delT [commonly referred to as 6174delT] in BRCA2) is typically performed prior to sequence analysis and rearrangement testing.

The possible outcomes of BRCA1/2 gene testing include a positive test result (the identification of a variant known to be deleterious); a negative test result (no deleterious variant identified); or the identification of a variant of unknown clinical significance (VUS). The interpretation of a specific BRCA1/2 gene test result may depend on the patient’s history (Palma et al., 2006; Berliner and Fay, 2007; ACOG, 2009; Petrucelli et al., 2010). For example, a negative result for someone whose family is transmitting a known BRCA1/2 gene variant would be considered a

Section L, Exhibit L-9 Sample Long Assessment, Evolving Practices, Devices, Medicines, Treatments and true negative (ACOG, 2009). However, a negative test result in an unaffected individual is considered uninformative when a deleterious variant is not first identified in an affected family member. Because of this possibility, it is recommended that BRCA1/2 gene testing be performed in an affected family member before unaffected family members seek predisposition testing (Berliner and Fay, 2007).

The vast majority of BRCA1/2 gene variants are sequence variants identifiable by direct sequence analysis.

However, a study of more than 2600 high-risk patients referred for clinical BRCA1/2 gene testing found that 2.5% carried 1 of 5 recurrent rearrangements in BRCA1 (Hendrickson et al., 2005). Additional studies indicate that large deletions or duplications in either BRCA1 or BRCA2 may be identified in approximately 3% to 4% of patients considered high-risk for hereditary breast and ovarian cancer (Petrucelli et al., 2010).

The chance of identifying a pathogenic BRCA1 or BRCA2 variant in a given patient depends on several factors, including the individual’s personal and family history of cancer (Petrucelli et al., 2010). Several tools have been developed to determine the probability of detecting a deleterious variant in order to identify the most appropriate patients for testing, although each model has its own advantages and disadvantages (Nelson et al., 2005; Petrucelli et al., 2010). The available models include the Couch model, the BRCAPro computer program, the Myriad prevalence tables, the Manchester Scoring System, the Family History Risk Assessment Tool (FHAT), and the Risk Assessment in Genetics (RAGs) program (Nelson et al., 2005; Palma et al., 2006; Berliner and Fay, 2007;

Petrucelli et al., 2010).

In addition, several groups have made recommendations regarding which patients are most suitable for testing.

The National Comprehensive Cancer Network (NCCN) recommends that BRCA1 and BRCA2 gene testing be considered in the following:

• Individuals from families transmitting a known BRCA1/2 variant

• Individuals with a history breast cancer and at least one of the following:

o Breast cancer diagnosed ≤ 45 years of age o Breast cancer diagnosed ≤ 50 years of age and a close family member with breast cancer ≤ 45 years of age or ovarian cancer at any age o Two breast primaries with one diagnosed at or before age 50 o A diagnosis of triple negative breast cancer at or before age 60 o Breast cancer diagnosed at any age and at least two close relatives with breast and/or ovarian cancer o Breast cancer diagnosed at any age and at least two close relatives diagnosed with pancreatic cancer o A close male relative with breast cancer o An ethnic background associated with a higher frequency of BRCA1/2 variants (i.e., Ashkenazi

Jewish)

• Individuals with a personal history of epithelial ovarian cancer

• Individuals with male breast cancer

• Individuals with a personal history of pancreatic cancer and at least two close relatives with breast, ovarian, and/or pancreatic cancer

• Unaffected individuals (with no personal history of cancer) who have one of the following:

o A first- or second-degree relative satisfying the above criteria

Section L, Exhibit L-9 Sample Long Assessment, Evolving Practices, Devices, Medicines, Treatments and o A third-degree relative with breast and/or ovarian cancer and at least 2 more relatives with breast cancer (at least one diagnosed before age 50) and/or ovarian cancer (NCCN, 2012)

Women who are found to carry a pathogenic BRCA1 or BRCA2 gene variant have several options for medical management (Daly et al., 2010; Petrucelli et al., 2010; NCCN, 2012). Extensive surveillance programs, aimed at detecting breast and ovarian cancers at the earliest stage possible, typically involve regular self-examination and clinical breast examinations, annual mammograms, magnetic resonance imaging (MRI) of the breast, transvaginal ultrasounds, and measurements of cancer antigen (CA-125) levels (Daly et al., 2010; Petrucelli et al., 2010; NCCN, 2012). Prophylactic surgeries are also available to minimize the chance of future breast and ovarian cancers.

Prophylactic mastectomy is estimated to decrease the risk of breast cancer by 90%, while bilateral salpingo-oophorectomy is estimated to decrease the risk of ovarian cancer by 80% to 96% and the risk of breast cancer by 53% to 68% (Klaren et al., 2003; Rebbeck et al., 2004; van Sprundel et al., 2005; Guillem et al., 2006; Palma et al., 2006; Berliner and Fay, 2007). In addition, patients may be candidates for chemoprevention; the selective estrogen receptor modulator tamoxifen has been shown to decrease the risk of breast cancer by up to 50% (Guillem et al., 2006; Palma et al., 2006; Berliner and Fay, 2007). For men carrying BRCA1/2 gene variants, surveillance includes self-examination and clinical breast examinations, mammography if breast tissue is present, and screening for prostate cancer by digital rectal examination and prostate-specific antigen (PSA) testing (Petrucelli et al., 2010). Specific recommendations regarding the surveillance of BRCA1/2 carriers, such as when to initiate screening and how frequently a given test should be performed, are provided by the NCCN (Daly et al., 2010; NCCN, 2012).

Given the complexity of risk assessment and test interpretation, as well as the importance of adequate medical management, genetic counseling is recommended for all individuals with or at risk of carrying a deleterious BRCA1 or BRCA2 gene variant (ASCO, 2003; Berliner and Fay, 2007; Robson et al., 2010). For any individual found to carry a BRCA1 or BRCA2 gene variant, the recurrence risk for siblings and offspring is 50% (Petrucelli et al., 2010; NCBI, 2012).

POLICY CONTEXT

Food and Drug Administration (FDA) approval is currently a requirement for coverage of any laboratory-determined test under TRICARE. The TRICARE MANAGEMENT AUTHORITY (TMA) has initiated a demonstration project to determine the utility of a variety of genetic tests that are currently not covered under TRICARE due to the lack of FDA approval.

DESCRIPTION

Testing of the breast cancer 1 (BRCA1) and the breast cancer 2 (BRCA2) genesis available commercially as BRACAnalysis and involves the direct sequence analysis of BRCA1 and BRCA2 coding regions and splice junctions (Myriad Genetic Laboratories Inc., 2012a). The BRACAnalysis Rearrangement Test (BART), typically performed in patients negative for gene variants detectable by sequence analysis, utilizes quantitative polymerase chain reaction or array comparative genomic hybridization (aCGH) to identify large deletions and duplications in the BRCA1 and BRCA2 genes (Myriad Genetic Laboratories Inc., 2012b). Targeted testing for Ashkenazi Jewish individuals uses direct sequence analysis to test for the three most common founder variants: c.68_69delAG

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(187delAG) and c.5266dupC (5385insC) in BRCA1 and c.5947delT (6174delT) in BRCA2 (Myriad Genetic Laboratories Inc., 2012a).

EVALUATION OF THE CLINICAL RESEARCH EVIDENCE

Search Strategy and Study Selection Criteria

Evidence evaluated for this report was obtained by searching the peer-reviewed medical literature in the MEDLINE and Embase databases spanning January 2007 to April 2012. For both databases, the title field was searched using the terms (BRCA1 OR BRCA2) AND (mutation OR variant OR polymorphism OR rearrangement), while the keyword field was searched using the term breast cancer AND (validity OR utility OR screening OR genetic). After limiting to English language and human subjects, this search yielded 641 citations. Studies were selected for detailed review if they were published in the peer-reviewed literature and evaluated the analytical validity, clinical validity, or clinical utility of BRCA1/2 gene testing.

Literature Review

Analytical Validity

Because of patent restrictions, clinical breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) gene testing is available only through Myriad Genetic Laboratories (Myriad Genetic Laboratories Inc., 2012a). According to the information provided in their Technical Specifications, the sensitivity, specificity, and overall test accuracy of BRCA1/2 gene sequencing are all greater than 99% (Myriad Genetic Laboratories Inc., 2012a). The reported sensitivity and specificity of BRCA1/2 rearrangement testing are also greater than 99% (Myriad Genetic Laboratories Inc., 2012b). Of 313 test samples used to validate the test for rearrangements, 37 were found to carry large rearrangements by both quantitative polymerase chain reaction (PCR) and array comparative genomic hybridization (aCGH). Additional details regarding the data from which the above figures were derived are not provided, and no published studies regarding the performance of BRACAnalysis or BART are available (Myriad Genetic Laboratories, 2012a; Myriad Genetic Laboratories Inc., 2012b).

Relevant published data regarding the analytical validity of BRCA1/2 gene testing are limited to an external quality assessment performed by the European Molecular Genetics Quality Network (Appendix III, Table 1) (Mueller et al., 2004). However, the laboratories participating in this study (as many as 50 laboratories per year over 3 years) used a variety of methods for detecting BRCA1/2 gene variants, including direct sequence analysis, denaturing high performance liquid chromatography (dHPLC), denaturing gradient gel electrophoresis (DGGE), and protein truncation testing (PTT). Since the study evaluated the diagnostic performance of the BRCA1/2 gene testing regardless of the methods used, specific data regarding direct sequence analysis of BRCA1 and BRCA2 were not available. Overall, the study found 17 of 297 (5.6%) cases analyzed over 3 years resulted in diagnostic errors. Nine of the 17 (3% overall) were cases in which a deleterious variant was missed (false-negative). The remaining errors were errors in reporting observed sequence changes or in interpreting the test results (Mueller et al., 2004).

No studies that specifically evaluate the analytical validity of BRCA1/2 gene sequencing were identified. In addition, no published data regarding the analytical validity of BRCA1/2 rearrangement testing were identified.

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Clinical Validity

Prevalence of BRCA1 and BRCA2 Gene Variants in High-Risk Populations

Numerous studies evaluated the diagnostic yield of BRCA1/2 gene testing, examining what percentage of patients considered high risk for hereditary breast and ovarian cancer are found to carry deleterious variants in one of these genes. Studies selected for this assessment included those that were published since January 2007, involved at least 200 index patients, and utilized direct sequence analysis to identify sequence variants and/or tested for large genomic rearrangements in one or both genes (Appendix III, Table 2). The selected studies were primarily retrospective analyses of clinic-based study populations, although two were retrospective, cross-sectional analyses of subpopulations tested at Myriad Genetics Laboratories (Simard et al., 2007; Palma et al., 2008; Haffty et al., 2009; Hall et al., 2009; Hansen et al., 2009; Seong et al., 2009; del Valle et al., 2010; Hall et al., 2010; Kang et al., 2010; Ticha et al., 2010; Zhang et al., 2010; Bayraktar et al., 2011; Robertson et al., 2012). The precise inclusion and exclusion criteria differed for each study, although all were designed to evaluate individuals with an increased chance of carrying a deleterious BRCA1 or BRCA2 gene variant, based on personal and/or family history.

Recent studies show that 14.5% to 33% of individuals with a personal or family history suggestive of hereditary breast and ovarian cancer have identifiable pathogenic variants in BRCA1 or BRCA2 (Simard et al., 2007; Palma et al., 2008; Haffty et al., 2009; Hansen et al., 2009; Seong et al., 2009; Kang et al., 2010). In addition, a study of more than 46,000 non-Ashkenazi Jewish individuals referred for testing at Myriad Genetic Laboratories (approximately 40,000 of whom were considered high-risk based on personal or family history) identified deleterious BRCA1 or BRCA2 gene variants in 12.5% of cases (Hall et al., 2009). The majority of studies that included testing for large rearrangements involving BRCA1 or BRCA2 indicate that between 0.9% and 5.9% of high-risk patients carry a large deletion or duplication in one of these genes (most often in BRCA1) (Palma et al., 2008;

Hansen et al., 2009; del Valle et al., 2010; Kang et al., 2010; Ticha et al., 2010;).

Studies evaluating the prevalence of BRCA1 and BRCA2 gene variants in specific patient populations revealed that BRCA1 gene variants are much more common among individuals with triple negative breast cancer (i.e., negative for estrogen receptor [ER], progesterone receptor [PR], and human epidermal growth factor receptor 2 [HER2] ) (Bayraktar et al., 2011). One study reported that 50% of women with triple negative breast cancer, who were considered high-risk for hereditary breast and ovarian cancer based on an early age at diagnosis or a significant family history, carried pathogenic BRCA1/2 gene variants, with approximately 82% of these variants occurring in BRCA1 (94/227; 41.4% for the frequency of BRCA1 variants specifically) (Bayraktar et al., 2011). A second study examining BRCA1 specifically reported an overall prevalence of 14% for patients with triple negative breast cancer, but 20.1% for those with early-onset disease or a family history of breast/ovarian cancer (Robertson et al., 2012).

Among 7295 non-Ashkenazi Jewish women diagnosed with ductal carcinoma in situ (DCIS) or lobular carcinoma in situ (LCIS), more than 700 of whom had no personal or family history of breast or ovarian cancer, the frequency of deleterious BRCA1 or BRCA2 gene variants was 5.9%, with another 5.2% of women receiving a result of variant of unknown significance (VUS) (Hall et al., 2010). A second smaller study involving 118 women with DCIS and a high risk of hereditary breast and ovarian cancer (based on family history or a diagnosis at or before age 50) identified

Section L, Exhibit L-9 Sample Long Assessment, Evolving Practices, Devices, Medicines, Treatments and pathogenic BRCA1/2 variants in 27% of patients (Bayraktar et al., 2012). In this study, the best predictors of a positive gene test were having at least 2 family members with a history of ovarian cancer or a BRCAPro probability of at least 10%.

The reported prevalence of BRCA1/2 gene variants among male breast cancer patients is also variable, and likely related to a patient’s personal and family history. A recent study that investigated the role of BRCA1/2 gene variants in male breast cancer cases (using single-stranded conformation polymorphism analysis and protein truncation testing) found that 10 of 108 (9.3%) affected men carried deleterious variants in BRCA1 (2/108; 1.9%) or BRCA2 (8/108; 7.4%) (Ottini et al., 2009). Similar to this study, an earlier examination of unselected male breast cancer cases reported that 12 of 154 (7.8%) affected men had identifiable BRCA2 gene variants considered to be pathogenic (Syrjäkoski et al., 2004). A smaller study of 41 male breast cancer patients, 31 of whom had a known family history of female breast cancer, ovarian cancer, prostate cancer, or pancreatic cancer, found that 15 (37%) were BRCA1 or BRCA2 carriers, although none carried large rearrangements (Tchou et al., 2007). A study that specifically examined the frequency of the 3 Ashkenazi Jewish founder variants among Israeli men reported that 12.8% of Ashkenazi Jewish men with breast cancer carried 1 of the 3 variants. The prevalence of the three founder variants among affected non-Ashkenazi Jews was slightly lower at 9.1% (Chodick et al., 2008).

An important limitation of the body of evidence relating to the diagnostic yield of BRCA1/2 gene testing is the use of different inclusion and exclusion criteria (Appendix III, Table 2). Another limitation of many studies examining diagnostic yield is that they did not include testing for large rearrangements in BRCA1 or BRCA2. Despite these limitations, the evidence clearly indicates that a significant proportion of individuals with a personal history of breast and/or ovarian cancer and a strong family history of BRCA1/2-related malignancies will prove to be BRCA1 or BRCA2 carriers.

Risk of Cancer for BRCA1 and BRCA2 Carriers

Relevant studies selected for this assessment were those that involved at least 200 index patients and were published since January 2007 (Appendix III, Table 3). These included four population-based case-control studies, three retrospective cohort studies, and one prospective case series (Begg et al., 2008; Evans et al., 2008; Milne et al., 2008; Evans et al., 2010; Figueiredo et al., 2010; Malone et al., 2010; Møller et al., 2010; Akbari et al., 2011).

A recent meta-analysis of 10 studies published between 1995 and 2006 reported that the lifetime risk (to age 70) of breast cancer was 57% (95% confidence interval [CI], 47-66%) for BRCA1 carriers and 49% (95% CI, 40-57%) for BRCA2 carriers, and that the corresponding risks for ovarian cancer were 40% (95% CI, 35-46%) and 18% (95% CI, 13-23%), respectively (Chen and Parmigiani, 2007). Several more recent studies report variable levels of risk for variant-positive individuals. The first study, which involved more than 300 families, reported that the risk of breast cancer to age 70 was 68% for BRCA1 carriers and 75% for BRCA2 carriers, and that the risk of ovarian cancer to age 70 was 60% for BRCA1 carriers and 30% for BRCA2 carriers (Evans et al., 2008). The second study, which also involved more than 300 families, reported that the risk of breast cancer to age 70 was 52% for BRCA1 carriers and 47% for BRCA2 carriers, and that the risk of ovarian cancer to age 70 was 22% for BRCA1 carriers and 18% for BRCA2 carriers (Milne et al., 2008) A third study involving 649 women reported that the annual incidence of breast or ovarian cancer was 3% for BRCA1 carriers and 2.5% for BRCA2 carriers (Møller et al., 2010). Evans et al.

(2010) specifically evaluated the risk of male breast cancer among men harboring a pathogenic BRCA2 gene

Section L, Exhibit L-9 Sample Long Assessment, Evolving Practices, Devices, Medicines, Treatments and variant. For male BRCA2 carriers, the average cumulative risk for male breast cancer to age 70 was 7.1% (Evans et al., 2010).

Two studies specifically evaluated the risk of contralateral breast cancer among BRCA1/2 carriers diagnosed with unilateral breast cancer. Malone et al. (2010) reported that, compared with noncarriers, the risk of contralateral breast cancer was 4 times greater for any patient with a deleterious BRCA1/2 variant, and 11times greater for carriers diagnosed with breast cancer prior to age 35 (Malone et al., 2010). Figueiredo et al. (2010) found that there was no statistically significant increase in the risk of contralateral breast cancer for BRCA1/2 carriers who have taken oral contraceptives or used hormone replacement therapy after menopause, compared with carriers who have not done so (Figueiredo et al., 2010).

Akbari et al. (2011) evaluated the risk of cancer in carriers of VUS in BRCA1 or BRCA2 by studying the family histories of 32 VUS carriers and 176 carriers of variants known to be deleterious. The risk of breast, ovarian, or fallopian tube cancer was 16.2% for the female first-degree relatives of VUS carriers and 40.2% for the female first-degree relatives of carriers with deleterious BRCA1/2 variants. However, when comparing the cancer risk for the relatives of VUS carriers with that of noncarriers, there was no statistically significant difference (hazard ration [HR] 1.62; 95% CI, 0.83-3.16) (Akbari et al., 2011).

The studies discussed in this section indicate a variable degree of cancer risk for BRCA1/2 carriers. This suggests that while it is clear the risk of breast and ovarian cancer is increased significantly for BRCA1/2 carriers, the precise risk for a given patient may depend on other factors, such as the person’s family history or the specific variant he/she carries. Supporting this theory, one study showed that the lifetime risk of breast cancer was higher for the relatives of BRCA1/2 carriers who have a history of bilateral breast cancer (48% for BRCA1 carriers; 59% for BRCA2 carriers) than it was for the relatives of carriers with a history of unilateral breast cancer (36% for BRCA1 carriers; 47% for BRCA2 carriers) (Begg et al., 2008). Another study reported that the risk of breast cancer to age 70 for patients with a specific Spanish founder variant in BRCA1 (c.330A>G) was 27%, compared with 52% for carriers of any pathogenic BRCA1 gene variant (Milne et al., 2008).

Two important limitations pertain to some of the above studies of cancer risk (Appendix III, Table 3). These include the acquisition of data (i.e., cancer history) through patient interview without confirmation from a second source in three studies and the retrospective and/or observational design of five studies. However, the available evidence is consistent with earlier findings and confirms a significantly increased risk for breast and ovarian cancer in BRCA1/2 carriers.

Test Limitations

A significant concern related to BRCA1/2 gene sequencing is the identification of VUS. The majority of recent studies that reported the frequency of VUS indicate that 4.4% to 8% of tested individuals carry such a variant (Simard et al., 2007; Palma et al., 2008; Haffty et al., 2009; Hall et al., 2009; Seong et al., 2009). As additional information becomes available, some VUS’s are reclassified as either pathogenic or benign. Others remain classified as a VUS (Murray et al., 2011).

Section L, Exhibit L-9 Sample Long Assessment, Evolving Practices, Devices, Medicines, Treatments and

A number of methods for classifying each VUS have been evaluated. Easton et al. (2007) examined the clinical significance of 1433 different BRCA1/2 variants considered unclassified. A combined likelihood ratio, which was based on the co-occurrence of a VUS with a deleterious variant, the personal or family history of the proband, and the co-segregation of a VUS with disease in a pedigree, was used to evaluate each VUS. A total of 133 variants had odds of at least 100:1 in favor of being benign, and 43 had odds of at least 20:1 in favor of being pathogenic (Easton et al., 2007). Lee et al. (2008) identified 147 VUS’s among 1467 female breast cancer patients. Five different methods were used to evaluate the likelihood of a VUS being neutral or deleterious: (1) allele frequency;

(2) the Polyphen algorithm (classifies missense variants as probably damaging, possibly damaging, or benign); (3) sequence conservation; (4) Grantham matrix score (measures the degree of amino acid substitution); and (5) a combination of Grantham matrix score and sequence conservation. All five methods yielded similar results regarding VUS classification and indicated that they may be more successful at classifying BRCA1 VUS than BRCA2 VUS (Lee et al., 2008). Similar to the previous studies, Spearman et al. (2008) developed and evaluated a model for classifying VUS. This model, which was based on co-occurrence of a VUS with a deleterious variant, sequence conservation, location within the gene, effect on splicing as predicted by two different programs, loss of heterozygosity in breast tumor cells, and tumor histopathology, had a sensitivity of 98% and a specificity of 76%, when used to evaluate 54 VUS and 43 BRCA1/ BRCA 2 variants known to be deleterious (Spearman et al., 2008).

Clinical Utility

Impact of BRCA1/2 Gene Testing on Medical Management

Numerous studies investigated the medical management options for BRCA1/2 carriers, including the uptake of prophylactic surgery, chemoprevention, and disease surveillance. Studies selected for this assessment included those that were published since January 2007 and involved at least 100 BRCA1/2-positive index patients, although the inclusion and exclusion criteria varied for each study (Appendix III, Table 4). Five retrospective analyses of patient choices and three prospective studies of elected procedures or treatments were included (Friebel et al., 2007; Gronwald et al., 2007; Metcalfe et al., 2008; Staton et al., 2008; Julian-Reynier et al., 2011; Murray et al., 2011; Schwartz et al., 2012; Sidon et al., 2012).

Recent studies examining the uptake of prophylactic mastectomy among those with deleterious BRCA1/2 gene variants report variable results, although all report that mastectomy is elected by some percentage of variant-positive patients. The frequency of prophylactic mastectomy among carriers with no personal history of breast cancer ranged from 7% to 21% (Friebel et al., 2007; Julian-Reynier et al., 2011). Among a population of women who had a personal history of breast cancer, 27.3% elected to have a contralateral prophylactic mastectomy (Metcalfe et al., 2008). The frequency of prophylactic mastectomy (bilateral or contralateral) among populations, including patients both with and without a previous history of breast cancer, ranged from 5% to 43.9% (Gronwald et al., 2007; Staton et al., 2008; Schwartz et al., 2012).

The uptake of risk-reducing mastectomy has been found to correlate with a younger age at diagnosis and a more recent diagnosis (Metcalfe et al., 2008; Schwartz et al., 2012). In addition, a survey of BRCA1/2 carriers indicated that factors likely to influence a patient’s choice to have mastectomy include their perceived cancer risk and concerns regarding appearance and/or sexuality (Staton et al., 2008). For carriers who have been diagnosed with breast cancer, prophylactic contralateral mastectomy was less likely among those who initially had breast-

Section L, Exhibit L-9 Sample Long Assessment, Evolving Practices, Devices, Medicines, Treatments and conserving therapy, and more likely among those who were younger at diagnosis (Metcalfe et al., 2008). Another factor that could explain the variability in uptake reported by the above studies is the method of subject recruitment. The study reporting the highest uptake (43.9%) involved a recruitment strategy that differed from all other studies (i.e., recruitment from an online advocacy organization) and could be associated with ascertainment biases (Staton et al., 2008).

Interestingly, two studies reported that prophylactic mastectomy was also chosen by some patients without clearly pathogenic BRCA1/2 variants. In one study, the 25.9% of women (77% with a history of breast or ovarian cancer) who elected to have a risk-reducing mastectomy included 14 of 261 (5.4%) patients who received an uninformative test result (Schwartz et al., 2012). In another study, which involved 107 women carrying VUS, 10.3% elected to have prophylactic mastectomy (Murray et al., 2011). A smaller study of 58 women with VUS found that 11% (3/27) of those with a history of breast cancer had a prophylactic contralateral mastectomy after receiving their VUS result; several more had the surgeries prior to genetic testing. In this study, none of the eight women with a history of ovarian cancer and none of the eight women with no history of cancer had risk-reducing mastectomy (Ready et al., 2011).

Recent studies investigating the uptake of risk-reducing salpingo-oophorectomy report that between 28.3% and 55% of women carrying deleterious BRCA1/2 gene variants opted for this prophylactic surgery (Friebel et al., 2007; Gronwald et al., 2007; Staton et al., 2008; Julian-Reynier et al., 2011; Schwartz et al., 2012; Sidon et al., 2012). Prophylactic salpingo-oophorectomy was significantly more common among carriers who were at least 40 years of age, compared with those who were younger (Friebel et al., 2007; Julian-Reynier et al., 2011; Sidon et al., 2012). In addition, the uptake of salpingo-oophorectomy has been correlated with parity, a family history of ovarian cancer, and time since diagnosis (Friebel et al., 2007; Schwartz et al., 2012).