This document addresses gene-based tests for the screening, detection and management of prostate cancer. Gene-based tests for the screening, detection and management of prostate cancer include, but are not limited to, gene hypermethylation, multiple gene tests (gene panels), prostate cancer antigen gene-3 (PCA3 [formerly known as DD3]), single-nucleotide polymorphisms (SNPs), and TMPRSS fusion genes.

Investigational and Not Medically Necessary: 

Gene-based tests for the screening, detection and management of prostate cancer are considered investigational and not medically necessary.

There has been a variety of research surrounding gene-based tests for the screening, detection and management of prostate cancer. Some products of this work have already been translated or are in the process of being translated into commercially available tests. These tests are currently without evidence of clinical utility for diagnosis, prognosis, or risk assessment. The National Comprehensive Cancer Network^® (NCCN) and the National Cancer Institute (NCI) do not include the use of gene-based tests for the screening or management of prostate cancer. Currently, the prostate specific antigen (PSA) test has been utilized along with digital rectal exams (DRE) to detect and manage prostate cancer.

Gene hypermethylation for diagnosis and prognosis

The association of a gene hypermethylation marker, GSTP1, with prostate cancer has been investigated. Several studies of GSTP1 hypermethylation using tissue samples reported significant results for identifying prostate cancer with a sensitivity of 92%, a percent specificity of 85%, and an area under curve (AUC) of about 0.9 (Eilers, 2007; Ellinger, 2008). However, two other studies did not find significant associations with disease (Henrique, 2007; Woodson, 2006). The published literature demonstrates conflicting results surrounding the association of GSTP1 with prostate cancer.

Gene panels for prostate cancer diagnosis

Because no single gene markers have been found that are both highly sensitive and highly specific for diagnosing prostate cancer, particularly in men already known to have elevated PSA levels, some investigators are combining several markers into a single diagnostic panel. While the concept may be promising, only single studies of various panels have been published.

In 2009, Clarient, Inc., Aliso Viejo, CA launched a "patent protected combination of four genes that have been shown to accurately identify the presence of Grade 3 or higher" prostate cancer in prostate tissue. This test is reportedly based on a study that has been submitted for publication but is not yet accepted or available for evaluation.

PCA3 for disease diagnosis

PCA3, a prostate cancer antigen gene, has been investigated as a possible additional tool in the detection of prostate cancer. The PCA3 gene (formerly known as DD3) is markedly upregulated in cancerous prostate cells and is not expressed, or expressed only at very low levels in normal or hyperplastic prostatic tissue. The identification of the PCA gene relies on detection of the overexpression of the associated messenger ribonucleic acid (mRNA) in blood or urine after a digital rectal examination.

A small non-randomized trial (Hessels, 2003) reported on the results of the PCA3 gene test in 108 men undergoing prostate biopsy prompted by a prostate specific antigen (PSA) level of greater than 3 ng/ml. Of these 108 men, 24 were found to have prostate cancer based on biopsy. Of these, 16 were shown to be positive for PCA3. The reported sensitivity was 67% and the negative predictive value was 90%. The authors hypothesize due to its negative predictive value; the PCA3 test could eliminate the need for unnecessary biopsies in those with marginally elevated PSA levels. Fradet and colleagues (2004) reported on a multicenter study of 517 men, in which the positive predictive value of the PCA 3 test and PSA greater than 4 ng/dL was 75% and 38%, respectively, while the negative predictive value of the 2 tests was similar. Tinzl and colleagues (2004) reported on a case series of 201 men, of whom 158 had an evaluable urine specimen. The positive and negative predictive value 67% and 87% for the PCA3 test compared to 40% and 83% for PSA level greater than 2.5 ng/dL. However, in this study, 39% of the subjects were found to have prostate cancer, suggesting that this population is not representative of a general screening population.

A prospective, multicenter European study (Haese, 2008) evaluated the clinical utility of PCA3 urine assay in men scheduled for repeat prostate biopsies. All of the participants had previously had one or two negative prostate biopsies. Urine samples were collected after a digital rectal exam (DRE) and prior to the biopsy procedure. Simultaneously, blood samples were obtained and utilized to determine total and free PSA levels. Using a PCA 3 assay, the urine samples were processed to quantify PCA3 and PSA messenger ribonucleic acid (mRNA) concentrations. Sensitivity and specificity were determined by comparing the PCA3 score to the biopsy results. Out of 470 participants, 467 urine samples had sufficient concentrations of both PCA3 and PSA mRNA to calculate the PCA3 score. Conclusive biopsy results were obtained in 463 men out of the 467. A total of 128 men (28%) had cancer diagnosed by the repeat biopsy. Participants with a positive biopsy had statistically significant higher age, higher total PSA, suspicious DRE and a higher mean PCA3 score compared to the participants with negative biopsy results. While this and other studies found that an optimal PCA3 score of 35 would optimize the balance between sensitivity and specificity, using this cutoff score would still result in missing 21% of cancers even though 67% of unnecessary biopsies would have been avoided. Conversely, using a lower cutoff score of 20 would miss only 9% of cancers while avoiding only 44% of unnecessary biopsies. Thus the authors agree that even though the score had greater diagnostic accuracy than free PSA percentage in this study, further studies are needed to better delineate its role in the diagnosis and management of prostate cancer.

Wang and colleagues (2009) evaluated the ability of the PCA3 with the PSA to detect prostate cancer. From September 2006 to December 2007, urine samples were collected in a urology outpatient clinic following digital rectal exam from 187 men before ultrasound-guided 12-core prostate biopsy. Urine PCA3/PSA mRNA ratio scores were assessed within one month and serum PSA within six months of biopsy. Overall, 87/187 (46.5%) biopsies were positive for cancer. Sensitivity and specificity of PCA3 score greater than or equal to 35 for positive biopsy were 52.9% and 80.0%; positive and negative predictive values were 69.7% and 66.1%. Study limitations included that study cohorts consisted only of pre-screened individuals undergoing biopsy for an elevated PSA. The authors concluded: "to date, there is no definitive evidence demonstrating that PCA3 prognosticates for lethal prostate cancer, and in the absence of such evidence, these biomarkers may only contribute to the continued over-diagnosis of prostate cancer."

In a more recent study, Roobol and colleagues (2010) investigated the performance characteristics of PCA3 and compared this to the PSA. A total of 721 men between the ages of 63-75 were screened for prostate cancer from September 2007 to February 2009. Both PCA3 scores and serum PSA levels were measured. Men with a PSA greater than or equal to 3.0 ng/ml or a PCA3 score greater than or equal to 10 underwent a DRE, transrectal ultrasounds, and biopsy. It was noted that the correlation between PSA and PCA3 was poor. The authors concluded that the value of PCA3 for improving detection in the low PSA ranges and after previous negative biopsies was hampered by small numbers, is unclear and needs to be further explored.

SNPs for risk assessment 

Studies have identified SNPs that are highly significant predictors of prostate cancer risk, although the genes and biologic mechanisms behind these associations are as yet unknown. Several SNPs combined explain a significant proportion of prostate cancer, but not all. A few different groups are commercializing specific SNP panels (Gudmundsson, 2008; Zheng, 2008), combined in one case with family history, as risk assessment tools. Additional research has been reported by other groups, e.g., in the United Kingdom, where results of a trial in progress may lead to a commercial test (Eeles, 2008); by the National Cancer Institute (Thomas, 2008; Yeager, 2007); and by the University of Washington (Salinas, 2009). The work cited in these example publications is supported by a large number of studies that searched for and validated common, inherited gene variations present in individuals with prostate cancer, but not in controls.

The men sampled in these studies were primarily of European Caucasian ancestry, which limited the generalizability of assays developed from these studies to other populations. However, these tests do not predict certainty of disease nor do they clearly predict aggressive versus indolent disease. While the monitoring of high-risk men identified by these assays may improve outcomes, it is also possible that these could be offset by the harms of identifying and treating additional cases of indolent disease.

Guidelines suggest that asymptomatic men with prostate specific antigen (PSA) results <3 ng/mL who will be regularly monitored by PSA testing should be given information on prostate cancer prevention with 5-alpha reductase inhibitors (Kramer, 2009). It is possible that future risk assessment assays with evidence supporting generalizability to a variety of populations will help identify those who would most benefit from preventive therapy. However, one study found that adding 5 SNP risk factors to standard clinical predictors (age, serum PSA, and family history) did not improve ROC prediction models for determining who is at high risk for getting prostate cancer (Salinas, 2009). Discovery of genetic variants that can predict likelihood of aggressive versus indolent prostate cancer would be much more effective at defining a population in need of preventive therapy and regular surveillance.

TMPRSS fusion genes for diagnosis and prognosis

TMPRSS2 fusion gene detection has been investigated as a means to identify aggressive disease or to predict disease recurrence. There is conflicting evidence regarding the association of TMPRSS2 fusion gene detection and biochemical recurrence or survival outcomes of prostate cancer (Demichelis, 2007; Fitzgerald, 2008; Mehra, 2007; Nam, 2007a; Nam, 2007b; Wang, 2006; Winnes, 2007). Fusion gene structure is complex and variable, making it a difficult assay target (Clark, 2007; Wang, 2006). As a result, assays have not yet been standardized; once they are, larger studies will be needed to determine clinical utility.

One small study (n=74) describes the ability of TMPRSS2-ERG fusion genes to predict prostate cancer screening biopsy outcome, and association with high versus low Gleason scores (Clark, 2008). Fusion gene detection improved on PSA plus DRE for predicting the biopsy result (from AUC 0.645 to 0.823) and for predicting Gleason score greater than 7 (from AUC 0.688 to AUC 0.844). These results need further validation in larger studies and also examined for utility in clinical decision-making.

Summary 

At this time, the evidence for genetic tests related to prostate cancer screening, detection, and management does not demonstrate clinical utility, that is, that using a test will change treatment decisions and improve subsequent outcomes that matter to the individual such as mortality, morbidity, or quality of life.

According to the American Cancer Society (ACS), prostate cancer is the most common form of cancer, other than skin cancer, among men in the United States. It is second only to lung cancer as a cause of cancer-related death among men. The American Cancer Society estimated that in 2010, about 217,730 new cases of prostate cancer would be diagnosed and 32,050 men would die of the disease. About two out of every three men diagnosed with prostate cancers are aged 65 years or older. The current available testing for the screening of prostate cancer involves a DRE and a blood test for a substance in the blood, PSA. Elevated levels of PSA in the blood are known to be associated with the presence of prostate cancer and this test is commonly used in the diagnosis and management of prostate cancer. The ACS (2010) recommends "men thinking about prostate cancer screening should make informed decisions based on available information, discussion with their doctor, and their own views on the benefits and side effects of screening and treatment."

The published literature surrounding gene-based tests for the screening, detection and management of prostate cancer initially focused on the technical feasibility of identifying a novel prostate cancer-specific gene, PCA3 gene and its possible function. Unfortunately, the PCA3 gene appears to be a non-coding gene, (i.e., there is no protein product that can be easily identified with an immunoassay), and thus its identification relies on the detection of the overall expression of the associated mRNA. mRNA is a molecule that results when a cell "reads" a DNA strand. PCA3 testing in clinical practice focuses on the detection of the PCA3-associated mRNA in blood and urine samples following a DRE. This test differs from traditional genetic testing for chromosome or single gene mutations in that PCA3 testing does not evaluate the genetic material of an individual (DNA). This type of test quantifies the amount of mRNA transcription product produced when the DNA is read by the cell, and is analogous to testing for a metabolite or biomarker in the blood or urine, rather than what one would normally consider a genetic test.

Currently, the role of gene-based tests for prostate cancer screening, detection and management remains under investigation. In addition to the PCA3, this group of gene-based tests has now evolved to include: gene hypermethylation, multiple gene tests (gene panels), SNPs, and TMPRSS fusion genes.

In the 2007 updated clinical guidelines for the management of prostate cancer, the American Urological Association noted serum PSA test and DRE were the two most commonly used tests for prostate cancer screening.

Fusion gene: A hybrid gene created by joining portions of two different genes.

Genetic testing: A type of test that is used to determine the presence or absence of a specific gene or genetic alteration that may indicate an increased risk for developing a specific disease or disorder.

Messenger ribonucleic acid (mRNA): A molecule that results when a cell "reads" a DNA strand.

Methylation: The attachment of methyl groups to DNA at cytosine bases; correlated with reduced transcription of the gene and thought to be the principal mechanism in X-chromosome inactivation and imprinting.

Screening: The testing of persons, in either the general population or those at high risk, for specific diseases or conditions.

Single-nucleotide polymorphisms (SNPs): DNA sequence variations that occur when a single nucleotide in the genome sequence is altered.

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When services are Investigational and Not Medically Necessary:
When the code describes a procedure indicated in the Position Statement section as investigational and not medically necessary.

Peer Reviewed Publications:

1. Bussemakers MJ, van Bokhoven A, Verhaegh GW, et al. DD3: a new prostate-specific gene, highly overexpressed in prostate cancer. Cancer Res. 1999; 59(23):5975-5979.
2. Clark J, Merson S, Jhavar S, et al. Diversity of TMPRSS2-ERG fusion transcripts in the human prostate. Oncogene 2007; 26(18):2667-2673.
3. Clark JP, Munson KW, Gu JW, et al. Performance of a single assay for both type III and type VI TMPRSS2:ERG fusions in noninvasive prediction of prostate biopsy outcome. Clin Chem, 2008; 54(12):2007-2017.
4. de Kok JB, Verhaegh GW, Roelofs RW, et al. DD3 (PCA3), a very sensitive and specific marker to detect prostate tumors. Cancer Res. 2002; 62(9):2695-2698.
5. Demichelis F, Fall K, Perner S, et al. TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort. Oncogene 2007; 26(31):4596-4599.
6. Eeles RA, Kote-Jarai Z, Giles GG, et al. Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet 2008; 40(3):316-321.
7. Eilers T, Machtens S, Tezval H et al. Prospective diagnostic efficiency of biopsy washing DNA GSTP1 island hypermethylation for detection of adenocarcinoma of the prostate. Prostate 2007; 67(7):757-763.
8. Ellinger J, Bastian PJ, Jurgan T et al. CpG island hypermethylation at multiple gene sites in diagnosis and prognosis of prostate cancer. Urology, 2008; 71(1):161-167.
9. FitzGerald LM, Agalliu I, Johnson K, et al. Association of TMPRSS2-ERG gene fusion with clinical characteristics and outcomes: results from a population-based study of prostate cancer. BMC Cancer 2008; 8:230.
10. Fradet Y, Saad F, Aprikian A, Dessureault J, et al. uPM3, a new molecular urine test for the detection of prostate cancer. Urology. 2004; 64(2):311-316.
11. Gandini O, Luci L, Stigliano A, et al. Is DD3 a new prostate-specific gene? Anticancer Res. 2003; 23(1A):305-308.
12. Gudmundsson J, Sulem P, Rafnar T, et al. Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat Genet 2008; 40(3):281-283.
13. Haese A, de la Taille A, van Poppel H, et al. Clinical utility of the PCA3 urine assay in European men scheduled for repeat biopsy. Eur Urol. 2008; 54(5):1081-1088.
14. Henrique R, Ribeiro FR, Fonseca D, et al. High promoter methylation levels of APC predict poor prognosis in sextant biopsies from prostate cancer patients. Clin Cancer Res, 2007; 13(20):6122-6129.
15. Hessels D, Klein Gunnewiek JM, van Oort I, et al. DD3 (PCA3)-based molecular urine analysis for the diagnosis of prostate cancer. Eur Urol. 2003; 44(1):8-16.
16. Marks LS, Fradet Y, Deras IL, et al. PCA3 molecular urine assay for prostate cancer in men undergoing repeat biopsy. Urology. 2007; 69(3):532-535.
17. Mehra R, Tomlins SA, Shen R, et al. Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer. Mod Pathol 2007; 20(5):538-544.
18. Nam RK, Sugar L, Yang W, et al. Expression of the TMPRSS2:ERG fusion gene predicts cancer recurrence after surgery for localised prostate cancer. Br J Cancer 2007a; 97(12):1690-1695.
19. Nam RK, Sugar L, Wang Z, et al. Expression of TMPRSS2:ERG gene fusion in prostate cancer cells is an important prognostic factor for cancer progression. Cancer Biol Ther 2007b; 6(1):40-45.
20. Roobol MJ, Schröder FH, van Leeuwen P, et al. Performance of the prostate cancer antigen 3 (PCA3) gene and prostate-specific antigen in prescreened men: exploring the value of PCA3 for a first-line diagnostic test. Eur Urol. 2010; 58(4):475-481.
21. Salinas CA, Koopmeiners JS, Kwon EM et al. Clinical utility of five genetic variants for predicting prostate cancer risk and mortality. Prostate 2009; 69(4):363-372.
22. Schalken JA, Hessels D, Verhaegh G. New targets for therapy in prostate cancer: differential display code 3 (DD3(PCA3)), a highly prostate cancer-specific gene. Urology. 2003; 62(5 Suppl 1):34-43.
23. Thomas G, Jacobs KB, Yeager M et al. Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet 2008; 40(3):310-315.
24. Tinzl M, Marberger M, Horvath S et al. DD3PCA3 RNA analysis in urine–a new perspective for detecting prostate cancer. Eur Urol 2004; 46(2):182-186.
25. Wang J, Cai Y, Ren C et al. Expression of variant TMPRSS2/ERG fusion messenger RNAs is associated with aggressive prostate cancer. Cancer Res, 2006; 66(17):8347-8351.
26. Wang R, Chinnaiyan AM, Dunn RL, et al. Rational approach to implementation of prostate cancer antigen 3 into clinical care. Cancer. 2009; 115(17):3879-3886.
27. Winnes M, Lissbrant E, Damber JE, et al. Molecular genetic analyses of the TMPRSS2-ERG and TMPRSS2-ETV1 gene fusions in 50 cases of prostate cancer. Oncol Rep 2007; 17(5):1033-1036.
28. Woodson K, O'Reilly KJ, Ward DE, et al. CD44 and PTGS2 methylation are independent prognostic markers for biochemical recurrence among prostate cancer patients with clinically localized disease. Epigenetics 2006; 1(4):183-186.
29. Yeager M, Orr N, Hayes RB et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 2007; 39(5):645-649.
30. Zheng SL, Sun J, Wiklund F, et al. Cumulative association of five genetic variants with prostate cancer. N Engl J Med 2008; 358(9):910-919.

Government Agency, Medical Society, and Other Authoritative Publications:

1. American Cancer Society. Overview: prostate cancer. Revised December 13, 2010. Available at: http://www.cancer.org/docroot/CRI/CRI_2_1x.asp?dt=36. Accessed on: March 16, 2011.
2. American Urological Association. Prostate Cancer. Guideline for the management of clinically localized prostate cancer: 2007 update. Reviewed and validity confirmed 2009. Available at: http://www.auanet.org/content/guidelines-and-quality-care/clinical-guidelines/main-reports/proscan07/content.pdf. Accessed on March 16, 2011.
3. Blue Cross and Blue Shield Association. TEC Special Report: Recent Developments in Prostate Cancer Genetics and Genetic Testing. TEC Assessment. 2009; 23(7).
4. Centers for Medicare and Medicaid Services. National Coverage Determination for Prostate Cancer Screening Tests. NCD #210.1. Effective June 19, 2006. Available at: http://www.cms.hhs.gov/mcd/index_list.asp?list_type=ncd. Accessed on: March 16, 2011.
5. Kramer BS, Hagerty KL, Justman S, et al. Use of 5-alpha-reductase inhibitors for prostate cancer chemoprevention: American Society of Clinical Oncology/American Urological Association 2008 Clinical Practice Guideline. J Clin Oncol 2009; 27(9):1502-1516.
6. National Cancer Institute. Prostate Cancer (PDQ^®): Screening. Last modified December 03, 2010. Available at: http://www.nci.nih.gov/cancertopics/pdq/screening/prostate/HealthProfessional. Accessed on March 16, 2011.
7. NCCN Clinical Practice Guidelines in Oncology^{™_. ©} 2011 National Comprehensive Cancer Network, Inc. For additional information: http://www.nccn.org/index.asp. Accessed on March 16, 2011.
   • Prostate Cancer (V.1.2011). Revised December 13, 2010.
   • Prostate Cancer Early Detection (V.2.2010). Revised August 7, 2009.

1. American Cancer Society. What Are Tumor Markers? Revised: December21, 2009. Available at: http://www.cancer.org/docroot/PED/content/PED_2_3X_Tumor_Markers.asp?sitearea=PED. Accessed on March 16, 2011.
2. National Cancer Institute. What You Need to Know about Prostate Cancer. Posted November 20, 2008. Available at: http://www.cancer.gov/cancerinfo/wyntk/prostate. Accessed on: March 16, 2011.

DD3
Gene-Based Tests for Screening, Detection and/or Management of Prostate Cancer
Glutathione S-transferase Gene (GSTP1, pi-class) Methylation Assay
PCA3
ProCa Assay
Prostate Cancer, Gene-Based Tests for
The Prostate Gene Expression Profile
uPM3 Test

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