ProstateNext

ProstateNext is a next generation sequencing panel that simultaneously analyzes 14 genes associated with increased risk for prostate, male breast, and other cancers.

PrintPrint

ProstateNext is a next generation sequencing panel that simultaneously analyzes 14 genes associated with increased risk for prostate, male breast, and other cancers.

Ambry utilizes next generation sequencing (NGS) to offer a comprehensive panel for hereditary prostate cancer.  Genes on this panel include: ATM, BRCA1, BRCA2, CHEK2, EPCAM, HOXB13, MLH1, MSH2, MSH6, NBN, PALB2, PMS2, RAD51D, and TP53.  Full gene sequencing is performed for 14 genes (excluding EPCAM).  Gross deletion/duplication analysis is performed for all 14 genes. Specific Site Analysis is available for individual gene mutations identified in a family.

"Read the blog"

Disease Name 
Prostate cancer
Male breast cancer
Hereditary breast and ovarian cancer (HBOC)
Hereditary cancer
Lynch syndrome
Disease Information 

Prostate cancer is the 2nd most common cancer in men in the United States, after skin cancer.1  The National Cancer Institute (NCI) estimates that approximately 180,890 new cases of prostate cancer will be diagnosed in the U.S. in 2016.2  The majority of prostate cancer is sporadic and diagnosed over the age of 65. Some prostate cancer may be hereditary and develop due to an inherited genetic mutation. Hereditary prostate cancer may be diagnosed at younger ages and may also be more aggressive. For example, BRCA1 and BRCA2 gene mutations have been shown to be associated with more aggressive prostate cancer, including a higher likelihood of nodal involvement and distant metastasis.3

Male breast cancer is a rare cancer that will be diagnosed in approximately 2,600 men in the U.S. in 2016.2 Men have a 0.1% lifetime risk to develop breast cancer; however, this risk can be higher for men with an inherited susceptibility to cancer. While most breast cancer is sporadic, men who are diagnosed with breast cancer may be more likely to have an inherited gene mutation increasing their risk for various types of cancer. For example, men with a BRCA2 mutation may have a >6% risk for breast cancer in their lifetime.4 Many men are diagnosed with breast cancer at the locally advanced or metastatic stages, therefore, it is important to determine if a man is at an increased risk for breast cancer, so that proper screening can be recommended. 

ProstateNext Genes:

ATM is a gene associated with an autosomal recessive condition called ataxia-telangiectasia (AT). AT is characterized by progressive cerebellar ataxia with onset between ages 1 and 4, telangiectases of the conjunctivae, oculomotor apraxia, immune defects, and a predisposition to malignancy, particularly leukemia and lymphoma. Women who carry ATM mutations also have an estimated 2-4 fold increased risk for breast cancer.5  Cancer risk estimates for male ATM mutation carriers are not currently available. Recent studies have also reported ATM germline mutations in individuals with familial pancreatic cancer. In one of these studies, ATM mutations were identified in 4/87 (4.6%) families with more than three affected members.6

BRCA1 and BRCA2 are tumor suppressor genes inherited in an autosomal dominant pattern. Mutations in these two highly penetrant genes increase the chance for cancer of the breast (female and male), ovaries (including primary peritoneal and fallopian tube), pancreas, prostate, and melanoma. Studies suggest female BRCA1 mutation carriers have a 57-87% risk to develop breast cancer and a 39-40% risk to develop ovarian cancer by age 70. 7-12 Male BRCA1 mutation carriers have a cumulative breast cancer risk of about 1.2% by age 70.413 Similar studies suggest female BRCA2 mutation carriers have a 45-84% risk to develop breast cancer and an 11-18% risk to develop ovarian cancer by age 70.7-9,14,15 Male BRCA2 mutation carriers have up a 15%  prostate cancer risk and a cumulative breast cancer risk of 6.8% by ages 65 and 70 respectively.4,13,15,16 BRCA1/2 mutation carriers may also be at an increased risk for melanoma, pancreatic cancer, and potentially other cancers.17 BRCA2 is also known as FANCD1.  Individuals who inherit a BRCA2/FANCD1 mutation from each parent may have a rare autosomal recessive condition called Fanconi anemia type D1 (FA-D1), which affects multiple body systems.  

CHEK2 is a gene that receives signals from damaged DNA, transmitted via ATM. CHEK2 interacts in vivo with BRCA1, BRCA2, and TP53, which have all been implicated in cellular processes responsible for the maintenance of genomic stability. Multiple studies indicate that mutations in CHEK2 confer an increased risk of developing many types of cancer including breast (female and male), colon, prostate, and other cancers. A female CHEK2 mutation carrier has approximately a two-fold increase in lifetime breast cancer risk, and has a 1% risk per year of developing a second breast primary cancer. Lifetime risks for other associated cancers are unknown.  An increased risk for ovarian cancer has also been suggested.18-21

HOXB13 encodes a transcription factor involved in epidermal differentiation and prostate gland development. Multiple studies have associated a recurrent HOXB13 mutation, p.G84E, with an increased risk for early-onset prostate cancer, however, lifetime cancer risk estimates are not currently available for mutation carriers.22-24 Data is insufficient to support increased cancer risks for other HOXB13 alterations at this time.

MLH1, MSH2, MSH6, PMS2, and EPCAM germline mutations are associated with Lynch syndrome (previously called hereditary non-polyposis colorectal cancer, HNPCC). Lynch syndrome is an autosomal dominant condition estimated to cause 2-5% of all colorectal cancer. It is associated with a significantly increased risk for colorectal cancer (up to 82% lifetime risk), uterine/endometrial cancer (25-60% lifetime risk in women), stomach cancer (6-13% lifetime risk), ovarian cancer (4-12% lifetime risk in women), and prostate cancer (up to 2 fold).55,56 Risk for cancer of the small bowel, hepatobiliary tract, upper urinary tract (including transitional cell carcinoma of the renal pelvis), brain, and sebaceous glands may also be elevated.25-29

NBN and RAD51D are genes involved in the Fanconi anemia (FA)-BRCA pathway, critical for DNA repair by homologous recombination, and interact in vivo with BRCA1 and/or BRCA2.30-32 Mutations in these genes are associated with an increased risk for female breast cancer.32-34  The ovarian cancer risk associated with mutations in RAD51D has been estimated to be up to 10-12%.35-37 NBN and RAD51D have more recently been associated an increased risk of prostate cancer.38,39  NBN is associated with a rare autosomal recessive disorder that affects multiple body systems. 

PALB2 germline mutations have been associated with an increased lifetime risk for pancreatic cancer, breast cancer (female and male), and Fanconi anemia type N (FA-N). Familial pancreatic and/or breast cancer due to PALB2 mutations is inherited in an autosomal dominant pattern, while FA-N is a rare autosomal recessive condition affecting multiple body systems. Females with a PALB2 mutation have a 2- to 4-fold increase in risk for breast cancer.40,41  A 2014 article concluded that in the context of a strong family history, mutations in PALB2 may be associated with up to a 58% risk of female breast cancer. Without a family history, the risk for female breast cancer was estimated to be 33% (the difference attributed to genetic and/or environmental modifiers).42  Studies have identified PALB2 mutations in 1-3% of families with pancreatic cancer; however, the exact lifetime pancreatic cancer risk has not yet been established.43-44 Recent studies have shown an increased risk for ovarian cancer. 18,45  Prostate cancer has also been reported.46

TP53 is a tumor suppressor gene, and germline mutations within it are associated with Li-Fraumeni syndrome (LFS). An individual carrying a TP53 mutation has a 21-49% risk of developing cancer by age 30 and a lifetime cancer risk of 68-93%.47 The most common tumor types observed in LFS families include soft tissue and osteosarcomas, breast cancer, brain tumors (including astrocytomas, glioblastomas, medulloblastomas and choroid plexus carcinomas), and adrenocortical carcinoma (ACC); other cancers, including colorectal, gastric, ovarian, pancreatic, prostate, and renal, have also been reported.48-50

 

Testing Benefits & Indication 

Indications for Testing

ProstateNext may be appropriate in the following situations, combined with common red flags for hereditary cancer:

  • Early-onset prostate cancer (diagnosed <40 years of age)
  • Multiple primary cancers in one person (e.g. prostate and male breast cancer)
  • Personal history of prostate cancer and 1 or more family members* with breast cancer (diagnosed <50 years of age) and/or invasive ovarian cancer
  • Personal history of prostate cancer and 2 family members* with breast, pancreatic, or prostate cancer
    *On the same side of family

Common Red Flags for Hereditary Cancer:

  • Cancer diagnosed at a younger age than expected for the general population (≤ 50 years, for most cancers)
  • Cancer diagnosed across generations, and in multiple generations within a family, especially when diagnosed younger than average
  • Individual with multiple primary cancers (either in paired organs or in different organs)
  • A pattern of cancer in the family that is typical of a known cancer predisposition syndrome (e.g. colon and uterine cancer in Lynch syndrome, or breast and pancreatic cancer with PALB2 mutations) 

The American Society of Clinical Oncology (ASCO) recommends that genetic testing be offered to individuals with suspected inherited (genetic) cancer risk in situations where test results can be interpreted, and when they affect medical management of the patient. It is sufficient for cancer risk assessment to evaluate genes of established clinical utility that are suggested by the patient’s personal and/or family history. 51-54

Benefits of Testing:
Identifying patients with an inherited susceptibility for certain cancers can help with medical management and risk assessment. For example, this information can:

  • Modify cancer surveillance options and age of initial screening
  • Suggest specific early screening measures (e.g. begin prostate cancer screening at 40 years old, in addition to self and clinical male breast exams at 35 years old with BRCA2 mutations)
  • Clarify and stratify personal and familial cancer risks, based on gene-specific cancer associations (e.g. risk for colon, stomach, and small bowel cancer with MLH1 mutations)
  • Offer treatment guidance (e.g. avoidance of radiation-based treatment methods for individuals with a TP53 mutation)
  • Identify other at-risk family members
  • Provide guidance with new gene-specific treatment options and risk reduction measures as they emerge

 

Test Description 

ProstateNext analyzes 14 genes (listed above). 13 genes (excluding EPCAM) are evaluated by next generation sequencing (NGS) or Sanger sequencing of all coding domains, and well into the flanking 5’ and 3’ ends of all the introns and untranslated regions. In addition, sequencing of the promoter region is performed for the following genes: MLH1 (c.-337 to c.-194), and MSH2 (c.-318 to c.-65). The inversion of coding exons 1-7 of the MSH2 gene and the BRCA2 Portuguese founder mutation, c.156_157insAlu (also known as 384insAlu) are detected by NGS and confirmed by PCR and agarose gel electrophoresis. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Additional Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, variants in regions complicated by pseudogene interference, and single nucleotide variant calls not satisfying 100x depth of coverage and 40% het ratio thresholds are verified by Sanger sequencing.57  Gross deletion/duplication analysis is performed for the covered exons and untranslated regions of all 14 genes using read-depth from NGS data with confirmatory multiplex ligation-dependent probe amplification (MLPA) and/or targeted chromosomal microarray. If a deletion is detected in exons 13, 14, or 15 of PMS2, double stranded sequencing of the appropriate exon(s) of the pseudogene, PMS2CL, will be performed to determine if the deletion is located in the PMS2 gene or pseudogene.

Mutation Detection Rate 

ProstateNext can detect >99.9% of described mutations in the included genes listed above, when present (analytic sensitivity).

Specimen Requirements 

Complete specimen requirements are available here or by downloading the PDF found above on this page.

Turnaround Time 
TEST CODE TEST NAME TURNAROUND TIME (days)
8845 ProstateNext 14-21
Specialty 
Genes 
ATM
BRCA1
BRCA2
CHEK2
EPCAM
HOXB13
MLH1
MSH2
MSH6
NBN
PALB2
PMS2
RAD51D
TP53
References 
  1. Surveillance, Epidemiology, and End Results Program. Cancer Stat Fact Sheets  [Accessed September 15, 2016]. Available from: http://seer.cancer.gov/
  2. National Cancer Institute.  [Accessed September 15, 2016]. Available from: http://www.cancer.gov/.
  3. Castro E. et al. Germline BRCA mutations are associated with higher risk of nodal involvement, distant metastasis, and poorsurvival outcomes in prostate cancer. J Clin Oncol. 2013 May 10;31(14):1748-57.
  4. Tai YC, et al. Breast cancer risk among male BRCA1 and BRCA2 mutation carriers. J Nat Cancer Inst. 2007;99(23):1811-4. 
  5. Renwick A, et al. ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles. Nat Genet. 2006;38(8):873-5. 
  6. Roberts NJ, et al. ATM mutations in patients with hereditary pancreatic cancer. Cancer Discovery. 2011;2(1):OF1-OF6.
  7. Antoniou A, et al. Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case series unselected for family history: a combined analysis of 22 studies. Am J Hum Genet. 2003;72(5):1117-30. 
  8. Chen S, Parmigiani G. Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol. 2007;25(11):1329-33. 
  9. Ford D, et al. Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am J Hum Genet. 1998;62(3):676-89.
  10. Janavicius R. Founder BRCA1/2 mutations in the Europe: implications for hereditary breast-ovarian cancer prevention and control. The EPMA Journal. 2010;1(3):397-412. 
  11. Ferla R, et al. Founder mutations in BRCA1 and BRCA2 genes. Ann Oncol. 2007;18 Suppl 6:vi93-8.
  12. Tulinius H, et al. The effect of a single BRCA2 mutation on cancer in Iceland. J Med Genet. 2002;39(7):457-62.
  13. Thompson D, Easton DF, Breast Cancer Linkage Consortium. Cancer Incidence in BRCA1 mutation carriers. J Natl Cancer Inst. 2002;94(18):1358-65.
  14. Folkins AK, Longacre TA. Hereditary gynaecological malignancies: advances in screening and treatment. Histopathology. 2013;62(1):2-30. 
  15. Shannon KM, Chittenden A. Genetic testing by cancer site: breast. Cancer Journal. 2012;18(4):310-9. 
  16. Kote-Jarai Z, et al. BRCA2 is a moderate penetrance gene contributing to young-onset prostate cancer: implications for genetic testing in prostate cancer patients. Br J Cancer. 2011;105(8):1230-4. 
  17. van Asperen CJ, et al. Cancer risks in BRCA2 families: estimates for sites other than breast and ovary. J Med Genet. 2005;42(9):711-9.
  18. Walsh T, et al. Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing. Proc Natl Acad Sci U S A. 2011;108(44):18032-7. 
  19. Bahassi EM, et al. The checkpoint kinases Chk1 and Chk2 regulate the functional associations between hBRCA2 and Rad51 in response to DNA damage. Oncogene. 2008;27(28):3977-85. 
  20. Cybulski C, et al. CHEK2 is a multiorgan cancer susceptibility gene. Am J Hum Genet. 2004;75(6):1131-5
  21. Walsh T, et al. Spectrum of mutations in BRCA1, BRCA2, CHEK2, and TP53 in families at high risk of breast cancer. JAMA. 2006;295(12):1379-88. 
  22. Ewing CM, et al. Germline mutations in HOXB13 and prostate cancer risk. N Engl J Med. 2012. 366(2):141-9.
  23. Lin X, et al. A novel germline mutation in HOXB13 is associated with prostate cancer risk in Chinese men. Prostate. 2013. 73(2):169-75.
  24. Maia S, et al. Identification of two novel HOXB13 germline mutations in Portuguese prostate cancer patients. PLoS One. 2015. 10(7):e0132728.
  25. Hegde MR, Roa BB. Genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC). Curr protoc Hum Genet. 2009;61(Unit 10.12):10.2.1-.2.28.
  26. Capelle LG, et al. Risk and epidemiological time trends of gastric cancer in Lynch syndrome carriers in the Netherlands. Gastroenterology. 2010;138(2):487-92. 
  27. Bonadona V, et al. Cancer risks associated with germline mutations in MLH1, MSH2, and MSH6 genes in Lynch syndrome. JAMA. 2011;305(22):2304-10. 
  28. Engel C, et al. Risks of less common cancers in proven mutation carriers with Lynch syndrome. J Clin Oncol. 2012;30(35):4409-15. 
  29. Win AK, et al. Colorectal and other cancer risks for carriers and noncarriers from families with a DNA mismatch repair gene mutation: a prospective cohort study. J Clin Oncol. 2012;30(9):958-64. 
  30. Walsh T, et al. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci U S A. 2010;107(28):12629-33. 
  31. Pennington KP and Swisher EM. Hereditary ovarian cancer: beyond the usual suspects. Gynecologic oncology. 2012;124(2):347-53. 
  32. Damiola F, et al. Rare key functional domain missense substitutions in MRE11A, RAD50, and NBN contribute to breast cancer susceptibility: results from a breast cancer family registry case-control mutation-screening study. Breast Cancer Res. 2014;16(3):R58.
  33. Seal S, et al. Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles. Nat Genet. 2006;38(11):1239-41. 
  34. Bogdanova N et al. Nijmegen Breakage Syndrome mutations and risk of breast cancer. Int J Cancer. 2008 Feb 15;122(4):802-6.
  35. Loveday C, et al. Germline mutations in RAD51D confer susceptibility to ovarian cancer. Nat Genet. 2011;43(9):879-82.
  36. Song et al. Contribution of germline mutations in the RAD51B, RAD51C, and RAD51D genes to ovarian cancer in the population. J Clin Oncol. 2015. 33 (26): 2901-7.
  37. Ramus et al. Germline mutations in the BRIP1, BARD1, PALB2, and NBN genes in women with ovarian cancer. J Natl Cancer Inst. 2015. 107(11). 
  38. Cybulski C et al. An inherited NBN mutation is associated with poor prognosis prostate cancer. Br J Cancer. 2013;108:461–468
  39. Pritchard CC et al. Inherited DNA-repair gene mutations in men with metastatic prostate cancer. N Engl J Med. 2016 Aug 4;375(5):443-53.
  40. Slater EP, et al. PALB2 mutations in European familial pancreatic cancer families. Clin Genet. 2010;78(5):490-4. 
  41. Casadei S, et al. Contribution of inherited mutations in the BRCA2-interacting protein PALB2 to familial breast cancer. Cancer Res. 2011;71(6):2222-9. 
  42. Antoniou AC, et al. Breast-cancer risk in families with mutations in PALB2. N Engl J Med. 2014;371(6):497-506. 
  43. Tischkowitz MD, et al. Analysis of the gene coding for the BRCA2-interacting protein PALB2 in familial and sporadic pancreatic cancer. Gastroenterology. 2009;137(3):1183-6. 
  44. Jones S, et al. Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science. 2009;324(5924):217.
  45. Norquist BM, et al. Inherited mutations in women with ovarian carcinoma. JAMA Oncol. 2016 Apr;2(4):482-90.
  46. Erkko H et al. A recurrent mutation in PALB2 in Finnish cancer families. Nature. 2007 Mar 15;446(7133):316-9.
  47. Hwang SJ, et al. Germline p53 mutations in a cohort with childhood sarcoma: sex differences in cancer risk. Am J Hum Genet. 2003;72(4):975-83. 
  48. Olivier M, et al. Li-Fraumeni and related syndromes: correlation between tumor type, family structure, and TP53 genotype. Cancer Res. 2003;63(20):6643-50. 
  49. Birch JM, et al. Prevalence and diversity of constitutional mutations in the p53 gene among 21 Li-Fraumeni families. Cancer Res. 1994;54(5):1298-304. 
  50. Gonzalez KD, et al. Beyond Li-Fraumeni syndrome: clinical characteristics of families with p53 germline mutations. J Clin Oncol. 2009;27(8):1250-6. 
  51. Statement of the American Society of Clinical Oncology: genetic testing for cancer susceptibility, Adopted on February 20, 1996. J Clin Oncol. 1996 May;14(5):1730-6.
  52. American Society of Clinical Oncology. American Society of Clinical Oncology policy statement update: genetic testing for cancer susceptibility. J Clin Oncol. 2003 Jun 15;21(12):2397-406.
  53. Robson ME et al. American Society of Clinical Oncology. American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility. J Clin Oncol. 2010 Feb 10;28(5):893-901.
  54. Robson ME et al. American Society of Clinical Oncology Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility. J Clin Oncol. 2015 Nov 1;33(31):3660-7.
  55. Ryan S et al. Risk of prostate cancer in Lynch syndrome: a systematic review and meta-analysis. Cancer Epidemiol Biomarkers Prev. 2014 Mar;23(3):437-49.
  56. Raymond VM et al. Elevated risk of prostate cancer among men with Lynch syndrome. J Clin Oncol. 2013 May 10;31(14):1713-8.
  57. Mu W, et al. Sanger confirmation is required to achieve optimal sensitivity and specificity in next-generation sequencing panel testing. J Mol Diagn. 2016. 18(6):923-932.