PancNext

PancNextTM is a next generation sequencing panel that simultaneously analyzes 13 genes associated with increased risk for pancreatic cancer.

PrintPrint

PancNextTM is a next generation sequencing panel that simultaneously analyzes 13 genes associated with increased risk for pancreatic cancer.

Ambry utilizes next generation sequencing (NGS) to offer a comprehensive hereditary pancreatic cancer panel.  Genes on this panel include APC, ATM, BRCA1, BRCA2, CDKN2A, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, STK11, and TP53. Full gene sequencing is performed for 12 of the genes (excluding EPCAM). Gross deletion/duplication analysis is performed for all 13 genes. Specific Site Analysis is available for individual gene mutations identified in a family.

Disease Name 
Hereditary cancer
Pancreatic cancer
Disease Information 

Pancreatic cancer affects about 1 in 65 (1.5%) of men and women in their lifetime.The National Cancer Institute (NCI) estimates that approximately 48,960 new cases of pancreatic cancer will be diagnosed in the U.S. in 2015. Approximately 95% of pancreatic cancers are pancreatic adenocarcinomas of the exocrine gland (which produces enzymes for food digestion). Neuroendocrine/islet cell tumors of the endocrine gland (a gland that produces insulin and regulates blood sugar) make up the other 5% of pancreatic cancer subtypes. While the majority of pancreatic cancers are sporadic, approximately 5-10% of pancreatic cancer cases are familial often occurring in families with multiple affected individuals.3 Multiple genes are associated with increased pancreatic cancer susceptibility. Most genes known to increase risk for pancreatic adenocarcinoma are included on the PancNext panel. 


PancNext Panel Genes

APC germline mutations are well established as the primary cause of familial adenomatous polyposis (FAP) and attenuated familial adenomatous polyposis (AFAP). FAP and AFAP are autosomal dominant colon cancer predisposition syndromes characterized by hundreds to thousands of adenomatous polyps in the internal lining of the colon and the rectum. They affect 1 in 8,000 to 1 in 10,000 individuals and account for about 1% of all colorectal cancers.4  In individuals affected with classic FAP, colonic polyps generally begin developing at an average age of 16 years.5  In these families, colon cancer is inevitable without surgical intervention like colectomy, and the mean age of colon cancer diagnosis in untreated individuals is 35-40 years.6  Individuals with FAP or AFAP may also have increased risks to develop duodenal cancer, pancreatic cancer, papillary thyroid cancer, hepatoblastoma in childhood, and medulloblastoma.  Some individuals may also have non-malignant features such as osteomas, congenital hypertrophy of the retinal pigment epithelium (CHRPE), and/or desmoid tumors.4

ATM is a gene classically 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.7  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.8

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, ovaries (including primary peritoneal and Fallopian tube), pancreas and prostate. Studies suggest female BRCA1 mutation carriers have a 57-87% lifetime risk to develop breast cancer and a 39-40% lifetime risk to develop ovarian cancer by age 70.9-14 Male BRCA1 mutation carriers have a cumulative breast cancer lifetime risk of about 1.2% by age 70.15,16 Similar studies suggest female BRCA2 mutation carriers have a 45-84% lifetime risk to develop breast cancer and an 11-18% risk to develop ovarian cancer by age 70.9-11,17,18 Male BRCA2 mutation carriers have up a 15% lifetime prostate cancer risk and a cumulative lifetime breast cancer risk of 6.8% by ages 65 and 70 respectively.15,16,18,19 BRCA1/2 mutation carriers may also be at an increased risk for melanoma, pancreatic cancer, and potentially other cancers.20 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.  

CDKN2A encodes two distinct proteins, p16 and p14ARF, which are both involved in cell cycle regulation. Germline p16/CDKN2A mutations are associated with familial atypical multiple mole melanoma (FAMMM) syndrome. FAMMM is an autosomal dominant disorder characterized by an increased risk for atypical mole malignant melanoma, often associated with dysplastic or atypical nevi. CDKN2A mutation carriers have an approximate 28-67% lifetime risk of developing melanoma, with penetrance estimates varying widely based on study design and geographic region.21-23 Individuals carrying CDKN2A mutations also have an approximate 17-25% lifetime risk for pancreatic cancer; however, recent reports suggest this risk may be as high as 58% and elevated further in smokers.24-26 Rare mutations that affect the p14ARF mutations have also been reported to predispose to melanoma and possibly pancreatic cancer.25,27,28

MLH1, MSH2, MSH6, PMS2 and EPCAM germline mutations are associated with Lynch syndrome (previously known as hereditary nonpolyposis colorectal cancer, HNPCC). Lynch syndrome is an autosomal dominant condition estimated to cause 2-5% of all colon 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), and ovarian cancer (4-12% lifetime risk in women). 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.29-33

PALB2 germline mutations have been associated with an increased lifetime risk for pancreatic cancer, breast cancer, 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.34,35 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).36   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.37,38Additionally, recent studies have shown an increased risk for ovarian cancer.39,49

STK11 germline mutations are associated with Peutz-Jeghers syndrome (PJS), an autosomal dominant disorder characterized by the development of gastrointestinal hamartomatous polyps, along with hyperpigmentation of the skin and mucous membranes. Overall, individuals affected with PJS have up to an 85% lifetime risk of developing cancer by the age of 70, with gastrointestinal and breast cancers being the most common.40,41  Individuals with PJS are also at elevated risk for tumors of the pancreas, lung, and, in females, ovarian tumors, specifically, sex cord tumors with annular tubules (SCTATs) and mucinous ovarian tumors.

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% lifetime risk of developing cancer by age 30 and a lifetime cancer risk of 68-93%.42  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, and renal, have also been reported.43,44  Studies have shown that a small percentage of women with early onset breast cancer who do not carry BRCA1 and BRCA2 mutations are identified to have mutations in TP53.45-47

Testing Benefits & Indication 

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

  • Early-onset pancreatic cancer (diagnosed < 60 years of age)
  • Multiple primary cancers in one person (e.g. pancreatic & colon or breast cancer)
  • ≥2 family members with pancreatic cancer* 
  • ≥3 family members with pancreatic, breast, colon, uterine, ovarian, and/or melanoma*
    *On the same side of the family

If increased risk of a hereditary cancer syndrome is suspected, the American Congress (formerly College) of Obstetricians and Gynecologists (ACOG) recommends referral to a specialist in cancer genetics or a healthcare provider with expertise in genetics for complete hereditary cancer risk assessment, which may lead to genetic testing.48 Establishing a molecular diagnosis can help guide preventive measures, direct surgical options and estimate personal and familial cancer risk.  

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
  • 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. breast and pancreatic cancer with PALB2-related cancer) 

 

Benefits of Testing

Identifying patients with an inherited susceptibility for certain cancers can help with medical management. Depending on the gene mutation identified, this information can:

  • Modify cancer surveillance options and age of initial screening
  • Suggest specific risk-reduction measures (e.g. considering prophylactic oophorectomy, after childbearing is complete, for women with increased risk for breast/ ovarian cancer)
  • Clarify and stratify familial cancer risks, based on gene-specific cancer associations, such as risk for uterine, colon, and ovarian 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 

PancNext analyzes 13 genes (APC, ATM, BRCA1, BRCA2, CDKN2A, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, STK11, and TP53). Twelve genes (excluding EPCAM) are evaluated by 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: PTEN (c.-1300 to c.-745), 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. Suspect variant calls are verified by Sanger sequencing. Gross deletion/duplication analysis is performed for the covered exons and untranslated regions of all 13 genes using read-depth from NGS data with confirmatory multiplex ligation-dependent probe amplification (MLPA) and/or targeted chromosomal microarray. Of note, the APC promoter 1B region is covered as part of this deletion/duplication analysis. 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 

PancNext 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)
8042 PancNext 14 - 21

 

Specialty 
Genes 
APC
ATM
BRCA1
BRCA2
CDKN2A
EPCAM
MLH1
MSH2
MSH6
PMS2
STK11
TP53
PALB2
References 
  1. National Cancer Institute. Cancer Stat Fact Sheets  October 22, 2014. Available from: http://seer.cancer.gov/.
  2.  National Cancer Institute. February 3, 2016. Available from: http://www.cancer.gov/.
  3. Shi C, et al. Familial pancreatic cancer. Arch Pathol Lab Med. 2009. 133(3):365-74.
  4. Lipton L and Tomlinson I. The genetics of FAP and FAP-like syndromes. Fam Cancer. 2006. 5(3):221-6.
  5. Petersen GM, et al. Screening guidelines and premorbid diagnosis of familial adenomatous polyposis using linkage. Gastroenterology. 1991. 100(6):1658-64.
  6. Pedace L, et al. Identification of a novel duplication in the APC gene using multiple ligation probe amplification in a patient with familial adenomatous polyposis. Cancer Genet Cytogenet. 2008. 182(2):130-5.
  7. Renwick A, et al. ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles. Nat Genet. 2006. 38(8):873-5.
  8. Roberts NJ, et al. ATM Mutations in patients with hereditary pancreatic cancer. Cancer Discovery. 2011. 2(1):OF1-OF6.
  9. 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.
  10. Chen S and Parmigiani G. Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol. 2007. 25(11):1329-33.
  11. 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.
  12. Janavicius R. Founder BRCA1/2 mutations in Europe: implications for hereditary breast-ovarian cancer prevention and control. EPMA J. 2010. 1(3):397-412.
  13. Ferla R, et al. Founder mutations in BRCA1 and BRCA2 genes. Ann Oncol. 2007. 18 Suppl 6:vi93-8.
  14. Tulinius H, et al. The effect of a single BRCA2 mutation on cancer in Iceland. J Med Genet. 2002. 39(7):457-62.
  15. Tai YC, et al. Breast cancer risk among male BRCA1 and BRCA2 mutation carriers. J Natl Cancer Inst. 2007. 99(23):1811-4.
  16. Thompson D, et al. Breast Cancer Linkage, Cancer Incidence in BRCA1 mutation carriers. J Natl Cancer Inst. 2002. 94(18):1358-65.
  17. Folkins AK and Longacre TA. Hereditary gynaecological malignancies: advances in screening and treatment. Histopathology. 2013. 62(1):2-30.
  18. Shannon KM and Chittenden A. Genetic testing by cancer site: breast. Cancer J. 2012. 18(4):310-9.
  19. 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.
  20. 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.
  21. Begg CB, et al. Lifetime risk of melanoma in CDKN2A mutation carriers in a population-based sample. J Natl Cancer Inst. 2005. 97(20):1507-15.
  22. Bishop DT, et al. Geographical variation in the penetrance of CDKN2A mutations for melanoma. J Natl Cancer Inst. 2002. 94(12):894-903.
  23. Cust AE, et al. Melanoma risk for CDKN2A mutation carriers who are relatives of population-based case carriers in Australia and the UK. J Med Genet. 2011. 48(4):266-72.
  24. Vasen HF, et al. Risk of developing pancreatic cancer in families with familial atypical multiple mole melanoma associated with a specific 19 deletion of p16 (p16-Leiden). Int J Cancer. 2000. 87(6):809-11.
  25. McWilliams RR, et al. Prevalence of CDKN2A mutations in pancreatic cancer patients: implications for genetic counseling. Eur J Hum Genet. 2011. 19(4):472-8.
  26. de Snoo FA, et al. Increased risk of cancer other than melanoma in CDKN2A founder mutation (p16-Leiden)-positive melanoma families. Clin Cancer Res. 2008. 14(21):7151-7.
  27. Laud K, et al. Comprehensive analysis of CDKN2A (p16INK4A/p14ARF) and CDKN2B genes in 53 melanoma index cases considered to be at heightened risk of melanoma. J Med Genet. 2006. 43(1):39-47.
  28. Binni F, et al. Novel and recurrent p14 mutations in Italian familial melanoma. Clin Genet. 2010. 77(6):581-6.
  29. Hegde MR and Roa BB. Genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC). Current Protocols in Human Genetics. 2009. 61(Unit 10.12):10.12.1-10.12.28.
  30. 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.
  31. 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.
  32. Engel C, et al. Risks of less common cancers in proven mutation carriers with Lynch syndrome. J Clin Oncol. 2012. 30(35):4409-15.
  33. 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.
  34. Slater EP, et al. PALB2 mutations in European familial pancreatic cancer families. Clin Genet. 2010. 78(5):490-4.
  35. 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.
  36. Antoniou AC, et al. Breast-cancer risk in families with mutations in PALB2. N Engl J Med. 2014. 371(6):497-506.
  37. 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.
  38. Jones S, et al. Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science. 2009. 324(5924):217.
  39. 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): p. 18032-7.
  40. Hearle N, et al. Frequency and spectrum of cancers in the Peutz-Jeghers syndrome. Clin Cancer Res. 2006. 12(10):3209-15.
  41. Lim W, et al. Relative frequency and morphology of cancers in STK11 mutation carriers. Gastroenterology. 2004. 126(7):1788-1794.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. Gonzalez KD, et al. Beyond Li-Fraumeni syndrome: clinical characteristics of families with p53 germline mutations. J Clin Oncol. 2009. 27(8):1250-6.
  47. McCuaig JM, et al. Routine TP53 testing for breast cancer under age 30: ready for prime time? Fam Cancer. 2012. 11(4):607-13.
  48. American Congress of Obstetricians and Gynecologists Committee on Genetics. Committee Opinion No. 634: Hereditary cancer syndromes and risk assessment. Obstet Gynecol. June 2015. 125(6):1538-1543.
  49. Norquist BM, et al. Inherited mutations in women with ovarian carcinoma. JAMA Oncol. 2015 Dec 30:1-9. [Epub ahead of print].