GYNplus

GYNplusTM is a next generation sequencing panel that simultaneously analyzes 13 high risk and moderate risk ovarian and uterine cancer susceptibility genes, all with published management guidelines.

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GYNplusTM is a next generation sequencing panel that simultaneously analyzes 13 high risk and moderate risk ovarian and uterine cancer susceptibility genes, all with published management guidelines.

GYNplus is a next generation sequencing (NGS) panel of 13 genes associated with an increased risk for ovarian and/or uterine cancer (BRCA1, BRCA2, BRIP1, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, PTEN, RAD51C, RAD51D, and TP53). These thirteen genes all have available management guidelines. Identification of a mutation in one of these genes can help estimate cancer risk and guide treatment, screening, and/or prevention decisions for the patient. Family members can be tested for the familial mutation to determine if they have an increased risk (positive for the familial mutation) or average risk (negative for the familial mutation) for cancer. Many individuals with a personal and/or family history of ovarian and/or uterine cancer may also have a personal and/or family history of breast and/or colorectal cancer and may be suspicious for more than one of the above syndromes. GYNplus may be ideal for such families.

Disease Name 
Uterine cancer
Ovarian cancer
Hereditary cancer
Hereditary breast and ovarian cancer (HBOC)
Lynch syndrome
Disease Information 

Ovarian cancer is the fifth most common cancer among women in developed countries, affecting approximately 1 in 71 (1.4%) women in their lifetime.  The National Cancer Institute (NCI) estimates that approximately 21,980 new cases of ovarian cancer will be diagnosed and 14,270 ovarian cancer deaths will occur in the U.S. in 2014.2  It is the leading cause of death from gynecologic malignancy, usually characterized by advanced presentation with regional dissemination in the peritoneal cavity. Epithelial ovarian cancer is the most common form, and up to 25% of epithelial cases may be due to inherited gene mutations.3,4 BRCA1 and BRCA2 are the most common causes of hereditary ovarian cancer, but several other genes are associated with increased ovarian cancer risk as well.3,5-7 However, many of these other genes are not included on this test. Please refer to OvaNext test information for additional details about these other genes.

Uterine cancer affects about 1 in 38 (2.6%)  women in their lifetime.1  The NCI estimates that approximately 54,870 new cases of uterine cancer will be diagnosed and 10,170 uterine cancer deaths will occur in the U.S. in 2015.2  Increased risk for uterine cancer has been identified in hereditary cancer syndromes, including Lynch syndrome and Cowden syndrome.

Breast cancer is the most common cancer in women in developed countries, affecting about 1 in 8 (12.5%) women in their lifetime.1 The National Cancer Institute (NCI) estimates that approximately 231,840 new cases of female breast cancer will be diagnosed in the U.S. in 2015. The majority of breast cancers are sporadic, but 5-10% are due to inherited causes.  Hereditary breast cancers tend to occur earlier in life than non-inherited sporadic cases and are more likely to occur in both breasts. The highly penetrant genes, BRCA1 and BRCA2, appear to be responsible for around half of hereditary breast cancer.8-10  However, additional genes have been discovered that are associated with increased breast cancer risk as well.8-12  Mutations in the genes on the GYNplus panel can confer an estimated 39–87% lifetime risk for breast cancer.  

Colorectal cancer (CRC) affects about 1 in 20 (5%) men and women in their lifetime.1 The NCI estimates that approximately 132,700 new cases will be diagnosed and 49,700 CRC deaths will occur in the U.S. in 2015. The majority of CRC is sporadic, but approximately 30% are familial, a subset of which have a strong genetic cause. Lynch syndrome is the most common form of hereditary CRC, but several other genes are associated with increased CRC risk as well.18

Lifetime cancer risks for ovarian, uterine, breast and colorectal cancers

GYNplus GENES

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 70.13-15,19-21 Male BRCA1 mutation carriers have a cumulative breast cancer lifetime risk of about 1.2% by age 70.22,23 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 70.13-15,24,25 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.22,23,25,26 BRCA1/2 mutation carriers may also be at an increased risk for melanoma, pancreatic cancer, and potentially other cancers.27 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.

BRIP1, RAD51C, 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 BRCA2.5,9,49 Mutations in these genes are associated with an increased risk for female breast cancer.49,50,51 The ovarian cancer risk associated with mutations in BRIP1, RAD51C, and RAD51D has been estimated to be up to 9%, 5-9% and 10-12%, respectively.6,7,51,52, 53. Of note, BRIP1 and RAD51C are each associated with a rare autosomal recessive disorder that affects multiple body systems.

MLH1, MSH2, MSH6, PMS2, and EPCAM ggermline 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.28-32

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.43,44 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).45 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.46,47 Additional studies have shown an increased risk for ovarian cancer.3, 48

PTEN is a gene associated with Cowden syndrome (CS), PTEN hamartoma tumor syndrome (PHTS), Bannayan-Riley-Ruvalcaba syndrome, Proteus syndrome, and autism spectrum disorder. CS is a multiple hamartoma syndrome with a high risk of developing tumors of the thyroid, breast, and endometrium. Mucocutaneous lesions, thyroid abnormalities, fibrocystic disease, multiple uterine leiomyomata, and macrocephaly can also be seen. Affected individuals have a lifetime risk of up to 50% for breast cancer, 10% for thyroid cancer, and 5-10% for endometrial cancer. Over 90% of individuals with CS will express some clinical manifestations by their twenties.33,34 Recent studies noted increased risks for renal cell cancer, colorectal cancer, and other cancers.17,35 One study quotes up to a 31-fold increase in RCC risk for PTEN mutation carriers as compared to the general population.36

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%.37 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.16,38 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 TP53.39-41

Testing Benefits & Indication 

Indications for Testing:

Families with a combination of the cancers below and some common red flags for hereditary cancer in the family would be appropriate to consider for GYNplus .

  • Ovarian cancer at any age
  • Early onset uterine cancer (diagnosed < 50 years of age)
  • Multiple primary cancers in one person (e.g. uterine and breast or thyroid cancer)
  • Multiple close family members with ovarian or uterine and other cancers (on the same side of the family)
  • Cancer histories that are suspicious for both HBOC and Lynch syndrome

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 if 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 (for example colon and uterine cancer in Lynch syndrome, or breast cancer and sarcoma with a TP53 mutation) 

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.42 Establishing a molecular diagnosis can help guide preventive measures, direct surgical options and estimate personal and familial cancer risk. 

Benefits of Testing:

Identifying patients with an inherited susceptibility for certain cancers can help with medical management. For example, 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 

GYNplus analyzes 13 genes (listed above). 12 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: 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 is detected by NGS and confirmed by PCR and agarose gel electrophoresis. The BRCA2 Portuguese founder mutation, c.156_157insAlu (also known as 384insAlu) is 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.54 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. 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 

GYNplus 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)
8835 GYNplus 14 - 21

 

Specialty 
Genes 
BRCA1
BRCA2
BRIP1
EPCAM
MLH1
MSH2
MSH6
PALB2
PMS2
PTEN
RAD51C
RAD51D
TP53
References 
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  2. National Cancer Institute. February 3, 2016. Available from: http://www.cancer.gov/.
  3. 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.
  4. Pennington KP, et al. Germline and somatic mutations in homologous recombination genes predict platinum response and survival in ovarian, fallopian tube, and peritoneal carcinomas. Clin Cancer Res. 2014. 20(3):764-75.
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  10. van der Groep P, et al. Pathology of hereditary breast cancer. Cell Oncol (Dordr). 2011. 34(2):71-88.
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  54. 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.