1. NGS panel - Genetic testing for ovarian cancer

Ovarian cancer

October 06, 2017

Clinical features

Ovarian cancer is the most lethal of all gynecological cancers, and the annual incidence of ovarian cancer is 12.1 per 100,000 women1, 3. Familial ovarian carcinoma has been described in the context of hereditary breast and ovarian cancer (HBOC) syndrome. Inherited in an autosomal dominant fashion, HBOC is characterized by an increased risk for female and male breast cancer, ovarian cancer and other cancers 2, 3. Known genetic causes of HBOC have largely been explained by germline pathogenic variants in the BRCA1 and BRCA2 genes. The prevalence of BRCA1/2 pathogenic variants in the general population (excluding Ashkenazim) is estimated at 1:400 to 1:500 whereas the frequency in Ashkenazim Jewish are above 1:40 3.

Approximately 1 in every 5 women with a diagnosis of ovarian cancer has a hereditary gene pathogenic variant that is responsible for the development of cancer 4. The ovarian cancer risk by age 70 is estimated to be 20–27% 5.

Ovarian tumors develop when the cells in the ovary proliferate without control. There are two types of tumors which can occur in the ovaries:

  • Benign, non-cancerous growth, the tumor can be surgically removed completely
  • Malignant, cancerous growth, which has to be treated according to the stage and histological type of ovarian cancer.

There are three main ovarian cancers, classified according to cellular types:

  • Germ cell tumors, which start from the cells which are responsible for producing the “egg” cells
  • Stromal tumors, which are connected to the tissue cells that hold the ovary together and produce the female hormones estrogen and progesterone
  • Epithelial cells, which cover the outer surface of the ovary. This is the most common type, comprising 90% of ovarian cancer cases.

Ovarian cancer used to be called ‘the silent killer’ as most women are not diagnosed until the cancer has already spread. However, repeated symptoms could alert women to the possibility of ovarian cancer. These symptoms may include the following:

Early stage ovarian cancer:

  • Pain in the lower abdomen or side
  • A feeling of fullness in the abdomen.

Later stage ovarian cancer:

  • Back, abdominal pain
  • Irregular periods
  • Increased passing of urine
  • Constipation
  • Swollen abdomen

Advanced stage ovarian cancer:

  • Constipation
  • Tiredness
  • Loss of appetite
  • Shortness of breath.

Although the exact causes are not known, there are high risk factors which may increase the chances of developing ovarian cancer. The major risks of ovarian cancer include the following:

  • Family history of cancer: if another woman in the family has ovarian cancer, or cancer of the breast, uterus, colon or rectum, there may be an increased risk.
  • Personal history of cancer: if a woman has previously been diagnosed with any of the above cancers.
  • Age: ovarian cancer is more likely to develop after menopause. It is most common in women aged 50 and older, and woman who began to menstruate before age of 12.
  • Previous pregnancies: if women have had children before age of 35, they have a lower risk of developing ovarian cancer. Breastfeeding may lower the risk even further.
  • Use of infertility drugs: the use of the oral contraceptive pill decreases the chances of developing ovarian cancer. A woman is more at risk if she has not used any birth control methods, but this varies with each individual.
  • Childhood obesity: women who are obese at the age of 18 are at a higher risk of developing ovarian cancer before menopause.

Germline pathogenic variants are involved in more than one-fifth of ovarian cancer cases. The lifetime risk of ovarian cancer in patients with BRCA1 or BRCA2 genetic variants is 10-40%. According to data from large genetic studies collected at GeneReviews 3, the general population risk of ovarian cancer caused by any associated gene is 1-2%, while the general population risk of ovarian cancer in patients who are carriers of a BRCA1 pathogenic variant is 24-40%, and for patients who are carriers of a BRCA2 pathogenic variant it is 11-18%3. An additional study indicated that general risk of contracting ovarian cancer for individuals with a BRCA1 pathogenic variant is 39% by age 70 6. More recently, in a large cohort of BRCA1 and BRCA2 heterozygotes the estimated cumulative risks of ovarian cancer by age 70 was 59% for BRCA1 heterozygotes and 16.5% for BRCA2 heterozygotes 7.

Some of the common BRCA1 pathogenic variants reported to cause hereditary ovarian cancer include the following:

Brasilian population 8:

  • c.5203delTT frameshift pathogenic variant
  • c.1446 A > T; p.K443X nonsense pathogenic variant
  • c.560 + 2 T > A splice site pathogenic variant
  • Exon 16–17 deletion

Mexican population 9:

  • 3020insCT/c.2901insCT, frameshift pathogenic variant

Spanish population 10:

  • c.2805_2808delAGAT, small deletion

Danish population 11:

  • Deleterious frame-shift pathogenic variant, intronic variants, and missense pathogenic variant.

USA population 12:

  • Protein-truncating pathogenic variants identified in 4.6% of ovarian cancer patients in large USA study.

Ashkenazi population3:

  • c.185delAG pathogenic variant with a frequency of 1%
  • c.5382insC pathogenic variant with estimated prevalence of 0.1-0.15%

African population 13:

  • c.5382insC pathogenic variant
  • E881X pathogenic variant in BRCA1 was identified in 5,56% of African ovarian cancer affected patients 13

The most commonly observed pathogenic variant in the BRCA2 gene which are known to cause hereditary ovarian cancer (or breast-ovarian cancer) include the following:

Mexican population 9:

  • c.2639_2640delTG, small deletion
  • c.5114_5117delTAAA, small deletion

Spanish population 10:

  • c.2999delCT, frameshift pathogenic variant

Danish population 11:

  • Deleterious pathogenic variant (frame-shift and nonsense), intronic variants, and missense pathogenic variant

Ashkenazi Jewish 3:

  • c.6174delT with a frequency of around 1.52%

In addition to BRCA1/2, a contribution of hereditary ovarian carcinoma risk has also been attributed to MLH1, MSH2, MSH6, PMS2 and EPCAM, the mismatch repair (MMR) or Lynch genes 14, 15 and tumor suppressor genes (TP53, PTEN, STK11). Germ-line pathogenic variants in ATM, CHK2, NBS1, RAD50, PALB2, BRIP1 and other genes also moderately increase breast cancer risk 3 (see table).

With genetic testing, we are able today to provide detection of increased genetic risk of ovarian cancer in order to prevent cancer development in affected patients and thereby reduce cancer mortality. Genetic testing for ovarian cancer is also the most accurate means of determining the risk of hereditary breast and ovarian cancer.

Genes included in CENTOGENE´s Ovarian cancer panel

chr. locus
Protein Allelic disorders
2q35 BRCA1-associated RING domain 1 Susceptibility to breast cancer (OMIM: 114480)
17q21.31 Breast cancer 1 gene Susceptibility to familial breast cancer type 1 (604370); Susceptibility to pancreatic cancer type 4 (614320)
13q13.1 BRCA2 gene Breast-ovarian cancer type 2 (612555); Fanconi anemia D1 (605724); Pancreatic cancer (613347); Prostate cancer (176807); Wilms tumor (194070); Susceptibility to Breast cancer, male (14480); Glioblastoma type 3 (613029); Medulloblastoma (155255)
17q23.2 BRCA1-interacting protein 1 Breast cancer, early-onset (114480); Fanconi anemia J (609054)
2p21 Epithelial cell adhesion molecule Colorectal cancer, hereditary nonpolyposis, type 8 (613244); Diarrhea 5, with tufting enteropathy, congenital (613217)
3p22.2 MutL homologue of E.Coli type 1 Colorectal cancer, hereditary nonpolyposis, type 2 (609310); Mismatch repair cancer syndrome (276300); Muir-Torre syndrome (158320)
11q21 Meiotic recombination 11, homolog of S. cerevisiae A Ataxia-telangiectasia-like disorder (604391)
2p21 MutS, homolog of E. Coli type 2 Colorectal cancer, hereditary nonpolyposis, type 1 (120435); Mismatch repair cancer syndrome (276300); Muir-Torre syndrome (158320)
2p16.3 MutS homolog of E. Coli type 6 Colorectal cancer, hereditary nonpolyposis, type 5 (614350); Endometrial cancer, familial (608089); Mismatch repair cancer syndrome (276300)
8q21.3 Nibrin Aplastic anemia (609135); Leukemia, acute lymphoblastic (613065); Nijmegen breakage syndrome (251260)
2q32.2 Postmeiotic segregation increased S. Cervisiae type 1 Colorectal cancer, non-polyposis (no OMIM); Breast and ovarian cancer (no OMIM)
7p22.1 Postmeiotic segregation increased S. Cervisiae type 2 Colorectal cancer, hereditary nonpolyposis, type 4 (614337); Mismatch repair cancer syndrome (276300)
5q31.1 RAD50, homolgue of S. Cervisiae 50 Nijmegen breakage syndrome-like disorder (613078)
17q22 RAD51 paralog C Fanconi anemia, complementation group O (613390); Susceptibility to breast-ovarian cancer type 3 (613399)
17q12 RAD51 paralog D Susceptibility to breast-ovarian cancer 4 (614291)
19p13.3 Serine/Threonine protein kinase 11 Melanoma, malignant, somatic (no OMIM); Pancreatic cancer (260350); Peutz-Jeghers syndrome (175200); Testicular tumor, somatic (273300)
17p13.1 Tumor protein 53 Breast cancer (114480)- Colorectal cancer (114500); Li-Fraumeni syndrome (151623); Adrenal cortical carcinoma (202300); Choroid plexus papilloma (260500); Hepatocellular carcinoma (114550); Nasopharyngeal carcinoma (607107); Osteosarcoma (259500); Pancreatic cancer (260350); Basal cell carcinoma type 7 (614740); Glioma susceptibility type 1 (137800)

The primary forms of treatment of ovarian cancer include surgery, chemotherapy, hormone therapy, targeted therapy, and radiation therapy. Several studies have documented a significant (80-96%) risk reduction in ovarian cancer following risk-reducing oophorectomy 3. Furthermore, recent advances in understanding the molecular events preceding ovarian cancer have established the fallopian tube as the origin of the majority of high-grade serous ovarian cancers, leading to the consideration of salpingectomy with ovarian retention until the age of natural menopause as a first step in primary prevention. Oral contraceptive use has been associated with a reduction in ovarian cancer risk by 14% among women who had ever used oral contraceptives and 38% among long-term users 3.

CENTOGENE experts have designed the Ovarian cancer panel, which includes these genes: BARD1, BRCA1, BRCA2, BRIP1, EPCAM, MLH1, MRE11A, MSH2, MSH6, NBN, PMS1, PMS2, RAD50, RAD51C, RAD51D, STK11, TP53.

Differential diagnosis

The differential diagnosis of ovarian cancer-related disorders – depending on the major symptoms in the initial case – includes the following diseases1:

  • Ovarian cysts
  • Endometriosis
  • Pelvic inflammatory disorders
  • Appendiceal, adnexal or peritoneal tumors
  • Colon uterine or pancreatic cancer
  • Gastric adenocarcinoma
  • Ovarian torsion
  • Pelvic abscess
  • Irritable bowel syndrome
  • Ectopic pregnancy.

Testing strategy

CENTOGENE offers an advanced, fast and cost-effective strategy to test large NGS panels and diagnose complex phenotypes based on PCR-free whole genome sequencing and NGS technology. This approach offers an unparalleled advantage by reducing amplification/capture biases and providing sequencing of the entire gene with more uniform coverage.

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for ovarian cancer using NGS Panel Genomic targeted towards this specific phenotype:

Step 1: Whole genome sequencing from a single filter card. The sequencing covers the entire gene (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the ovarian cancer panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no pathogenic variants is identified after analysis of the Ovarian cancer panel, we further recommend continuing the bioinformatics analysis of the data using whole genome sequencing to cover those genes which are either implicated in an overlapping phenotype or could be involved in a similar pathway but are not strongly clinically implicated based on the current information in literature.

Referral reasons

Genetic testing for ovarian cancer is recommended for persons who show one or more of the following features:

  • History of breast cancer
  • Positive family history of the disease, e.g. when there are ovarian cancer cases in individual family members or multiple cases of breast cancer and/or ovarian cancer on the same side of the family
  • Present endometriosis and/or inability for pregnancy.

Women diagnosed with epithelial ovarian, tubal, and peritoneal cancers should receive genetic counseling and be offered genetic testing, even in the absence of a family history.

Test utility

Sequencing, deletion/duplication of ovarian cancer related genes should be performed in all individuals suspected of having ovarian cancer. In parallel, other genes reported to be related with this clinical phenotype should also be analyzed for the presence of pathogenic variants, due to the overlap in many clinical features caused by those particular genes.

Confirmation of a clinical diagnosis through genetic testing can allow for genetic counseling and may direct medical management. Genetic counseling can provide a patient and/or family with the natural history of ovarian cancer, identify at-risk family members, provide information about reproductive risks as well as preconception/prenatal options, and allow for appropriate referral for patient support and/or resources.

More information on CENTOGENE´s Ovarian cancer panel can be found in our genetic test catalogue.