Hereditary Endometrial Cancer Panel

Endometrial cancer (EC) is the 6^th most common diagnosed cancer among women worldwide. The vast majority of cases are sporadic, however it is estimated that 2%-5% are familial and linked to germline variants in genes associated with mismatch repair and Lynch syndrome (O'Hara and Bell. 2012. PubMed ID: 22888282). Approximately 75% of ECs are diagnosed in the early stages of tumor development, with a reported average survival rate of 75% (Siegel et al. 2013. PubMed ID: 23335087). Epidemiological studies have reported White women have a 2.9% lifetime risk of developing EC, compared to their African-American counterparts with a reported 1.7% lifetime risk (Burke et al. 2014. PubMed ID: 24905773). In women with a family history of Lynch Syndrome (LS), EC incidence is greater than or equal to that of colorectal cancer. In many cases, endometrial or ovarian cancer presents as the woman’s first malignancy (Aarnio et al. 1999. PubMed ID: 10188721; Vasen et al. 1999. PubMed ID: 10348829; Watson et al. 2008. PubMed ID: 18398828; Gayther and Pharoah. 2010. PubMed ID: 20456938).

The predominant EC histotypes are endometrioid, serous, and clear cell; however more rare carcinosarcomas, mucinous carcinomas, squamous cell carcinomas, and transitional cell carcinomas histotypes have been reported (O'Hara and Bell. 2012. PubMed ID: 22888282; Acharya et al. 2005. PubMed ID: 16321764; Dedes et al. 2011. PubMed ID: 21221135). Endometrioid ECs are estrogen-dependent tumors (Type I tumors) that are low-grade and diagnosed early in tumor progression. Surgical intervention is curative in most cases (5 year survival rate is ~90%). Established risk factors for endometrioid ECs are associated with unopposed estrogen exposure associated with obesity, nulliparity, early age of menarche, late age at menopause, and estrogen therapy in post-menopausal women (O'Hara and Bell. 2012. PubMed ID: 22888282). Serous and clear cell ECs are estrogen-independent (Type II tumors) that predominantly arise in post-menopausal women with no clear associated risk factor(s) besides increased age. Serous and clear cell histotypes have a worse prognosis than their endometrioid EC counterparts, accounting for 40-50% of all deaths from endometrial cancer, but only represent ~10-20% of cases (O'Hara and Bell. 2012. PubMed ID: 22888282; Hamilton et al. 2006. PubMed ID: 16495918, Hamilton et al. 2008. PubMed ID: 18197002; Setiawan et al. 2013. PubMed ID: 23733771).

Women with Lynch syndrome (LS) or hereditary nonpolyposis colorectal cancer, both autosomal dominant conditions, are at an increased risk for the development of colon, ovarian, and endometrial cancers (Burke et al. 2014. PubMed ID: 24905773). Lynch syndrome is characterized by germline variants within mismatch repair pathway genes, which include (but are not limited to) MLH1, MSH2, MSH6, and PMS2. Single stranded DNA breaks are repaired via the base excision repair or nucleotide excision repair systems with components encoded by the genes described above. Inheritance of a pathogenic germline variant in any of these genes results in a LS diagnosis, with a second variant occurring somatically later in life. LS-associated endometrial cancers are usually diagnosed after menopause, with only 15% diagnosed before the age of 50 and only 5% before the age of 40 (Gallup and Stock. 1984. PubMed ID: 6462572; Burke et al. 2014. PubMed ID: 24905773).

Several other genes have been implicated in the development of hereditary endometrial cancers. While BRCA1 and BRCA2 pathogenic variants are known to contribute to elevated risks of breast and ovarian cancer, studies support that pathogenic variants in BRCA1 particularly contribute to increased risk of endometrial cancer (Segev et al. 2015. PubMed ID: 25838159). Approximately 5% of women with uterine serous carcinoma have germline pathogenic variants in BRCA1, CHEK2, or TP53 (Pennington et al. 2013. PubMed ID: 22811390). 3’ end deletions of the EPCAM gene can result in LS via silencing of the adjacent MSH2 promoter and subsequently MSH2-deficiency. Carriers of EPCAM deletions have a 12% cumulative risk for endometrial cancer development, particularly when the deletion extends close to the MSH2 promoter region (Kempers et al. 2011. PubMed ID: 21145788). PTEN pathogenic variants are associated with autosomal dominant Cowden syndrome, which is characterized by hamartomatous tumors in multiple organ systems and an increase risk of multiple cancers. Lifetime risk of endometrial cancer in women with Cowden syndrome is approximately 10%-28%, and variants within PTEN account for a small proportion of endometrial cancer cases (Shai et al. 2014. PubMed ID: 24838932). Germline variants in POLD1 have been identified in European families with a history of colorectal cancer, colonic adenomas, and predispose individuals to endometrial and brain cancers. However, to date the incidence of POLD1 germline variants in endometrial cancer cases is unclear (Shai et al. 2014. PubMed ID: 24838932).

There is little information regarding the role of MUTYH in endometrial cancer. At least one MUTYH compound heterozygote with endometrial cancer has been identified (Barnetson et al. 2007. PubMed ID: 17956577), however other reports have failed to identify a genetic basis for MUTYH in endometrial cancer (Ashton et al. 2009. PubMed ID: 19338676).

Cumulative risk for endometrial cancer rises significantly after the age of 40, and by 70 varies depending on the gene in which a pathogenic variant is inherited. Women with endometrial cancer under the age of 50 having a first-degree relative diagnosed with a LS-related malignancy have a 43% chance of carrying a germline pathogenic variant in a mismatch repair gene and a 9% chance if two or more first-degree relatives have had an EC diagnosis (Gayther and Pharoah. 2010. PubMed ID: 20456938). For MLH1, the cumulative risk is reported to be 54%, while for MSH2 and MSH6 the cumulative risk is 21% and 16%-71%, respectively (Bonadona et al. 2011. PubMed ID: 21642682; Burke et al. 2014. PubMed ID: 24905773; Gayther and Pharoah. 2010. PubMed ID: 20456938).

Compared to other familial cancers, there have been relatively few studies investigating the familial risk of endometrial cancer (Gayther and Pharoah. 2010. PubMed ID: 20456938). Overall, Lynch syndrome is attributed to pathogenic variants predominantly in the MLH1, MSH2, MSH6, and PMS2 genes in approximately 50%, 40%, 7%-10% and < 5% of cases, respectively (Kohlmann and Gruber. 2012). The majority of these variants are single nucleotide substitutions or small insertions and deletions. Missense, nonsense and splicing EPCAM mutations are involved in congenital tufting enteropathy (Human Gene Mutation Database), whereas EPCAM deletions account for 1-3% of Lynch syndrome cases (Kohlmann and Gruber. 2012). Large deletions and genetic rearrangements account for 20%, 5%, 20%, 7%, and 100% of identifiable pathogenic variants in the MSH2, MLH1, PMS2, MSH6, and EPCAM genes respectively (Kohlmann and Gruber. 2012).

This panel typically provides ≥98% coverage of all coding exons of the genes listed, plus ~10 bases of flanking noncoding DNA. We define coverage as ≥20X NGS reads or Sanger sequencing.

DNA analysis of the PMS2 gene is complicated due to the presence of several pseudogenes. One particular pseudogene, PMS2CL, has high sequence similarity to PMS2 exons 11 to 15 (Blount et al. 2018. PubMed ID: 29286535). Next-generation sequencing (NGS) based copy number variant (CNV) analysis can detect deletions and duplications involving exons 1 to 10 of PMS2 but has less sensitivity for exons 11 through 15. Multiplex ligation-dependent probe amplification (MLPA) can detect deletions and duplications involving PMS2 exons 1 to 15.  Of note PMS2 MLPA is included in this test.