Genomic examination of endometrial precancers: serial analysis and diagnostic utility

The diagnosis of endometrial precancer (endometrioid intraepithelial neoplasia/EIN) is sometimes uncertain, with variable criteria and disagreements among gynecologic pathologists, leading to under/overtreatment. The endometrium is unique as an accessible anatomic location where diagnostic biopsies do not extirpate neoplastic lesions. Our purpose was to exploit these features to characterize serial genomic alterations along the pre-EIN/EIN/cancer continuum in individual women to ascertain if genomic analysis could add diagnostic value to histopathological review. Cases were selected based on 1) endometrial cancer diagnosis/hysterectomy 2) preceding endometrial biopsies including for some patients an early biopsy before an EIN diagnosis. A comprehensive panel was designed for genes recurrently mutated in endometrial cancer, including hereditary cancer loci. Formalin-fixed/paraffin-embedded specimens for each cancer, preceding samples, and matched germline DNA were subjected to barcoded high-throughput sequencing to identify mutations, hereditary and acquired, and track their origin and allelic frequency progression. In total, 98 samples from 24 patients with cancer/EIN were analyzed. Notably, more than one mutations were detectable for the majority of patients in pre-EIN biopsies. Serial analysis provided unique insights into the progression of individual cancers. In 18/21 cases, more than one mutation was confirmed by immunohistochemistry, providing unique views of histologic correlates. Class-defining mutations (e.g. POLE, TP53) were identified in several cases. A germline mutation was identified in one patient with a known cancer predisposition syndrome. Canonical driver mutations were not identified in 19 age-matched control (normal) endometria, arguing that with appropriate thresholds, age-related endometrial mutations should not frequently confound analyses of endometrial biopsy DNA. We conclude that genomic analysis of selected endometrial biopsies can be a valuable diagnostic adjunct to histology, also replacing in one assay diverse screening methods to identify cancer predisposition syndromes.