No evidence of somatic DNA copy number alterations in eutopic and ectopic endometrial tissue in endometriosis

De novo somatic copy number aberrations (SCNAs) in eutopic and ectopic endometria are thought to be involved in the pathogenesis of endometriosis. In this study we used, for the first time, high-density single nucleotide polymorphism-array technology for accurate detection of SCNAs, inherited DNA copy number variations (CNVs) and copy-neutral loss of heterozygosity (cn-LOH) patterns in patients with endometriosis. The Illumina HumanOmniExpress array was used to detect de novo somatic genomic alterations in eutopic and ectopic endometria from 11 women (eight with Stage III endometriosis and three with Stage IIIIV endometriosis) by comparatively analysing DNA from peripheral blood, eutopic endometrium and a pure population of endometriotic cells harvested from endometriotic lesions by laser capture microdissection (LCM). The frequency of the CNV in 3p14.1 from blood DNA of 187 endometriosis patients (94 with Stage III endometriosis and 93 with Stage IIIIV endometriosis) and 171 healthy women from the Estonian general population was evaluated. Analysis of array data showed that LCM DNA can be used successfully for detection of genetic changes as all inherited CNVs were identified in all tissues studied. No unique SCNAs or cases of cn-LOH were found in either eutopic or ectopic endometrium when compared with blood DNA. The frequency of the deletion allele in 3p14.1 did not differ between studied groups. In the present study no endometriosis-specific SCNAs or regions of cn-LOH in eutopic or ectopic endometrium were found. Nevertheless, as we studied only 17 endometriotic tissues derived from 11 patients we cannot entirely exclude the occurrence of rare SCNAs. Based on our results we suggest that molecular mechanisms other than chromosomal rearrangements most likely underlie the onset and progression of endometriosis.