15. THE INCIDENCE AND ORIGIN OF CHROMOSOME ANEUPLOIDIES IN HIGH QUALITY KARYOMAPPING SNP PROFILES

Abstract

Introduction Karyomapping serves as the universal PGT-M platform based on Mendelian inheritance of SNP markers which assist in identifying haplotypes linked to a mutated gene. Moreover, karyomapping enables detection of aneuploidies by interrogating genome-wide SNP data in embryo samples and assists in a selection of euploid embryos for a transfer. We have found out that high quality SNP profiles, characterized by overall call rate ≥95%, might be reliably used for the identification of mitotic chromosome errors, aneuploidies in mosaic or segmental chromosome aberrations. Since karyomapping utilizes parental DNA samples, the origin of identified aneuploidies might be tracked in embryo samples. Our study describes the incidence and origin of aneuploidy, aiming at segmental chromosomes errors and mosaic aneuploidies which represents hot topic in respect to their clinical significance. Material & methods SNP data obtained by HumanKaryomap-12 BeadChips, Illumina SNP arrays were analysed in 2085 trophectoderm (TE) samples derived from 319 couples requesting PGT-M. Mean maternal age was 32.4 ± 4.5. Based on the karyomapping SNP data QC metrics, mean and median call rate was 90.4% and 95%, respectivelly. In total, 936 embryos fulfilled criteria of high quality SNP profiles (call rate ≥95%). A subset of twenty TE samples detected with mitotic trisomies, mosaic aneuploidies and segmental chromosome abnormalities by karyomapping were reanalysed using PG-Seq™ kit, which is the fully validated PGT-A platform in our laboratory. We have observed full concordance between both platforms. Results Analysing 936 high quality TE samples, we have observed that 617 (65.9%) of them were euploid. The remaining 319 TE samples were detected with the following aberrations: a) only aneuploid 234 (73.4%) samples; b) only mosaic 43 (13.5%) samples; c) aneuploid + mosaic 42 (13.2%) samples. In other words, overall mosaicism rate in 936 TE samples was 9.1% (85/936) in our study. This number tend to be underestimated, since we did not report low level mosaicism due to a lack of proper sensitivity validation of the karyomapping in last years. We have detected segmental aneuploidies in 12.6% (118/936) of TE samples, 56 (47.4%) of them were present in mosaic form. Regarding the origin of aneuploidies, 87% (220/253) of whole chromosome aneuploidies affected maternal chromosomes, the ratio difference was even more highlighted in whole chromosome trisomies (93%; 91 out of 98). In contrast, segmental chromosome abnormalities affected more frequently paternal chromosomes (61,3%; 38 out of 62). Notably, this trend towards paternally related segmental aneuploidies were also followed in segmental chromosome abnormalities in mosaic (60,7%; 34 out of 56). Conclusions 1. According to our validation, high quality SNP profiles (overall SNP call rate ≥95%) enables detection of mitotic trisomies, mosaicism at 25% sensitivity level and segmental chromosome abnormalities (in 5Mb resolution). 2. Meiotic whole chromosome trisomies prevail over mitotic whole chromosome trisomies (in full or mosaic state) in the ratio 4:1. 3. Segmental chromosome abnormalities (in full or mosaic state) affects more frequently paternal chromosomes (P value 4. Whole chromosome aneuploidies in mosaic affect equally maternal and paternal chromosomes.