Use of single nucleotide polymorphism (SNP) arrays and next generation sequencing (NGS) to study the incidence, type and origin of aneuploidy in the human preimplantation embryo

Abstract

To perform a thorough investigation using a combination of the most advanced technologies available in an effort to decipher the aneuploidy ‘code’ in the human preimplantation embryo. Quantitative assessment and genotyping were undertaken concurrently for human blastocysts using SNP arrays and NGS. Single trophectoderm biopsies were obtained from blastocysts of couples undergoing in vitro fertilization (IVF) with preimplantation genetic diagnosis (PGD) for single gene disorders (SGD) and aneuploidy screening. Karyomapping SNP array (Illumina, USA) was used for PGD of SGD while, NGS via the VeriSeq PGS assay (Illumina) was utilized for comprehensive chromosome screening. Fisher’s exact test (GraphPad Software, USA) was used for statistical analysis. In total, over 19,000 chromosomes were screened in 417 embryos from 75 couples [maternal age: 34.1±0.5 years (mean ± SE)]. At least one chromosomal abnormality was detected in 49.2% (205/417) of the embryos assessed, with 48.3% of the embryos exhibiting only abnormalities of meiotic origin, 40% having only mitotic abnormalities and the remainder of the embryos presenting both types of abnormalities. Notably, maternal meiosis was associated with an equal number of events leading to gain vs. loss of chromosomal material (74 gains vs. 75 losses) and prevailed over paternal meiosis which consisted of events mainly involving loss of chromosomal material (27 losses vs. 1 gain) with almost half of the losses (40.7%) being partial. Of the overall number of aneuploidies detected, 15.7% were determined to be partial with the size of segments gained or lost ranging from 7.8 to 145.6 megabases. Incidences of maternally-derived meiotic errors and overall mitotic errors detected are presented in the table below in relation to maternal age: The incidence of maternal meiotic abnormalities was associated with increasing age, consistent with the higher rates of implantation failure and miscarriage experienced by older women. Mitotic errors, potentially producing mosaicism, were also common. Interestingly, aneuploidy of male meiotic origin was characterized by a predominance of monosomies compared with that of female origin, suggesting a sex-specific difference in the mechanism underlying segregation errors.Tabled 1No. of embryos with meiotic or mitotic errors vs. overall No. of embryos per maternal age groupMaternal Age GroupMaternal Meiotic ErrorsOverall Mitotic Errors< 3445/257 (17.5%)a,b63/257 (24.5%)35-3956/131 (42.7%)a,c34/131 (26.0%)> 4022/29 (75.9%)b,c9/29 (31.0%)Meiotic errors: a difference statistically significant at P<0.0001; b difference statistically significant at P<0.0001; c difference statistically significant at P<0.01.Mitotic errors: No difference detected between the different age groups (P>0.05). Open table in a new tab