Oligonucleotide Arrays vs. Metaphase-Comparative Genomic Hybridisation and BAC Arrays for Single-Cell Analysis: First Applications to Preimplantation Genetic Diagnosis for Robertsonian Translocation Carriers

Abstract

Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers.

Novel Double Factor PGT strategy analyzing blastocyst stage embryos in a single NGS procedure

“…When using mCGH and aCGH to analyze embryos, these chromosomes usually present artifacts regions. [ 14 , 33 ] A positive correlation between DMSO addition and ADO rate reduction in the GEH-MDA method has been demonstrated in this work ( Table 3 ). Moreover, results also showed that the RG-MDA method produces less ADO and better coverage than any experimental condition tested for GEH-MDA.…”

“…These bands correspond to GC-rich regions and consequently prone to generate artifacts, as has been previously described by mCGH in chromosomes 1p, 16, 17, 19 and 22. [ 14 , 26 ]…”

“…An increasing number of studies have focused on developing new technologies for embryo screening in order to select the most viable for transfer. [ 11 ] These comprehensive cytogenetic techniques, such as metaphase comparative genomic hybridization (mCGH), single-nucleotide polymorphism arrays (SNP-arrays) or array-CGH (aCGH), have allowed the detection of both aneuploidies and segmental chromosome imbalances in oocytes,[ 12 ] cleavage-stage embryos[ 12 – 14 ] and blastocysts. [ 15 , 16 ]…”

Genomic and expression profiling reveal molecular heterogeneity of disseminated tumor cells in bone marrow of early breast cancer

“…Detection of genomic aberrancy in DTCs in these studies may have been limited by the low resolution of the cCGH method, which makes it less sensitive in detecting small copy number aberrations. 50 However, Holcomb and colleagues 49 used high-resolution array-based CGH analysis in small pools of EPCAM-positive DTCs; they reported that cells isolated from patients with localized prostate cancer had significantly fewer aberrations vs. their corresponding primary tumors. 49 …”