Oligonucleotide arrays vs. metaphase-comparative genomic hybridisation and BAC arrays for single-cell analysis: first applications to preimplantation genetic diagnosis for Robertsonian translocation carriers

PLoS One. 2014 Nov 21;9(11):e113223. doi: 10.1371/journal.pone.0113223. eCollection 2014.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blastomeres / cytology
  • Blastomeres / metabolism
  • Cell Line
  • Chromosome Banding
  • Chromosome Disorders / diagnosis
  • Chromosome Disorders / genetics
  • Chromosomes, Artificial, Bacterial / genetics
  • Comparative Genomic Hybridization / methods*
  • Female
  • Humans
  • Karyotyping
  • Metaphase / genetics
  • Oligonucleotide Array Sequence Analysis / methods*
  • Pregnancy
  • Preimplantation Diagnosis / methods*
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Single-Cell Analysis / methods*
  • Translocation, Genetic*

Grants and funding

This work was funded by the Fondo de Investigaciones Sanitarias, Instituto Carlos III (PI 08/0012, PI 11/00625) and Grup de Suport a la Recerca of the Generalitat de Catalunya (2009SGR1107). The first author had a pre-doctoral grant from the Universitat Autònoma de Barcelona. Qgenomics Laboratory provided support in the form of salaries for authors MG & LA, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.