2018 ISPD Conference

Haplotyping and copy number profiling of single cells by using extended family members: broadening the applicability of PGD
Jia Ding1, Aspasia Destouni2, Joris Vermeesch3

1UZ Leuven, Leuven, Belgium
2KUL, Leuven, Belgium
3Center for Medical genetics, Katholieke Universiteit Leuven, Leuven, Belgium
Objectives
Genome-wide linkage-analysis by haplotyping the entire genome of preimplantation embryos is being implemented as a generic approach for genetic diagnosis of inherited mutations. To enable the phasing of the genotypes into haplotypes, genotyping direct family members of the prospective parent carrying the mutation is required. Currently, the algorithm uses either (1) both parents of the affected prospective parent or (2) an affected or unaffected child of the affected couple. However, in many cases DNA from offspring and grandparents might not be available to phase the parental genotypes. This limitation deprives couples of gaining access to the generic genome-wide haplotyping-based PGD.
Methods
To expand the dynamic range of the technology in clinical practice, we optimized the algorithmic workflow to phase the parental genotypes using parental siblings. Our method exploits allelic states between family members and is independent of pedigree structure. As the genetic mutation is embedded in a local haplotype, it is possible to deduce the affected haplotype and copy number profiling of the embryo.
Results
Retrospective phasing of the parental haplotypes in twelve concluded PGD cases involving the analysis of 67 embryos in the Centre for Human Genetics, UZ Leuven between 2015-2016. We compared the genome-wide haplotypes and copy number states of each embryo, which were obtained with the new phasing approach to those initially obtained with the validated phasing strategy using grandparents and offspring during clinical PGD. In accordance to the expected degree of genetic relatedness between full siblings, new phasing approach could establish a diagnostic result in six out of the twelve (50%) of PGD couples included in this study.
Conclusions
We developed a method to enable generic haplotyping and genome-wide copy number profiling without the need to genotype grandparents or affected/unaffected offspring. This service significantly reduces the emotional stress imposed to the couple higher costs and increased waiting times in case a “private” protocol has to be set-up. More families can benefit from this new option without the need for customized test development. By including more than one extended family member, the chance of diagnosis the embryo will get increased. A rapid Pre-PGD work-up defines whether the carrier couple can benefit from this technology.