Whole-genome single-cell haplotyping, a generic method for preimplantation genetic diagnosis. M. Zamani Esteki1, E. Dimitriadou1, L. Mateiu1, C. Melotte1, N. Van der Aa1, P. Kumar1, R. Das1, K. Theunis1, J. Cheng1, 2, E. Legius1, Y. Moreau2, S. Debrock3, T. DHooghe3, P. Verdyck4, M. De Rycke4, 5, K. Sermon5, J. R. Vermeesch1, T. Voet1, 6 1) Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, Belgium; 2) Department of Electrical Engineering, ESAT-STADIUS, KU Leuven, Belgium; 3) Leuven University Fertility Center, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium; 4) Centre for Medical Genetics, Universitair Ziekenhuis Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium; 5) Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB) Laarbeeklaan 101, 1090 Brussels, Belgium; 6) Single-cell Genomics Centre, Welcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.

   Preimplantation genetic diagnosis (PGD) is the genetic testing of embryos prior to implantation to avoid the transmission of germline genetic disorders or of unbalanced chromosomal rearrangements when a parent is a balanced carrier. Current single-cell PCR or FISH PGD-assays require family-specific designs and labor-intensive workup. Array comparative genomic hybridization (aCGH)-based methods, which are mainly applied for preimplantation genetic screening (PGS) to discern diploid from aneuploid embryos, enable genome-wide aneuploidy detection but do not allow diagnosing single gene disorders. Here, we present a generic method that detects in single blastomeres not only the presence of Mendelian disorders genome wide, but also chromosomal rearrangements and aneuploidies, including their parental origin as well as the meiotic or mitotic nature of chromosomal trisomies. The method interrogates single nucleotide polymorphisms (SNPs) and uses a novel computational pipeline for single-cell genome-wide haplotyping and imputation of linked disease variants (siCHILD). Following stringent single-cell QC-metrics, a bimodal approach, based on discrete SNP-calls and continuous SNP B-allele fractions, respectively, reconstructs the parental haplotypes of the biopsied single cell. The approach proved accurate on 55 embryos from 12 couples carrying either autosomal dominant, recessive or X-linked Mendelian disorders, or simple or complex translocations. The method allowed diagnosing an embryo for multiple monogenic disorders at once, and, in contrast to current PGD for translocation cases, it enabled distinguishing embryos that inherited normal chromosomes from embryos that inherited a balanced configuration of the rearranged derivative chromosomes. The method facilitates genetic selection of embryos, and broadens the range of classic PGD.

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