Figure 1.

Genome-wide haplotyping and haplotype block copy number analysis in PGT-M. The figure has been adapted from Vermeesch et al. (2016). In this schematic we describe the principles for the simultaneous haplotyping and copy number analysis of a single-cell applied in the context of preimplantation genetic testing for a monogenic disorder (PGT-M). These principles are implemented in a series of algorithmic modules comprising siCHILD/Haplarithmisis. (A) (i) Shown here is a pedigree where the father is affected by an autosomal dominant disorder caused by a variant, which is passed on to the affected offspring. Haplotype phase (the string of linked informative single nucleotide polymorphisms (SNPs) belonging to one homologue) can be established with the use of the affected offspring genotypes or other relatives such as grandparents, parental siblings etc. To simplify the description we present only phasing of the paternal haplotypes but the same principles apply to the maternal ones. Informative paternal SNPs are those that are heterozygous (AB) in the father and homozygous in the mother. The offspring genotypes are used to phase the paternal SNPs and obtain the paternal haplotypes. Following this step, the single-cell genotypes corresponding to a biopsied blastomere, can be allocated to the inherited paternal haplotypes and the haplotype block harbouring the disease variant can be traced in the embryo (ii). This analytical procedure makes use of discrete genotypes (letters A and B) and it is implemented in Karyomapping. (iii) siCHILD/Haplarithmisis entails additional steps whereby the single-cell B-allele frequencies (BAF) (embryo) which correspond to the paternal informative SNP loci are assigned to paternal haplotype sub-categories. These ‘haplotype-assigned’ BAFs are segmented into blocks. The output of the analysis represents the copy number state (frequency) of each paternal haplotype block inherited by the embryo. This analysis is performed at the genome-wide level and provides the genome-wide copy-number state of haplotype blocks inherited by the embryo. (B) Schematic examples of haplarithm profiles corresponding to different ploidy scenarios. Shown here are single-chromosomes but in case of genome-wide ploidy anomalies the signature is detected along the entire genome. With siCHILD/Haplarithmisis, reciprocal haplotype block signatures are obtained for each parental genome. This feature increases the accuracy of copy number aberration detection. It also provides insights into the mechanism of aneuploidy or genome-wide ploidy detection. For example in the triploid digynic signature, a mitotic error contributed to the extra maternal chromosome because both maternal haplotypes are similar (i.e. the same breakpoint is detected in the maternal haplarithm = haplotype block copies). SGD = single gene disorder; Pat = paternal; Mat = maternal.