scHaplotyper: haplotype construction and visualization for genetic diagnosis using single cell DNA sequencing data

Abstract

Background: Haplotyping reveals chromosome blocks inherited from parents to in vitro fertilized (IVF) embryos in preimplantation genetic diagnosis (PGD), enabling the observation of the transmission of disease alleles between generations. However, the methods of haplotyping that are suitable for single cells are limited because a whole genome amplification (WGA) process is performed before sequencing or genotyping in PGD, and true haplotype profiles of embryos need to be constructed based on genotypes that can contain many WGA artifacts.

Results: Here, we offer scHaplotyper as a genetic diagnosis tool that reconstructs and visualizes the haplotype profiles of single cells based on the Hidden Markov Model (HMM). scHaplotyper can trace the origin of each haplotype block in the embryo, enabling the detection of carrier status of disease alleles in each embryo. We applied this method in PGD in two families affected with genetic disorders, and the result was the healthy live births of two children in the two families, demonstrating the clinical application of this method.

Conclusion: Next generation sequencing (NGS) of preimplantation embryos enable genetic screening for families with genetic disorders, avoiding the birth of affected babies. With the validation and successful clinical application, we showed that scHaplotyper is a convenient and accurate method to screen out embryos. More patients with genetic disorder will benefit from the genetic diagnosis of embryos. The source code of scHaplotyper is available at GitHub repository: https://github.com/yzqheart/scHaplotyper.

Keywords: Haplotyping; Preimplantation genetic diagnosis; Single cell DNA sequencing; Single gene disorder.

Fig. 1

a The principle of scHaplotyper. First, trio father-mother-child and father-mother-embryo “core families” are constructed, and the affected child and embryos are phased to paternal and maternal inheritance. The affected child-inherited paternal and maternal haplotypes are shown as red and yellow, respectively. Second, the haplotypes of the embryos are reconstructed by regarding the affected child as a reference. The horizontal line indicates the mutation position on the chromosome. The embryo is diagnosed as carrying paternal and/or maternal mutations when the embryo inherits the same paternal and/or maternal haplotype block as the affected child at the mutation position on the chromosome

Fig. 2

a Constructed maternal haplotype inheritance in an autosomal dominant disorder family in which the mother and child (daughter) were affected with polycystic kidney disease. The inherited paternal haplotype is not shown. The horizontal line indicates the mutation position in the PKD1 gene on the chromosome. Yellow and blue represent maternal haplotype blocks that are in and not in the affected child’s genome, respectively. The E1, E2, E5, and E7 embryos had the mutation as determined by the inheritance of the same haplotype block as that identified in the affected child at the PKD1 gene location. The E3, E4, and E6 embryos were free of the mutation because they inherited a different haplotype block than was found in the affected child at the PKD1 gene location. A recombination was identified in the PKD1 gene in E8. b Constructed haplotypes (paternal and maternal) of a family with an autosomal recessive disorder in which the father and mother were unaffected carriers, but a child (son) was affected with mucopolysaccharidosis. The horizontal line indicates the mutation position of the GALNS gene on the chromosome. Red and green represent paternal haplotype blocks in and not in affected child genome, respectively. Yellow and blue represent maternal haplotype blocks in and not in the affected child’s genome, respectively. The results show that embryos E1 and E3 had only the paternal mutations, and embryos E2 and E4 had only the maternal mutations. All embryos were therefore unaffected carriers