A precise and cost-efficient whole-genome haplotyping method without probands: preimplantation genetic testing analysis

Abstract

Research questionIs there a precise and efficient haplotyping method to expand the application on preimplantation genetic testing (PGT)? DesignIn this study, 8 cell line families and 18 clinical families including 99 embryos, were used to construct whole-genome haplotyping based on link-read sequencing and optimized analytical workflow with correction algorithm. Correction algorithm was based on differentiation of assembly errors and homologous recombination, in which the main feature of parental assembly error was that all embryos (embryo number >=2) had breakpoints at the same chromosome position. ResultsWith our method, parental assembly errors and homologous recombination were accurately distinguished and corrected, and using the link-reads (that ≥30 kilobases (KB) were more than 25%), complete genome-wide parental haplotypes were constructed, and the consistency of the typing results of each chromosome with conventional method requiring other family members was more than 95%. Besides, the length of N50 contigs was from 11.03 to 16.2 million bases (MB), which was far beyond to N50 contigs from long-read sequencing (148 KB∼863 KB). The complete haplotype analysis of all embryos could be exhibited by our method, and revealed 100% concordance with the available diagnostic results obtained by conventional method requiring other family members. ConclusionsOur method has high clinical value as a precise and cost-efficient whole-genome haplotyping method without probands as part of preimplantation genetic testing (PGT) and other genetic research, which could promote the application of PGT to decrease the birth of children with genetic diseases and the development of linkage-related genetic research.