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

Abstract

Research question: Is there a precise and efficient haplotyping method to expand the application of preimplantation genetic testing (PGT)?

Design: In this study, eight cell-line families and 18 clinical families including 99 embryos were used to construct whole-genome haplotyping based on link-read sequencing (Phbol-seq) and optimized analytical workflow with a correction algorithm. The correction algorithm was based on a 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.

Results: With Phbol-seq, parental assembly errors and homologous recombination were accurately distinguished and corrected. Using the link-reads (>25% long-reads were ≥30 kilobases [kb]), complete genome-wide parental haplotypes were constructed, and the consistency of the typing results of each chromosome with a conventional method requiring other family members was more than 95%. In addition, the length of N50 contigs was 11.03-16.2 million bases (mb), which was far beyond the N50 contigs from long-read sequencing (148-863 kb). The complete haplotype analysis of all embryos could be performed by Phbol-seq and revealed 100% concordance with the available diagnostic results obtained by the conventional method requiring other family members.

Conclusions: Phbol-seq has high clinical value as a precise and cost-efficient whole-genome haplotyping method without probands as part of 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.

Keywords: Correction algorithm; Haplotyping; Link-read; Without proband.