6. IDENTITY-BY-STATE BASED COMPREHENSIVE PGT: ADVANTAGES AND CHALLENGES

• Published in: Reproductive biomedicine online 2019-08, Vol.39, p.e30-e30
• Main Authors: Melotte, C., Ding, J., Dimitriadou, E., Tsuiko, O., Bogaert, K. Van Den, Debrock, S., Peeraer, K., Breckpot, J., Denayer, E., Vermeesch, J.R.
• Format: Article
• Language: English
• Subjects: haplarithmisis; identity-by-state; PGT-A; PGT-M
• ISSN: 1472-6483; 1472-6491
• DOI: 10.1016/j.rbmo.2019.04.059

Genome-wide haplotyping strategies, such as karyomapping, haplarithmisis and OnePGT, have paved the way for comprehensive PGT, leveraging PGT-M, PGT-A and PGT-SR in a single workflow. Nevertheless, family-specific challenges can complicate the implementation of current methods. First, to enable haplotype reconstruction, genotyping the prospective parents and direct family members, i.e. offspring of the couple or their parent(s), is required. However, if these references are not available or suitable for phasing, such approaches cannot be used, prompting investigation towards alternative phasing modules. Additionally, the advancement of current technologies leads to the identification of an increasing number of variants of unknown significance. Development of novel analysis approaches can assist further evaluation and interpretation of such variants, based on the familial segregation of the variant, in order to assess if PGT is an appropriate clinical option. Twelve couples i) burdened with a known hereditary genetic disorder participating in the genome-wide haplotyping-based PGT-M program and ii) with at least one parental sibling from the parental side carrying the genetic disorder available, were recruited for the development of the new method. Genotyping data from both prospective parents and parental sibling(s) were used to trace the shared and/or different allele and impute the disease-carrying allele based on identity-by-state (IBS) information. Concurrent haplotyping and copy number typing of embryo biopsies was then performed using an adapted version of siCHILD/haplarithmisis. Six out of 12 (50%) PGT-M couples could be phased using parental sibling(s). This is in line with the theoretical expectations of allele-sharing between sibling-pairs. Genome-wide haplotypes and copy-number profiles generated for each embryo using the new phasing approach were consequently compared to the clinical results, showing 100% concordancy. Clinical implementation of the method has resulted in the analysis of 7 families so far. Additionally, IBS analysis has enabled the inclusion of two special cases in the PGT program. In the first, PGT-M was offered for an X-linked disorder. The female partner had karyotype 47,XXX with presence of both maternal X chromosomes, so that no distinction could be made between the affected and unaffected allele. In the second, IBS analysis revealed the de novo and consequently pathogenic nature of an autosomal dominant variant in the mater