1. EVALUATION AND IMPLEMENTATION OF ONEPGT FOR MONOGENIC CONDITIONS

Abstract

Introduction Preimplantation genetic testing for monogenic disorders (PGT-M) offers couples who carry a known inherited genetic condition the chance of having children free of the disorder. Currently, a bespoke genetic test is developed for each new condition which can take up to 6 months to implement; over 300 gene specific tests have been produced at our centre. OnePGT (Agilent) utilises genome-wide Next Generation Sequencing (NGS), allowing most genetic conditions to be tracked within families and embryos. Availability of a commercially developed genetic test eliminates the time involved with new test development. Evaluation of OnePGT for the testing of embryos for familial monogenic conditions has been undertaken. Material & methods Whole genome amplified (WGA) biopsy DNA was available for 33 embryos from 13 couples who previously underwent PGT-M; all embryo biopsies consisted of ∼5 trophectoderm cells. The genetic status of the embryos had been determined using an ISO15189 accredited STR haplotyping approach. 13 single gene disorders were tested including 9 autosomal dominant, 2 autosomal recessive and 2 X-linked. The embryo samples and respective reference family gDNA samples were processed using the OnePGT workflow, sequenced on a NextSeq550 and the data analysed using Alissa software for SNP haplotyping of the monogenic disorder, in conjunction with targeted assessment of copy number of the chromosome on which the gene was located, to aid interpretation of the monogenic results in embryos. Results OnePGT results were all in concordance with the outcomes from the STR results (33/33). The automated PGT-M call rate was 28/33 whilst 5 required manual inspection. Of these, 3 were because there was less than 1Mb between the genes to the end of the chromosome, 1 was due to the proximity of the gene to a chromosome crossover breakpoint and 1 was due to a reduced number of concordant SNPs which was caused by the low-level presence of both maternal haplotypes in the embryo. In one case, an affected embryo was successfully used as the reference for phasing for the couple and in another, the availability of chromosome copy number identified an embryo as having uniparental Inheritance. Conclusions The NGS approach of OnePGT has been successfully evaluated for determining the genetic status of embryos for monogenic disease. Due to the sequencing costs involved with NGS, it may not be merited when there is an established ‘in-house’ test. On balance, taking all laboratory aspects into consideration, OnePGT is a contender to evaluate new disorders. It is an anxious time for couples as they wait to know whether they have embryos suitable for replacement. Implementing OnePGT will eliminate test development and expedite genetic testing for couples requesting PGT-M for rare monogenic diseases. Declaration of Interest The OnePGT kits were provided by Agilent as part of an early access programme