Universal preimplantation genetic testing for monogenic disease (Karyomapping): diagnosis of >1000 unique disorders with no detected misdiagnoses

STUDY QUESTION

Can a universal diagnostic test (Karyomapping) be applied for preimplantation genetic testing for multiple monogenic disorders (PGT-M) and what is the misdiagnosis rate?

SUMMARY ANSWER

Among 9020 cases of PGT-M, >1000 different disorders were diagnosed by Karyomapping; independent validation of >70% of cases did not detect a misdiagnosis.

WHAT IS KNOWN ALREADY

PGT-M, first performed in 1992, has been used for ∼40 000 clinical cases worldwide. A limiting factor in direct testing for disease mutations, however, is the need to design assays specific for each affected allele. Karyomapping, based on haplotype phasing using SNP microarrays, was developed in 2010 as a single, method tracing inheritance of any monogenic disorder. Karyomapping eliminates the impact of allele drop-out and DNA contamination on test accuracy and facilitates a short work-up time as the same assay platform is used for every case.

STUDY DESIGN, SIZE, DURATION

Here, we used Karyomapping on a large PGT-M series from one diagnostic base from January 2014 to December 2021.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The 9020 individual Karyomapping cases were performed in three CooperSurgical genetic testing laboratories, in Livingston NJ, Michigan, or London (UK). All cases involved trophectoderm biopsy with embryo vitrification. DNA from cheek brush samples was obtained from both parents and an affected reference family member where possible. Genomic DNAs and that of whole genome amplified DNA from embryo biopsies were subjected to SNP microarray. Karyomapping was performed according to manufacturer’s instructions by first importing into BlueFuse Multi software. Inheritance was determined as to where at-risk allele(s) were inherited, with 10 supporting 5′ and 3′ Key SNPs in a 2 Mbp flanking window. Wherever possible, direct mutation testing was performed using Sanger sequencing.

MAIN RESULTS AND THE ROLE OF CHANCE

A total of 1017 unique disorders were detected from mutations in 912 genes. Validation of 4120 mutations was possible in 73% of cases by direct sequencing, which confirmed that all diagnoses that could be assayed were accurate.

LIMITATIONS, REASONS FOR CAUTION

Karyomapping can be limited by the availability of a reference, as well as parental genomic DNA, and some loci near the telomere may be more difficult to detect because of the limitations of the SNP array rather than the Karyomapping algorithm. Of the 27% of cases where we could not confirm the findings, we cannot comment on the misdiagnosis rate.

WIDER IMPLICATIONS OF THE FINDINGS

Karyomapping is now the single most used approach for PGT-M. As new approaches increasingly involve DNA sequencing, PGT for all genetic disease becomes possible by encapsulating the principles of Karyomapping and incorporating chromosome copy number analysis.

TRIAL REGISTRATION NUMBER

N/A.

STUDY FUNDING/COMPETING INTEREST(S)

This research was funded by CooperSurgical. The PhD programs of A.S. and O.W. were supported by CooperSurgical (paid to institution). A.S. has received travel support and IT equipment from CooperSurgical. O.W. has received travel support and provision of a company laptop from CooperSurgical. L.X., P.C., E.B., and T.G. are employees of and hold stock/share ownership in CooperSurgical. N.-N.G. is an employee of, has received meeting registration fees from, and holds stock/share ownership in CooperSurgical. L.R. is an employee of CooperSurgical. D.K.G. has received consulting fees and travel support from CooperSurgical. P.E. has nothing to declare.