# The Insufficient Number of Informative SNPs in a Preclinical Karyomapping Test for PGT-M Depends on the Reference Selected

## TL;DR

This study shows that the choice of family member used as a reference in karyomapping affects the success rate of preimplantation genetic testing for monogenic disorders.

## Contribution

The study is the first to analyze how the choice of reference family member impacts the availability of informative SNPs in karyomapping for PGT-M.

## Key findings

- Using a child or parent as a reference resulted in fewer non-applicable karyomapping cases compared to using a sibling.
- Neurofibromatosis type 1 and Kennedy disease had the highest rates of non-applicable karyomapping cases.
- The success rate of karyomapping was 91.6% across 263 couples tested.

## Abstract

Background/Objectives: Karyomapping, a genome-wide SNP analysis, has drastically changed the approach to preimplantation genetic testing for monogenic disorders (PGT-M). However, there are cases in which karyomapping cannot be applied due to an insufficient number of informative SNPs. In this study, we aimed to analyze for the first time whether an insufficient number of informative SNPs is related to the family member used as a reference. Methods: For the karyomapping pre-clinical test, in addition to the couple, one of the DNA samples from an additional family member (children, parent, sibling) is used as a reference for phasing the SNP allele. We analyzed 263 couples who underwent karyomapping for PGT-M at the CHA Fertility Center from May 2020 to December 2022. karyomapping data was scanned on an Illumina NextSeq and analyzed through the BlueFuse Multi software version 4.5. Results: Preclinical karyomapping tests were performed in 263 couples with 58 monogenic diseases. Karyomapping was applicable to PGT-M for 241 (91.6%) couples and not applicable for 22 (8.4%) couples. The percentages of “not applicable” cases according to the reference family member were 1.3% (1/80) in the children group, 5.4% (8/148) in the parent group, and 37.1% (13/35) in the sibling group. Among the genetic diseases studied, couples with neurofibromatosis type 1 (6/27, 22.2%) and Kennedy disease (5/5, 100%) had the highest rate of non-applicable cases. Conclusions: Our results suggest that a child or parent may be better than the sibling for karyomapping in PGT-M. These data provide useful information for selecting a reference among the family members for preclinical karyomapping tests.