Salvage of fetal karyotype information from SNP array data obtained from products of conception with maternal cell contamination

Objective Maternal cell contamination (MCC) is known to increase the risk of misdiagnosis in prenatal diagnosis as well as in diagnostic tests for the products of conception (POC) from miscarriages. We aimed to develop a data correction method to salvage fetal karyotype information from SNP array data for POC with MCC when parental genotype data are available. Methods We obtained SNP array data from mixed genomic DNAs of a mother-child pair and used the dataset to assess the accuracy of data correction. We subsequently applied our method to miscarriage specimens with MCC. Results We adopted a linear interpolation model as a data correction method and implemented the method in an R package, snpsal. We successfully determined the fetal karyotypes of two miscarriage specimens that were previously undiagnosed due to MCC to be normal in one case and trisomy 16 in the other case using snpsal. Conclusion The R package, snpsal, developed in this study facilitates rapid and accurate estimation of the fetal karyotype from SNP array data for POC with MCC.