Related Experiment Video
Updated: Mar 1, 2026
FISH for Pre-implantation Genetic Diagnosis
Published on: February 23, 2011
Salvage of fetal karyotype information from SNP array data obtained from products of conception with maternal cell
Karin Sasaki1,2, Kosei Abe1, Takahide Mori3
1Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
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 single-nucleotide polymorphism (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. © 2017 John Wiley & Sons, Ltd.
Insights
Maternal cell contamination (MCC) can lead to misdiagnosis. A new R package, snpsal, corrects single-nucleotide polymorphism (SNP) array data to accurately determine fetal karyotypes from miscarriage products of conception (POC) with MCC.
Area of Science:
- Genetics
- Reproductive Medicine
- Bioinformatics
Background:
- Maternal cell contamination (MCC) poses a significant risk of misdiagnosis in prenatal and miscarriage testing.
- Accurate fetal karyotyping is crucial for genetic counseling and reproductive health decisions.
Purpose of the Study:
- To develop a data correction method for salvaging fetal karyotype information from SNP array data in products of conception (POC) with MCC.
- To enable accurate fetal karyotype determination when parental genotype data are available.
Main Methods:
- Utilized SNP array data from mixed maternal and fetal DNA samples to develop and validate a data correction method.
- Implemented the correction method as an R package named snpsal.
- Applied the snpsal package to miscarriage specimens with MCC.
Main Results:
- A linear interpolation model was adopted as the data correction method.
- The snpsal R package successfully corrected SNP array data for POC with MCC.
- Previously undiagnosed miscarriage specimens were accurately diagnosed with normal and trisomy 16 karyotypes using snpsal.
Conclusions:
- The snpsal R package provides a rapid and accurate solution for estimating fetal karyotypes from SNP array data in POC with MCC.
- This method aids in overcoming diagnostic challenges posed by MCC in miscarriage testing.
- Facilitates improved genetic diagnosis and counseling for products of conception.
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