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Allele-counting based non-invasive prenatal paternity testing for trisomy 21 fetuses:Methodology and case-based
Guosong Shen, Lvyan Chen1, Wenwen Li2
1Institut for Neuroscience, Technical University of Munich, 80802 Munich, Germany.
Legal Medicine (Tokyo, Japan)
|July 13, 2026
Summary
Non-invasive SNP testing accurately determines paternity in fetuses with Down syndrome, overcoming limitations of traditional STR analysis. This advanced method offers reliable prenatal paternity testing even with chromosomal aneuploidy.
Area of Science:
- Genetics
- Molecular Biology
- Forensic Science
Background:
- Prenatal paternity testing presents challenges with fetal chromosomal aneuploidies like Down syndrome.
- Traditional short tandem repeat (STR) analysis can be confounded by aneuploidy, affecting accuracy.
Purpose of the Study:
- To compare the efficacy of STR analysis and non-invasive single nucleotide polymorphism (SNP)-based testing for prenatal paternity determination.
- To evaluate the impact of trisomy 21 on paternity testing accuracy using both methods.
Main Methods:
- Collected amniotic fluid and parental blood samples from two Down syndrome pregnancies.
- Performed STR typing using the STRtyper-21G system.
- Conducted non-invasive prenatal paternity testing (NIPPT) using maternal plasma cell-free fetal DNA and a 5180 autosomal SNP capture panel, followed by high-throughput sequencing and analysis with the Prenatal Paternity Test Analysis System (PTAS).
Main Results:
- STR analysis showed tri-allelic patterns and dosage imbalance at chromosome 21 loci, necessitating exclusion and reducing the Combined Paternity Index (CPI).
- NIPPT yielded significantly higher CPIs (e.g., 2.40 × 10^183) with >99.999999% Cumulative Probability of Exclusion, unaffected by aneuploidy.
- SNP analysis demonstrated consistent numbers and distribution between trisomy 21 and euploid samples.
Conclusions:
- SNP-based NIPPT provides robust and reliable prenatal paternity evidence, unaffected by fetal chromosomal copy number variations.
- STR analysis is significantly confounded by aneuploidy, whereas SNP-based NIPPT offers a superior alternative for paternity testing in pregnancies with fetal chromosomal aneuploidy.
