Interpreting noninvasive prenatal paternity tests

Non-invasive prenatal paternity testing using cell-free fetal DNA from maternal plasma: DNA isolation and genetic marker studies

Invasive prenatal paternity tests can result in miscarriage and congenital malformations; therefore, a non-invasive method of testing is preferable. However, little progress could be made in this field until the introduction of cell-free fetal DNA (cffDNA) in 2009. In this review, two aspects regarding the history and development of non-invasive prenatal paternity testing (NIPAT) are summarized: (1) extraction and enrichment of cffDNA and (2) genetic marker-based studies. Although column-based kits are used widely for NIPAT, some researchers have suggested that an automated method, such as magnetic extraction, generally has a higher cffDNA yield than that of manual column-based extraction; therefore, its popularity might increase in the near future. In addition, size- and methylation-based enrichment methods are expected to perform better than formaldehyde-based methods. On the other hand, single nucleotide polymorphism-based techniques have contributed to NIPAT, whereas the application of short tandem repeat testing has so far been restricted to pregnant women bearing male fetuses only. Additional methods and techniques are expected to be innovated to facilitate the forensic practice of NIPAT.

Noninvasive fetal genotyping of paternally inherited alleles using targeted massively parallel sequencing in parentage testing cases

BACKGROUND

Researchers have sought to develop a noninvasive protocol for paternity analysis that uses fetal cell-free DNA (cfDNA) in maternal plasma. Massively parallel sequencing (MPS) is expected to overcome this challenge because it enables the analysis of millions of DNA molecules at a single-base resolution.

STUDY DESIGN AND METHODS

Seven women were involved in prenatal paternity testing cases. Before conventional invasive procedures, cfDNA was isolated from maternal plasma. Fetal tissues were then collected, as were blood samples from the alleged fathers. A custom array was designed that targeted 1497 regions containing single-nucleotide polymorphisms. These regions were massively parallel sequenced.

RESULTS

In these seven cases, the mean nonmaternal allele fractions in maternal plasma ranged from 3.22% to 6.17%. Setting the allele fraction cutoff of 2.5%, 300 to 491 loci were considered informative for paternal origin and no genetic incompatibilities with the alleged fathers were found. These results were concordant with those of conventional short tandem repeat genotyping. Validation results performed using fetal samples showed that sequencing noise was completely filtered out, and 78.35% to 99.19% of the paternal alleles were accurately genotyped. The fetal cfDNA concentrations ranged from 7.12% to 13.81%, and the overall sequencing error rates ranged from 0.40% to 0.93%.

CONCLUSION

In our study, we evaluate a straightforward method that can be used to identify paternal alleles based on analyses of paternal alleles and sequencing errors in maternal plasma. Our results support the notion that an MPS-based method could be utilized in noninvasive fetal genotyping and prenatal paternity analyses.