Evaluation of a Microhaplotype-Based Noninvasive Prenatal Test in Twin Gestations: Determination of Paternity, Zygosity, and Fetal Fraction.

Zhaochen Bai,Huan Wang,Linhuan Huang,Shaobin Lin,Hu Zhao,Xueling Ou,Zhiming He

doi:10.3390/genes12010026

Abstract

As a novel type of genetic marker, the microhaplotype has shown promising potential in forensic research. In the present study, we analyzed maternal plasma cell-free DNA (cfDNA) samples from twin pregnancies to validate microhaplotype-based noninvasive prenatal testing (NIPT) for paternity, zygosity, and fetal fraction (FF). Paternity was determined with the combined use of the relMix package, zygosity was evaluated by examining the presence of informative loci with two fetal genome complements, and FF was assessed through fetal allele ratios. Paternity was determined in 19 twin cases, among which 13 cases were considered dizygotic (DZ) twins based on the presence of 3~10 informative loci and the remaining 6 cases were considered monozygotic (MZ) twins because no informative locus was observed. With the fetal genomic genotypes as a reference, the accuracy of paternity and zygosity determination were confirmed by standard short tandem repeat (STR) analysis. Moreover, the lower FF, higher FF, and combined FF in each DZ plasma sample were closely related to the estimated value. This present preliminary study proposes that microhaplotype-based NIPT is applicable for paternity, zygosity, and FF determination in twin pregnancies, which are expected to be advantageous for both forensic and clinical settings.

Highlights

In recent years, the identification of fetal cell-free DNA in the maternal circulation has facilitated noninvasive prenatal testing (NIPT) for investigating monogenic diseases [1], identifying aneuploidies [2], and determining paternity [3,4,5,6]
(h) of LRH1,Hypothesis 3 (H3) and LRH2,H3 both twins, values for case 2 were all below 1 (Table S1, Figure 2), indicating the inclusion of alleged father (AF) as a biological father in relation to both twins in 18 cases but the exclusion of AF with regard to both twins where or d (H)i represents the fetus-specific allele with the lowerwas or higher sequencin case d2.(l)i
The targeted test described here constitutes an integrated microhaplotypebased assay that incorporates simultaneous determination of paternity, zygosity, and fetal fraction based on the same specimen in twin pregnancies, as a preliminary study

Summary

Introduction

The identification of fetal cell-free DNA (cfDNA) in the maternal circulation has facilitated noninvasive prenatal testing (NIPT) for investigating monogenic diseases [1], identifying aneuploidies [2], and determining paternity [3,4,5,6]. Pregnancies because the two fetuses could be either MZ, and genetically identical, or DZ, where they are likely to have different genotypes. In the field of forensic science, the validation of single-nucleotide polymorphism (SNP)based NIPT in twin pregnancies and the performance to assign zygosity and paternity have been reported in several studies previously [13,14,15]. The bioinformatic model utilized for paternity determination was based on the hypothesis that the twin fetuses had the same biological father, ignoring the probability of heteropaternity superfecundation (HS) among

Methods

Results

Discussion

Conclusion