Genotyping of STR and DIP-STR Markers in Plasma Cell-Free DNA for Simple and Rapid Noninvasive Prenatal Diagnosis of Zygosity of Twin Pregnancies

Microchimerism: The mystery of multiple DNA and its implications in forensic sciences

Microchimerism (MC) refers to the presence of small amounts of foreign cells or DNA in the tissues or circulation of an individual. It generally occurs through mother-fetus interaction, twin pregnancies, and intergenerational transmission. MC is influenced by genetic and environmental factors such as toxic conditions, immunological suppression, and various diseases (influenza, COVID-19, etc.). Progenitor cells transferred from the fetus to the mother through fetal MC are known to differentiate into neurons in the maternal brain. Although the relationship between these cells and the brain is not fully understood, it is thought that they may play a role in the emergence of some mental illnesses. The long-term presence of microchimeric cells in the body by differentiating into various cell types such as the brain, heart, bone, liver, and lung can lead to the presence of two or more DNA sets in an individual. This can lead to confusion in forensic identification and sex determination processes. This review aims to provide a comprehensive review of the definition, transmission pathways, detection duration in the human body, associated diseases, analytical detection techniques, and the importance of MC in forensic sciences. In this context, it is aimed to draw attention to the potential dangers of MC and contribute to the justice system. Furthermore, this study emphasizes the need for scientific research on this topic by creating a starting point for future research in the field of MC.

Noninvasive detection of twin zygosity using genome-wide linkage disequilibrium information

Dear Editor, in this study, we propose a novel linkage disequilibrium information-based noninvasive zygosity (LDNZ) assessment method in twin pregnancies. It combines fetus-specific allele frequency analysis with LD block to reduce the number of required single nucleotide polymorphism markers and experiment costs. LDNZ method offers a noninvasive, accurate, and cost-effective solution for zygosity assessment, addressing the need for precise obstetric care in twin pregnancies.

Early noninvasive prenatal paternity testing by targeted fetal DNA analysis

Today the challenge in paternity testing is to provide an accurate noninvasive assay that can be performed early during pregnancy. This requires the use of novel analytical methods capable of detecting the low fraction of circulating fetal DNA in maternal blood. We previously showed that forensic compound markers such as deletion/insertion polymorphisms-short tandem repeats (DIP-STR) can efficiently resolve complex mixed biological evidence including the target analysis of paternally inherited fetal alleles. In this study, we describe for the first time the validation of this type of markers in the first trimester of pregnancies, in addition to defining the statistical framework to evaluate paternity. To do so, we studied 47 DIP-STRs in 87 cases, with blood samples collected throughout gestation starting from the seven weeks of amenorrhea. Fetal DNA detection in the first trimester shows a false negative rate as low as 6%. The combined paternity index (CPI) results indicate that seven markers with fully informative genotypes are sufficient to determine the paternity. This study demonstrates that DIP-STR markers can be used from early pregnancy and that a small set of markers (about 40) is sufficient to address the question of paternity. The novel method offers substantial improvements over similar approaches in terms of reduced number of markers, lower costs and increased accuracy.

Identification and characterization of novel DIP-STRs from whole-genome sequencing data

In an attempt to enhance forensic DNA mixture deconvolution several alternative DNA typing approaches have been developed. Among these, DIP-STR compound markers can resolve extremely unbalanced two-source DNA mixtures of same-or-opposite sex donors, up to a 1:1000 minor:major DNA ratio. A forensic set of 10 markers was validated for casework and a larger set of 23 DIP-STRs has proven suitable to biogeographic ancestry inference and for prenatal paternity testing. Yet, to promote the widespread use of this original approach, more markers and multiplex panels need to be developed. To this end, here we describe an extended set of forensic DIP-STRs identified using currently available whole-genome sequencing datasets. Complete lists of Indels and STRs were obtained from reported frequencies of genetic variants of 76,156 genomes. About 3000 identified DIP-STRs candidates were shorter than 200 bp and 500 showed high haplotype variability estimated using the genotypes of individuals homozygous for the DIP or the STR. Here, we present 23 additional DIP-STRs validated for sensitivity, specificity and Swiss population variability. Finally, a set of 30 markers comprising seven previously validated ones is proposed for the prospective development of a forensic DIP-STR multiplex panel.

Non-invasive prenatal testing in the management of twin pregnancies

Twin pregnancies are common and associated with pregnancy complications and adverse outcomes. Prenatal clinical management is intensive and has been hampered by inferior screening and less acceptable invasive testing. For aneuploidy screening, meta‐analyses show that non‐invasive prenatal testing (NIPT) through analysis of cell‐free DNA (cf‐DNA) is superior to serum and ultrasound‐based tests. The positive predictive value for NIPT is driven strongly by the discriminatory power of the assay and only secondarily by the prior risk. Uncertainties in a priori risks for aneuploidies in twin pregnancies are therefore of lesser importance with NIPT. Additional information on zygosity can be obtained using NIPT. Establishing zygosity can be helpful when chorionicity was not reliably established early in pregnancy or where the there is a concern for one versus two affected fetuses. In dizygotic twin pregnancies, individual fetal fractions can be measured to ensure that both values are satisfactory. Vanishing twins can be identified by NIPT. Although clinical utility of routinely detecting vanishing twins has not yet been demonstrated, there are individual cases where cf‐DNA analysis could be helpful in explaining unusual clinical or laboratory observations. We conclude that cf‐DNA analysis and ultrasound have synergistic roles in the management of multiple gestational pregnancies.

What's already known about this topic?

In singleton pregnancies, non‐invasive prenatal testing (NIPT) for fetal aneuploidy is more effective than conventional serum and ultrasound‐based screening tests.

NIPT is more complex in dizygotic twin pregnancies due to the presence of two fetal genotypes.

Overall fetal fraction is higher in twin pregnancies but the individual contribution for each fetus is lower.

What does this study add?

A review of cell‐free DNA testing in twin pregnancies.

Individual fetal fractions in dizygotic twin pregnancies can be measured.

Zygosity can be established using NIPT and this can be particularly useful when there are concerns about chorionicity or determining whether one versus two fetuses are affected.

Vanishing twins can be detected through NIPT and this testing could be considered for some apparently singleton pregnancies with complications.

Detection of cell-free fetal DNA in maternal plasma using two types of compound markers

With the discovery of circulating cell-free fetal DNA (cffDNA) in maternal plasma, noninvasive prenatal testing became possible. However, analysis of low-level cffDNA against high background maternal DNA remains complicated and challenging. To circumvent this limitation, selective amplification of cffDNA was used in this study. Two kinds of compound markers (namely DIP-STR and SNP-STR), both based on selective amplification, were used here for targeting fetal DNA. By designing two allele-specific forward primers for DIP-STR and SNP-STR, DNA fragments with different DIP/SNP alleles can be selectively amplified. When analyzing maternal plasma DNA, these markers can selectively target paternally inherited fetal alleles whose DIP/SNP allele was not shared with the mother. In this study, 21 families were studied with six DIP-STRs and 11 SNP-STRs. Fetal DNA was successfully detected across plasma samples for at least one marker. Detection rate varied between DIP-STR and SNP-STR markers, and DIP-STR outperforms SNP-STR. Fetal alleles obtained from maternal plasma were double confirmed by genotyping paternal genomic DNA and fetal genomic DNA from amniocentesis. This study demonstrated that selective amplification strategy can be used to target cffDNA in maternal plasma, which will be a promising method for noninvasive prenatal paternity testing.

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

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.