Overview of Five-Years of Experience Performing Non-Invasive Fetal Sex Assessment in Maternal Blood

Droplet Digital PCR for Non-Invasive Prenatal Detection of Fetal Single-Gene Point Mutations in Maternal Plasma

Non-invasive prenatal testing (NIPT) is based on the detection and characterization of circulating cell-free fetal DNA (ccffDNA) in maternal plasma and aims to identify genetic abnormalities. At present, commercial NIPT kits can detect only aneuploidies, small deletions and insertions and some paternally inherited single-gene point mutations causing genetic diseases, but not maternally inherited ones. In this work, we have developed two NIPT assays, based on the innovative and sensitive droplet digital PCR (ddPCR) technology, to identify the two most common β thalassemia mutations in the Mediterranean area (β⁺IVSI-110 and β⁰39), maternally and/or paternally inherited, by fetal genotyping. The assays were optimized in terms of amplification efficiency and hybridization specificity, using mixtures of two genomic DNAs with different genotypes and percentages to simulate fetal and maternal circulating cell-free DNA (ccfDNA) at various gestational weeks. The two ddPCR assays were then applied to determine the fetal genotype from 52 maternal plasma samples at different gestational ages. The diagnostic outcomes were confirmed for all the samples by DNA sequencing. In the case of mutations inherited from the mother or from both parents, a precise dosage of normal and mutated alleles was required to determine the fetal genotype. In particular, we identified two diagnostic ranges for allelic ratio values statistically distinct and not overlapping, allowing correct fetal genotype determinations for almost all the analyzed samples. In conclusion, we have developed a simple and sensitive diagnostic tool, based on ddPCR, for the NIPT of β⁺IVSI-110 and β⁰39 mutations paternally and, for the first time, maternally inherited, a tool, which may be applied to other single point mutations causing monogenic diseases.

Evaluation of the efficiency of TaqMan duplex real-time PCR assay for non-invasive pre-natal assessment of foetal sex in equine

Accurate diagnosis of foetal sex in pregnant mare is helpful for many breeders, both for private or commercial purposes. In this study, in order to pre-natal foetal sexing in equine, we used TaqMan duplex real-time PCR to detect the specific regions of SRY and TSPY genes on extracted cell-free foetal DNA from maternal blood. Peripheral blood samples from 50 pregnant Arabian mares with singleton foetuses were collected. Cell-free foetal DNA was extracted from maternal plasma, and duplex real-time PCR assays were performed with TaqMan probes and primers. Amplification of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene was used as control of DNA extraction procedure. From the 50 sampled mares, 28 cases had female and 22 mares had male foetuses. The final results for 46 samples were conclusive, and from them, 43 cases were predicted correctly. Sensitivity, specificity and accuracy of the test were 90.48%, 96% and 93.48%, respectively. In conclusion, a TaqMan duplex real-time PCR was set up to pre-natal detection of foetal sex in equine. The method was fast and decreased the false-positive and false-negative results. The technique can be used as a routine procedure in farms by collecting only a blood sample.

Assessment of Fetal Rhesus D and Gender with Cell-Free DNA and Exosomes from Maternal Blood

The detection of fetal cell-free DNA (cfDNA) from maternal plasma has enabled the development of essential techniques in prenatal diagnosis during recent years. Extracellular vesicles including exosomes were determined to carry fetal DNA fragments. Considering the known difficulties during isolation and stability of cfDNA, exosomes might provide a new opportunity for prenatal diagnosis and screening. In this study, comparison of cfDNA and exosome DNA (exoDNA) for predicting the fetal sex and Rhesus D (RHD) genotype was performed by using real-time polymerase chain reaction with simultaneous amplification of sequences of SRY and RHD genes. Fetal sex and RHD were determined in 100 and 81 RHD-negative pregnant women with cfDNA and exoDNA, respectively. The gestation ages of pregnant women were between 9 and 40 weeks. The results were compared with the neonatal phenotype for gender and a serological test for RHD. The cfDNA revealed 95.75% sensitivity and 100% specificity in RHD positivity and 100% sensitivity and 95.45% specificity in SRY positivity. Cohen's agreement coefficient in the Kappa test ranged from 0.8 to 1.0 (P < 0.00001). Although the exoDNA failed to amplify 16 cases, the remaining 65 cases revealed a true estimate for both fetal RHD and SRY genes with 100% sensitivity and specificity. Successful application of exoDNA and cfDNA with real-time PCR for fetal genotyping enables this technique to be applied in the assessment of fetal RHD and gender during pregnancy, allowing initiation of early treatment methods and avoiding unnecessary interventions and cost.

Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis: a review

The animal’s blood is the most complicated and important biological liquid for veterinary medicine. In addition to standard methods that are always in use, recent technologies such as dynamic tensiometry (DT) of blood serum and PCR analysis of particular markers are in progress. The standard and modern biochemical tests are commonly used for general screening and, finally, complete diagnosis of animal health. Interpretation of major biochemical parameters is similar across animal species, but there are a few peculiarities in each case, especially well-known for cattle. The following directions are discussed here: hematological indicators; “total protein” and its fractions; some enzymes; major low-molecular metabolites (glucose, lipids, bilirubin, etc.); cations and anions. As example, the numerous correlations between DT data and biochemical parameters of cattle serum have been obtained and discussed. Changes in the cell-free nucleic acids (cfDNA) circulating in the blood have been studied and analyzed in a variety of conditions; for example, pregnancy, infectious and chronic diseases, and cancer. CfDNA can easily be detected using standard molecular biological techniques like DNA amplification and next-generation sequencing. The application of digital PCR even allows exact quantification of copy number variations which are for example important in prenatal diagnosis of chromosomal aberrations.

Non-invasive Prenatal Testing Using Fetal DNA

Non-invasive prenatal diagnosis (NIPD) is based on fetal DNA analysis starting from a simple peripheral blood sample, thus avoiding risks associated with conventional invasive techniques. During pregnancy, the fetal DNA increases to approximately 3-13% of the total circulating free DNA in maternal plasma. The very low amount of circulating cell-free fetal DNA (ccffDNA) in maternal plasma is a crucial issue, and requires specific and optimized techniques for ccffDNA purification from maternal plasma. In addition, highly sensitive detection approaches are required. In recent years, advanced ccffDNA investigation approaches have allowed the application of non-invasive prenatal testing (NIPT) to determine fetal sex, fetal rhesus D (RhD) genotyping, aneuploidies, micro-deletions and the detection of paternally inherited monogenic disorders. Finally, complex and innovative technologies such as digital polymerase chain reaction (dPCR) and next-generation sequencing (NGS) (exhibiting higher sensitivity and/or the capability to read the entire fetal genome from maternal plasma DNA) are expected to allow the detection, in the near future, of maternally inherited mutations that cause genetic diseases. The aim of this review is to introduce the principal ccffDNA characteristics and their applications as the basis of current and novel NIPT.

Bovine foetal sex determination-Different DNA extraction and amplification approaches for efficient livestock production

Foetal sex determination using polymerase chain reaction (PCR) in mammals is based on the amplification of gender-specific foetal DNA sequences circulating in maternal blood. The bovine synepitheliochorial placenta does not allow a direct contact between the trophoblast and the maternal blood, resulting in difficult passage of foetal DNA and, consequently, its very small amounts in maternal bloodstream. Circulating cell-free foetal DNA (ccffDNA) encompasses short nucleotide fragments (300-600 bp) in maternal circulation. The aim of this study was to assess this non-invasive method in accurate prenatal sexing in early and late gestational periods in comparison with ultrasound diagnostics. As various DNA isolation and amplification methods were tested, their success in obtaining reliable results was evaluated. Two groups were tested, each consisting of 20 pregnant cows. Blood of a bull and a non-pregnant heifer was the controls. Extraction of foetal DNA was accomplished by three different methods: using tubes with silicone membranes, a single-tube extraction without silicone membranes and phenol-chloroform extraction. Following each extraction method, foetal DNA was amplified using PCR and real-time PCR with both bAML and TSPY primers in a separate reaction. Positive results were obtained only after amplification of foetal DNA extracted with a single-tube extraction kit. In comparison with ultrasound examination results and foetal gender recorded at birth, the sensitivity of the PCR test was 90% in Group I, but the technique failed to detect male foetuses in Group II. The real-time PCR test sensitivity in Group I was 90% and in Group II 91.6%.

Cell-free Fetal Nucleic Acid Identifier Markers in Maternal Circulation

From the discovery of cell-free fetal (cff)-DNA in 1997 so far, many studies have been performed on various aspects of cff-nucleic acid. It is undoubted that currently, invasive prenatal diagnosis progresses to the noninvasive test. However, there are many problems. One of the most challenging issues in this field is differentiation and detection of the small amount of cff-nucleic acid in maternal plasma. Many markers and methods have been used for this purpose. This review makes an attempt to review and compare the studies in the field. Six identifier markers including Y-specific sequence, polymorphisms, epigenetic difference, DNA size difference, fetal mRNA, and microRNA as well as the advantages and disadvantages of each marker are discussed. This review provides a relatively perfect set on cff-nucleic acid biomarkers in various physiological and pathological status of pregnancy, helping to review and compare the prior obtained results, and improving designation in future studies.

Noninvasive Diagnosis of Fetal Gender: Utility of Combining DYS14 and SRY

OBJECTIVE

Diagnosis of fetal gender early in pregnancy is very useful as it would prevent invasive fetal sampling in almost half the cases at risk of inheriting X-linked disorders or those affecting sexual differentiation. Noninvasive prenatal diagnosis (NIPD) using circulating cell-free fetal (cff) DNA from maternal circulation has emerged as a useful alternative to existing methods for prenatal diagnosis of gender. NIPD eliminates the risk of miscarriage from invasive prenatal diagnosis and the necessity of possessing specialized obstetric skills for fetal tissue sampling. The aim of this study was to compare two Y chromosome markers-SRY and DYS14-for their utility in the diagnosis of fetal gender.

SUBJECTS AND METHODS

Forty-eight plasma samples from pregnant women between 9 and 25 weeks of gestation were analyzed. Real-time polymerase chain reaction was performed on cff DNA extracted from maternal plasma to detect fetal Y chromosome with SRY (n=27) and DYS14 (n=48) markers.

RESULTS

We observed 100% sensitivity and 85.6% specificity in noninvasive Y chromosome detection with the combined use of DYS14 and SRY markers (n=27) compared with the results obtained on using DYS14 (n=48 sensitivity 94%; specificity 71.4%) and SRY (n=27, sensitivity 84%; specificity 92.8%) markers alone.

CONCLUSION

Our results show that the test performance improved with the employment of two Y-amplification assays.