Assessment of QF-PCR as the first approach in prenatal diagnosis

The Rapid Evaluation of Down Syndrome With Quantitative Fluorescence Polymerase Chain Reaction (QF-PCR): A Pilot Study Among the Population in Eastern Uttar Pradesh, India

Background and objective Down syndrome (DS) is characterized by the presence of an additional chromosome; it is a typical chromosomal disorder causing intellectual disability in individuals. The diagnostic process for DS often involves conventional karyotyping, which can be time-consuming. Trisomy 21 and other chromosomal abnormalities may now be quickly and accurately diagnosed using quantitative fluorescence polymerase chain reaction (QF-PCR). In light of this, this study aimed to investigate chromosomal abnormalities in DS using conventional karyotyping and QF-PCR among the population in eastern Uttar Pradesh, India. Methods Blood samples from 40 individuals with clinically diagnosed DS were collected. Conventional karyotyping involved standard cytogenetic techniques, while QF-PCR utilized DNA extraction and analysis with chromosome-specific short tandem repeat (STR) markers. Results Various distinct physical characteristics were observed in the DS individuals, such as mongoloid slant and low-set ears. Karyotyping and QF-PCR analyses revealed different chromosomal configurations associated with DS trisomy 21, with additional chromosomal abnormalities found in some individuals, including partial monosomy 18 and mosaic trisomy 21. However, in a few cases, neither karyotyping nor QF-PCR revealed any abnormalities. Conclusions The study demonstrated that QF-PCR is a reliable and rapid method for diagnosing DS, providing results within 24 hours. This approach allows for the simultaneous diagnosis of a large number of samples and reduces the time required to obtain results. In the diagnostic procedure for DS, we believe QF-PCR will prove to be a useful tool. Furthermore, therapeutic interventions based on their clinical traits and molecular karyotyping can enhance the quality of life of people with DS.

Cilia and Nodal Flow in Asymmetry: An Engineering Perspective

Over the past several years, cilia in the primitive node have become recognized more and more for their contribution to development, and more specifically, for their role in axis determination. Although many of the mechanisms behind their influence remain undocumented, it is known that their presence and motion in the primitive node of developing embryos is the determinant of the left-right axis. Studies on cilial mechanics and nodal fluid dynamics have provided clues as to how this asymmetry mechanism works, and more importantly, have shown that direct manipulation of the flow field in the node can directly influence physiology. Although relatively uncommon, cilial disorders have been shown to have a variety of impacts on individuals from chronic respiratory infections to infertility, as well as situs inversus which is linked to congenital heart disease. After first providing background information pertinent to understanding nodal flow and information on why this discussion is important, this paper aims to give a review of the history of nodal cilia investigations, an overview of cilia mechanics and nodal flow dynamics, as well as a review of research studies current and past that sought to understand the mechanisms behind nodal cilia's involvement in symmetry-breaking pathways through a biomedical engineering perspective. This discussion has the additional intention to compile interdisciplinary knowledge on asymmetry and development such that it may encourage more collaborative efforts between the sciences on this topic, as well as provide insight on potential paths forward in the field.

Detection of partial deletion and mosaicism using quantitative fluorescent polymerase chain reaction: Case reports and a review of the literature

Background

Aneuploidy of chromosomes 13, 18, 21, X, and Y can be detected by the quantitative fluorescence polymerase chain reaction (QF‐PCR) performed with short tandem repeat (STR) markers. Although QF‐PCR is designed to detect whole chromosome trisomy, the partial deletion or mosaic of chromosomes may also be detected.

Methods

Partial deletion or mosaic of chromosomes in three cases was detected by QF‐PCR. Karyotyping and chromosome microarray analysis(CMA) were performed. We further reviewed the clinical utility of QF‐PCR in detecting mosaicisms and deletions/duplications.

Results

QF‐PCR demonstrated structurally abnormal 21, X, and Y chromosomes in primary amniotic cells. QF‐PCR results in these three cases showed abnormal peak height/peak area, which could not be interpreted according to the kit instructions. QF‐PCR results suggested that there were partial deletions or mosaicism, which were confirmed by karyotyping and CMA.

Conclusion

In addition to detecting trisomies of whole chromosomes, QF‐PCR can also detect deletion and mosaicism of chromosomes 13, 18, 21, X, and Y, which could suggest the presence of copy number variants (CNVs). Additional testing with genetic technologies, such as karyotyping or microarrays, is recommended when an uninformative pattern is suspected.

QF-PCR: a valuable first-line prenatal and postnatal test for common aneuploidies in South Africa

Quantitative fluorescence-polymerase chain reaction (QF-PCR) is useful for the detection of aneuploidies involving chromosomes 13, 18, 21, X and Y. Due to the rapid turn-around time and reduced cost compared to traditional karyotyping, QF-PCR has been used as an alternative test for both pre- and postnatal aneuploidy detection in Johannesburg, South Africa since 2001. An internal review of 13,396 aneuploidy tests processed using QF-PCR between January 2015 and December 2019 was performed, and the results showed that the majority (~ 88%) of cases were postnatal tests, with prenatal samples accounting for only ~ 12% of cases. The most common aneuploidies detected were Trisomy 21 (20.6%), Trisomy 18 (3.7%) and Trisomy 13 (2.4%), while sex chromosome aneuploidies were only detected in < 1% of cases. The average percentage of positive cases over the 5-year period was 32.1% for postnatal samples and 11.3% for prenatal samples. QF-PCR testing of the common aneuploidies is being used appropriately, and the high percentage of positive cases demonstrates the value of QF-PCR as prenatal and postnatal tests, particularly in limited resource settings. The higher proportion of positive postnatal cases suggests that referrals are clinically appropriate. However, there is under- and uneven utilization of genetic services in many provinces in South Africa, and the state of prenatal genetic services is poor, as reflected by the low number of prenatal referrals. These results demonstrate the need for programs which will improve the genetic knowledge of referring doctors and the general public, thereby improving the broader utilisation of QF-PCR aneuploidy diagnostic testing, so that patients receive appropriate diagnoses and subsequent management.

Prenatal diagnosis of syndromic alobar holoprosencephaly associated with digynic triploidy fetus

Holoprosencephaly (HPE) is a dramatic human brain malformation sequence with an extreme variable phenotypic spectrum and genetic heterogeneity, variable degree of severity and unknown etiology, in many cases. HPE is classified into syndromic, chromosomal, and non-syndromic, non-chromosomal. The most cases of HPE are syndromic. We present an atypical case of syndromic alobar HPE associated with digynic triploidy fetus, prenatally diagnosed, early at 18 weeks of gestation, by ultrasound (US) and complex genetic investigations. The US examination was performed with a specialized US machine, General Electric Voluson E10 OLED BT18, using two-dimensional (2D) scanning, three-dimensional (3D) image reconstruction, four-dimensional (4D) spatiotemporal image methodology and the highest power Doppler US technology. A detailed US examination of the fetus revealed several major abnormalities of the fetal head and severe facial malformations. Based on the antenatal US findings, the fetus was diagnosed with alobar HPE. After a careful examination and genetic counseling, additional cytogenetic investigations and molecular genetic analyses were performed, which revealed an abnormal number of 69 chromosomes, digynic triploidy (69,XXY). Two days later, the parents choose to interrupt the current gestation because of major fetal malformations. The pathological examination of the embryo reaffirmed the antenatal diagnostics.

A New Stepwise Molecular Work-Up After Chorionic Villi Sampling in Women With an Early Pregnancy Loss

Objective: To explore the use of a new molecular work-up based on the stepwise use of Quantitative Fluorescence PCR (QF-PCR) extended to eight chromosomes and single nucleotide polymorphism array (SNP-array) in chorionic villi obtained by chorionic villi sampling (CVS) offered to women experiencing an early pregnancy loss.

Methods: During a 3-year period (January 2016–December 2018), CVS was offered to women experiencing an early pregnancy loss before the evacuation of the products of conception (POC) to retrieve chorionic villi, irrespective of the number of previous losses. A new molecular work-up was prospectively assayed encompassing a first QF-PCR round (with the 21, 18, 13, 7, X, and Y chromosomes), a second QF-PCR round (with the 15, 16, and 22 chromosomes), and a high resolution SNP-array in those cases with normal QF-PCR results. A control group in which POC were collected after surgical uterine evacuation was used to be compared with the intervention group.

Results: Around 459 women were enrolled in the intervention group (CVS) and 185 in the control group (POC after uterine evacuation). The QF-PCR testing success rates were significantly higher in the intervention group (98.5%: 452/459) as compared to the control group (74%: 109/147; p < 0.001), while the chromosomal anomaly rate at the two QF-PCR rounds was similar between the two groups: 52% (234/452) in the intervention and 42% (46/109) in the control group (p = 0.073). The SNP-array was performed in 202 QF-PCR normal samples of the intervention group and revealed 67 (33%) atypical chromosomal anomalies (>10 Mb), 5 (2.5%) submicroscopic pathogenic copy number variants, and 2 (1%) variant of uncertain significance (VOUS).

Conclusion: Eighty-two percent of women experiencing an early pregnancy loss opted for a CVS. The testing success rates were higher in the intervention group (CVS; 98%) as compared to the control group (POC; 74%). The overall yields were 52% by QF-PCR (including three complete hydatiform moles), and 16% by SNP-array, including 15% atypical chromosomal anomalies and 1.1% submicroscopic pathogenic copy number variants.

An experience in prenatal diagnosis via QF-PCR of a female child with a 9.9 Mb pure deletion at 18p11.32-11.22

Quantitative Fluorescent - Polymerase Chain Reaction (QF-PCR) is a rapid prenatal diagnosis test for 21, 18, 13 and sex chromosomal aneuploidy detection. However, it could not detect partial trisomy or partial monosomy of those chromosomes. Here, we report a 19-month-old Vietnamese female with a 9.9 Mb pure deletion of chromosome 18 at 18p11.32-11.22 confirmed by next generation sequencing. The patient was short statured with facial dysmorphic features as well as motor skill and speech delays. First trimester screening showed high risk of trisomy 21 with only increased nuchal translucency (NT 3.9 mm) by ultrasound as an indication. Prenatal diagnosis by QF-PCR from amniotic DNA revealed normal disomy. Noticeably, two short tandem repeat (STR) markers D18S391 and D18S976 located on 18p exhibited uninformative patterns (one peak). Thus, our case suggested that the combination of both D18S391 and D18S976 markers with uninformative patterns in QF-PCR for prenatal diagnosis and increased NT in the first trimester ultrasound may be a significant indication of 18p monosomy.

Comparison of quantitative fluorescent polymerase chain reaction and karyotype analysis for prenatal screening of chromosomal aneuploidies in 270 amniotic fluid samples

Background Quantitative fluorescent polymerase chain reaction (QF-PCR) technique is a rapid prenatal aneuploidy detection method. This method can diagnose abnormality in chromosome 13, 18, 21, X and Y. Karyotyping is a technique in which, by the process of pairing and painting, all the chromosomes of an organism are displayed under a microscope. In the present study, a statistical comparison was made between karyotyping and QF-PCR for prenatal diagnosis. Methods A total of 270 samples were tested for QF-PCR and the results were compared with karyotyping. We also investigated heterozygosity of short tandem repeat (STR) markers by QF-PCR. Deoxyribonucleic acid (DNA) samples (n = 270) were extracted from amniotic fluid (AF) cells. After PCR amplifications, analysis was performed using GeneMarker. A Devyser QF-PCR kit containing 26 primers was used to estimate the observed heterozygosity of STR markers located on chromosome 13, 18, 21, X and Y. Results The results of karyotyping and QF-PCR were as follows: trisomy 13 (one case), trisomy 18 (five cases), trisomy 21 (five cases) and triploidy (one case). Chromosomal rearrangements and mosaicisms were not detected by QF-PCR but were detected by karyotyping. Maternal cell contamination (MCC) made the karyotyping fail but not the QF-PCR. Conclusion The QF-PCR method is especially important because it is fast, accurate, low cost and has a short turnaround time. This method will avoid ambiguity of karyotype results and parental anxiety. It will also shorten clinical management for high-risk families.

Multilevel regression modeling for aneuploidy classification and physical separation of maternal cell contamination facilitates the QF-PCR based analysis of common fetal aneuploidies

Background

The quantitative fluorescent polymerase chain reaction (QF-PCR) has proven to be a reliable method for detection of common fetal chromosomal aneuploidies. However, there are some technical shortcomings, such as uncertainty of aneuploidy determination when the short tandem repeats (STR) height ratio is unusual due to a large size difference between alleles or failure due to the presence of maternal cell contamination (MCC). The aim of our study is to facilitate the implementation of the QF-PCR as a rapid diagnostic test for common fetal aneuploidies.

Methods

Here, we describe an in-house one-tube multiplex QF-PCR method including 20 PCR markers (15 STR markers and 5 fixed size) for rapid prenatal diagnosis of chromosome 13, 18, 21, X and Y aneuploidies. In order to improve the aneuploidy classification of a given diallelic STR marker, we have employed a multilevel logistic regression analysis using "height-ratio" and "allele-size-difference" as fixed effects and "marker" as a random effect. We employed two regression models, one for the 2:1 height ratio (n = 48 genotypes) and another for the 1:2 height ratio (n = 41 genotypes) of the trisomic diallelic markers while using the same 9015 genotypes with normal 1:1 height ratio in both models. Furthermore, we have described a simple procedure for the treatment of the MCC, prior DNA isolation and QF-PCR analysis.

Results

For both models, we have achieved 100% specificity for the marker aneuploidy classification as compared to 98.60% (2:1 ratio) and 98.04% (1:2 ratio) specificity when using only the height ratio for classification. Treatment of the MCC enables a successful diagnosis rate of 76% among truly contaminated amniotic fluids.

Conclusions

Adjustment for the allele size difference and marker type improves the STR aneuploidy classification, which, complemented with appropriate treatment of contaminated amniotic fluids, eliminates sample re-testing and reinforces the robustness of the QF-PCR method for prenatal testing.

High accuracy of quantitative fluorescence polymerase chain reaction combined with non-invasive pre-natal testing for mid-pregnancy diagnosis of common fetal aneuploidies: A single-center experience in China

Quantitative fluorescence polymerase chain reaction (QF-PCR) may be used as a mid-pregnancy test to confirm the diagnosis of common fetal aneuploidies, but its use is controversial. The present study aimed to determine the value of QF-PCR for diagnostic confirmation of karyotyping and the impact of parental origin and meiosis stage on the detected aneuploidy. The present prospective cohort study included pregnant women (age, 21-45 years; gestational age, 17-25 weeks) who consulted between May 2015 and December 2016. Women were screened and only consecutive high-risk individuals were included (n=428). QF-PCR analysis of amniocytes was performed. Karyotype analysis was considered the gold standard. Parental karyotyping was performed if the embryo exhibited any aneuploidy. GeneMapper 3.2 was used for data analysis. There were no false-negative or false-positive QF-PCR results, with 100% concordance with the karyotype. The aneuploidy distribution (n=105) was 68.6% for trisomy 21, 19.0% for trisomy 18, 7.6% for sex chromosome aneuploidy, 3.8% for trisomy 13 and 1.0% for 48,XXX,+18. Regarding trisomy 21, most cases (86.1%) were of maternal origin, 8.3% paternal and 6.5% undefined. Trisomy 18 was 88.2% maternal and 11.8% paternal. Maternal meiosis stage errors in trisomy 21 mainly occurred in meiosis I, while the origin of trisomy 18 exhibited similar proportions between meiosis I and II. The combination of non-invasive pre-natal testing and QF-PCR may become a rapid and effective method for fetal aneuploidy detection. QF-PCR may provide more genetic information for clinical diagnosis and treatment than karyotyping alone.

Development and validation of a novel panel of 16 STR markers for simultaneous diagnosis of β-thalassemia, aneuploidy screening, maternal cell contamination detection and fetal sample authenticity in PND and PGD/PGS cases

Prenatal diagnosis (PND) may be complicated with sample mix-up; maternal cell contamination, non-paternity and allele drop out at different stages of diagnosis. Aneuploidy screening if combined with PND for a given single gene disorder, can help to detect any common aneuploidy as well as aiding sample authenticity and other probable complications which may arise during such procedures. This study was carried out to evaluate the effectiveness of a novel panel of STR markers combined as a multiplex PCR kit (HapScreen™ kit) for the detection of β-thalassemia, aneuploidy screening, ruling in/out maternal cell contamination (MCC), and sample authenticity. The kit uses 7 STR markers linked to β-globin gene (HBB) as well as using 9 markers for quantitative analysis of chromosomes 21, 18, 13, X and Y. Selection of the markers was to do linkage analysis with β-globin gene, segregation analysis and to perform a preliminary aneuploidy screening of fetal samples respectively. These markers (linked to the β-globin gene) were tested on more than 2185 samples and showed high heterozygosity values (68.4-91.4%). From 2185 fetal cases we found 3 cases of non-paternity, 5 cases of MCC, one case of sample mix-up and one case of trisomy 21 which otherwise may have end up to misdiagnosis. This kit was also successfully used on 231 blastomeres for 29 cases of pre-implantation genetic diagnosis (PGD) and screening (PGS). The markers used for simultaneous analysis of haplotype segregation and aneuploidy screening proved to be very valuable to confirm results obtained from direct mutation detection methods (i.e. ARMS, MLPA and sequencing) and aneuploidy screening.

Segmental Duplications as a Complement Strategy to Short Tandem Repeats in the Prenatal Diagnosis of Down Syndrome

BACKGROUND

Quantitative fluorescence-polymerase chain reaction (QF-PCR) is an inexpensive and accurate method for the prenatal diagnosis of aneuploidies that applies short tandem repeats (STRs) as a chromosome-specific marker. Despite its apparent advantages, QF-PCR is not applicable in all cases due to the presence of uninformative STRs. This study was carried out to investigate the efficiency of a method based on applying segmental duplications (SDs) in conjunction with STRs as an alternative to stand-alone STR-based QF-PCR for the diagnosis of Down syndrome.

METHODS

Fifty amniotic fluid samples from pregnant women carrying Down syndrome fetuses, 9 amniotic fluid samples with 1 or without any informative STR marker (inconclusive), and 100 normal samples were selected from Shiraz, Iran, between October 2015 and December 2016. Analysis was done using an in-house STR-SD-based multiplex QF-PCR and the results were compared. Statistical analysis was performed using MedCalc, version 14.

RESULTS

All the normal, Down syndrome, and inconclusive samples were accurately identified by the STR-SD-based multiplex QF-PCR, yielding 100% sensitivity and 100% specificity. Karyotype analysis confirmed all the cases with normal or trisomic results.

CONCLUSION

The STR-SD-based multiplex QF-PCR correctly identified all the normal and trisomy 21 samples regardless of the absence of informative STR markers. The STR-SD-based multiplex QF-PCR is a feasible and particularly useful assay in populations with a high prevalence of homozygote STR markers.

A Challenging Prenatal QF-PCR Rapid Aneuploidy Test Result Caused by a Maternally Inherited Triplication within Chromosome Xq26.2

The aim of this study was to investigate the origin of the biallelic trisomic amplification pattern of the X chromosome microsatellite marker DXS1187 in an otherwise normal male fetus, identified on routine rapid aneuploidy detection (RAD) testing by quantitative fluorescent-polymerase chain reaction (QF-PCR). Amniocentesis was performed on a 35-year-old female at 15 weeks, 2 days gestation for a positive first trimester screen. QF-PCR, metaphase FISH, and chromosomal microarray were carried out on both maternal and fetal DNA. Fetal QF-PCR showed a biallelic trisomic pattern for the X chromosome microsatellite marker DXS1187, with an otherwise normal male amplification pattern at all other sex chromosome markers. Chromosome analysis performed on cultured amniocytes showed a normal male karyotype. Chromosome microarray analysis identified a maternally inherited 304-kb copy number triplication within chromosome Xq26.2 encompassing the DXS1187 marker. The maternally inherited X chromosome harbors an apparently tandem 304-kb triplication that overlaps the DXS1187 marker. As the triplicated region is devoid of clinically relevant genes, it was considered as likely benign in the fetus. Postnatal follow-up reported a healthy male newborn. To our knowledge, this is a unique case demonstrating a "benign" copy number imbalance involving the DXS1187 marker detected by prenatal QF-PCR RAD.

Genetic testing of XY newborns with a suspected disorder of sex development

PURPOSE OF REVIEW

The current review focuses on the neonatal presentation of disorders of sex development, summarize the current approach to the evaluation of newborns and describes recent advances in understanding of underlying genetic aetiology of these conditions.

RECENT FINDINGS

Several possible candidate genes as well as other adverse environmental factors have been described as contributing to several clinical subgroups of 46,XY DSDs. Moreover, registry-based studies showed that infants with suspected DSD may have extragenital anomalies and in 46,XY cases, being small for gestational age (SGA), cardiac and neurological malformations are the commonest concomitant conditions.

SUMMARY

Considering that children and adults with DSD may be at risk of several comorbidities a clear aetiological diagnosis will guide further management. To date, a firm diagnosis is not reached in over half of the cases of 46,XY DSD. Whilst it is likely that improved diagnostic resources will bridge this gap in the future, the next challenge to the clinical community will be to show that such advances will result in an improvement in clinical care.

Application of Neural Networks for classification of Patau, Edwards, Down, Turner and Klinefelter Syndrome based on first trimester maternal serum screening data, ultrasonographic findings and patient demographics

Background

The usage of Artificial Neural Networks (ANNs) for genome-enabled classifications and establishing genome-phenotype correlations have been investigated more extensively over the past few years. The reason for this is that ANNs are good approximates of complex functions, so classification can be performed without the need for explicitly defined input-output model. This engineering tool can be applied for optimization of existing methods for disease/syndrome classification. Cytogenetic and molecular analyses are the most frequent tests used in prenatal diagnostic for the early detection of Turner, Klinefelter, Patau, Edwards and Down syndrome. These procedures can be lengthy, repetitive; and often employ invasive techniques so a robust automated method for classifying and reporting prenatal diagnostics would greatly help the clinicians with their routine work.

Methods

The database consisted of data collected from 2500 pregnant woman that came to the Institute of Gynecology, Infertility and Perinatology “Mehmedbasic” for routine antenatal care between January 2000 and December 2016. During first trimester all women were subject to screening test where values of maternal serum pregnancy-associated plasma protein A (PAPP-A) and free beta human chorionic gonadotropin (β-hCG) were measured. Also, fetal nuchal translucency thickness and the presence or absence of the nasal bone was observed using ultrasound.

Results

The architectures of linear feedforward and feedback neural networks were investigated for various training data distributions and number of neurons in hidden layer. Feedback neural network architecture out performed feedforward neural network architecture in predictive ability for all five aneuploidy prenatal syndrome classes. Feedforward neural network with 15 neurons in hidden layer achieved classification sensitivity of 92.00%. Classification sensitivity of feedback (Elman’s) neural network was 99.00%. Average accuracy of feedforward neural network was 89.6% and for feedback was 98.8%.

Conclusion

The results presented in this paper prove that an expert diagnostic system based on neural networks can be efficiently used for classification of five aneuploidy syndromes, covered with this study, based on first trimester maternal serum screening data, ultrasonographic findings and patient demographics. Developed Expert System proved to be simple, robust, and powerful in properly classifying prenatal aneuploidy syndromes.

Validation of QF-PCR for prenatal diagnoses in a Brazilian population

OBJECTIVES:

Quantitative fluorescence polymerase chain reaction (QF-PCR) is a rapid and reliable method for screening aneuploidies, but in Brazil, it is not used in public services. We investigated the accuracy of QF-PCR for the prenatal recognition of common aneuploidies and compared these results with cytogenetic results in our laboratory.

METHOD:

A ChromoQuant QF-PCR kit containing 24 primer pairs targeting loci on chromosomes 21, 13, 18, X and Y was employed to identify aneuploidies of the referred chromosomes.

RESULTS:

A total of 162 amniotic fluid samples analyzed using multiplex QF-PCR were compared with karyotyping analysis. The QF-PCR results were consistent with the results of cytogenetic analysis in 95.4% of all samples.

CONCLUSION:

QF-PCR was demonstrated to be efficient and reliable for prenatal aneuploidy screening. This study suggests that QF-PCR can be used as a rapid diagnostic method. However, rearrangements and some mosaic samples cannot be detected with this test; thus, those exceptions must undergo cytogenetic analysis.

Quantitative-fluorescent-PCR versus full karyotyping in prenatal diagnosis of common chromosome aneuploidies in southern Spain

BACKGROUND

Quantitative-fluorescent polymerase chain reaction (QF-PCR) is a reliable, rapid, and economic technique for prenatal diagnosis of the most common abnormalities. However, conventional karyotyping is expensive and requires a much longer time to yield results. It is currently under debate whether the replacement or restriction of karyotyping reduces the quality of prenatal test results. This study was undertaken to determine the percentage of clinically significant chromosomal abnormalities that would not be detected if QF-PCR was the main analysis method and karyotyping reserved for cases with increased nuchal translucency (NT) and/or abnormal ultrasound findings and to estimate the difference in cost between QF-PCR and full karyotyping.

METHODS

Nine hundred twenty-eight pregnant women underwent an invasive procedure at our center between May 2009 and December 2012, yielding 580 (62.5%) chorionic villous samples and 348 (37.5%) amniotic fluid samples. Samples were studied by both QF-PCR and full karyotyping. Karyotyping and detailed ultrasound findings were retrospectively analyzed.

RESULTS

If QF-PCR was the main analytic method and full karyotyping reserved for cases with elevated NT (≥4.5) and/or abnormal ultrasound findings, 12.7% of the patients would have required full karyotyping, 99% of the clinically significant chromosomal abnormalities would have been detected, and the cost would have been 54% lower than a policy of full karyotyping for all.

CONCLUSIONS

Detailed prenatal ultrasound scan can reduce the need for conventional karyotyping as a complement to QF-PCR in most prenatal samples, offering rapid results and reducing parental anxiety and healthcare costs.

Soft markers for aneuploidy following reassuring first trimester screening: what should be done?

PURPOSE OF REVIEW

The present article aims to review the current role of the soft markers on the second trimester ultrasound (STUS) in women after reassuring first trimester screening (FTS) in singleton pregnancies.

RECENT FINDINGS

Improvements in the FTS and the recent implementation of noninvasive prenatal testing (NIPT) for common aneuploidies have important impact on the prevalence of these conditions in the STUS. Some studies suggest that soft markers in the second trimester of the fetus without structural anomalies have a minor or no role in Down syndrome detection in a prescreened population with reassuring results. However, NIPT could be offered as a next step in the management of such pregnancies if the calculated new composite risk (NCR) for aneuploidy is increased. In the case of reassuring results, pregnancy follow-up for certain markers is advised.

SUMMARY

NIPT has emerged as a new method of prenatal testing and is feasible in the second trimester in women with increased NCR. However, apart from the Down syndrome screening, STUS screening remains a powerful tool in screening for other fetal aneuploidies, structural anomalies and pathological placental conditions and detection of specific soft markers that require pregnancy follow-up.

Performance of QF-PCR in targeted prenatal aneuploidy diagnosis: Indian scenario

OBJECTIVE

Among the rapid aneuploidy detection methods, QF-PCR has now become an alternative tool for prenatal aneuploidy diagnosis concomitant with karyotyping. This method has been validated in many of the western clinics but in India no study was conducted to assess its utility as standalone procedure. The study was designed to answer the question whether QF-PCR can be implemented as a standalone diagnostic method for rapid aneuploidy diagnosis in our present clinical setup?

MATERIALS AND METHODS

Study was conducted during March 2012 to August 2014 consisting of 270 prenatal samples that underwent for aneuploidy diagnosis. In addition to karyotyping, QF-PCR was also performed on these samples and the results were compared.

RESULTS

Of 270 samples screened, 262 samples showed euploid genome (125 normal male and 137 normal female). Eight samples were consistent with aneuploidy--four trisomy 21 male sample, 2 trisomy 21 female sample, 1 trisomy 18 samples and 1 Klinefelter sample. The specificity, sensitivity, positive prediction value and negative prediction values were 100% while false positive rate and false negative rate were 0%.

CONCLUSION

Outcome of this study strongly suggests that QF-PCR can be used as standalone procedure for targeted rapid aneuploidy diagnosis.

An Overview on Prenatal Screening for Chromosomal Aberrations

This article is a review of current and emerging methods used for prenatal detection of chromosomal aneuploidies. Chromosomal anomalies in the developing fetus can occur in any pregnancy and lead to death prior to or shortly after birth or to costly lifelong disabilities. Early detection of fetal chromosomal aneuploidies, an atypical number of certain chromosomes, can help parents evaluate their pregnancy options. Current diagnostic methods include maternal serum sampling or nuchal translucency testing, which are minimally invasive diagnostics, but lack sensitivity and specificity. The gold standard, karyotyping, requires amniocentesis or chorionic villus sampling, which are highly invasive and can cause abortions. In addition, many of these methods have long turnaround times, which can cause anxiety in mothers. Next-generation sequencing of fetal DNA in maternal blood enables minimally invasive, sensitive, and reasonably rapid analysis of fetal chromosomal anomalies and can be of clinical utility to parents. This review covers traditional methods and next-generation sequencing techniques for diagnosing aneuploidies in terms of clinical utility, technological characteristics, and market potential.

Use of Quantitative Fluorescent Polymerase Chain Reaction (QF PCR) in Prenatal Diagnostic of Fetal Aneuploidies in a 17 Month Period in Parallel with Karyotyping

Introduction:

QF PCR has recently entered diagnostic practice as a possible way to bypass culturing of the fetal cells, as well as to provide a rapid response following amniocentesis.

Material and methods:

The effective value of the QF PCR remains a much debated issue, positions ranging from that it makes classic kayotyping obsolete except in special occasions, to that it is no more than a guideline for a mandatory karyotype. Current practices of the gynecology specialists generates samples in such fashion that kariotyping of samples quickly falls behind to the point of obsoleteness, because, by the time a karyotype has been finished, a window of opportunity for termination of pregnancy has closed.

Results:

QF PCR provides a rapid response alternative, but it is necessary to establish its reproducibility, as well as an algorithm of its use along classic kariotyping. This study contains samples processed in a period from August 1, 2012 to December 31 2013 in both QF PCR and classic karyotype. Object of this study was compare results obtained by two methods, and establish confidence interval of the QF PCR testing. Overall, 661 amniotic fluid samples were processed and typed with QF PCR, out of which 221 were done in parallel with karyiotyping, as an confirmation of results.

Prenatal diagnosis of haemophilia B: the Italian experience

This article describes prenatal diagnosis (PND) of haemophilia B (HB) within the framework of Italian haemophilia centres and genetics laboratories. The study details the experience from six haemophilia genetic centres (three in the North, one in the Centre and two in the South of Italy) and summarizes the different techniques used to perform PND of HB during the last 15 years. To date, the Italian HB database includes 373 characterized unrelated patients and their genetic information has permitted the identification of 274 carriers of childbearing age. This database represents the main instrument for timely and precise PND. Sixty-six prenatal diagnoses were performed on 52 HB carriers whose average age at the time was 34 (ranging from 24 to 44 years). In 44 cases, genetic counselling for carrier status determination was performed before pregnancy, while eight were not studied prior to pregnancy. Foetal samples were obtained by chorionic villus sampling in 52 cases, by amniocentesis in 12 while two were diagnosed by analysis of free foetal DNA obtained from maternal peripheral blood. In 35 (53%) pregnancies the foetus was female. For 31 men (47%), haemophilia status was determined by analysis of previously determined informative markers or familial mutations (12 affected and 19 unaffected). There may be more than one laboratory involved in the PND diagnostic pathway (providing DNA extraction, karyotype analysis, gender determination, maternal contamination detection, molecular diagnosis and sequencing). Good communication between all the parties, coordinated by the haemophilia centre, is essential for a successful and rapid process.

Slovenian five-year experiences with rapid prenatal diagnosis of common chromosome aneuploidies using quantitative-fluorescence polymerase chain reaction

OBJECTIVE

Quantitative-fluorescence polymerase chain reaction (QF-PCR) was used to detect common fetal aneuploidies in pregnancies with increased (maternal age) or high risk (increased nuchal translucency, abnormal fetal ultrasonography, positive biochemical hormone test, or positive family history) for fetal aneuploidy.

METHODS

The QF-PCR testing was performed on 642 prenatal samples (73.3% amniotic fluids, 26.7% chorionic villus). DNA from prenatal samples were analyzed using an in-house-developed QF-PCR method with 20 micro-satellite markers located on the chromosomes 13, 18, 21, X and Y. Karyotyping of the 392 samples was done and both results were compared.

RESULTS

634/642 samples were successfully analyzed. In 7.1% of 634 cases numerical chromosome abnormalities were detected. Results of QF-PCR and karyotyping were compared in 392 cases. In the group, with increased risk of fetal trisomy the specificity and sensitivity of QF-PCR method was 100%. Among cases with high risk for fetal aneuploidy, sensitivity was 100% (86.6%-100%); however, the specificity was lower, 91.1% to 100%, depending on the referral reason.

CONCLUSIONS

In women, at advanced age QF-PCR can be used alone without karyotyping. In cases with higher risk, especially those with abnormal ultrasound findings, analysis performed only with QF-PCR is not a sufficient diagnostic method.

Toward optimal detection of the common prenatal aneuploidies by quantitative fluorescent-polymerase chain reaction: comparison of two commercial assays

BACKGROUND/AIM

To evaluate and compare the performance of the recently released Aneufast™ v2 (MolgentixSL) and QST*RplusV2 commercial assays (Gen-Probe), both designed for the quantitative fluorescent-polymerase chain reaction (PCR) detection of the common aneuploidies during pregnancy.

METHODS

A series of 160 consecutive fetal samples referred for rapid aneuploidy detection testing and an additional 25 samples enriched for the presence of an abnormality were selected for comparison.

RESULTS

To confidently rule out a chromosome abnormality, a second round of short tandem repeat typing was required for 14.1% (26) and 9.7% (18) of the specimens analyzed with Aneufast v2 and QST*RplusV2, respectively. Reflex testing was required for 7.6% (14) and 5.9% (11) of the specimens analyzed with respective assays to confidently rule out an autosomal trisomy. For the sex chromosomes, the difference in the amount of follow-up testing is greater between the assays, as a result of the inclusion in the initial PCR of the TAF9L paralogous marker in the QST*RplusV2 assay.

CONCLUSIONS

Overall, both assays performed similarly in the detection of aneuploidies. In this sample set, the QST*RplusV2 kit required less frequent reflex testing, which translates into shorter turnaround time and cost savings. The incorporation of the TAF9L paralogous sequence in the initial PCR is advantageous for diagnostic use.

Dual testing with QF-PCR and karyotype analysis for prenatal diagnosis of chromosomal abnormalities. Evaluation of 13,500 cases with consideration of using QF-PCR as a stand-alone test according to referral indications

OBJECTIVE

Evaluate the results obtained from Quantitative Fluorescent (QF)-PCR and conventional karyotype analysis to determine the advantages and disadvantages of dual testing in prenatal diagnosis.

METHODS

From 1 June 2006 to 1 June 2010, dual testing by QF-PCR and karyotype analysis was performed in 13,500 prenatal samples. The rates of concordant results between the two methods were evaluated and the rates of clinically significant chromosomal abnormalities undetected by QF-PCR were assessed.

RESULTS

Abnormal karyotype was found in 320 out of 13,500 cases (2.37%, 95% confidence interval (CI) 2.11-2.63%). From these, QF-PCR did not detect the abnormality in 70 cases (0.52%, 95% CI 0.4-0.64%), whereas 34 had a high/unknown risk of adverse outcome (0.25%, 95% CI 0.17-0.33%). By selectively applying dual testing only at cases with ultrasound findings and/or genetic history, 13 cases of high/unknown risk would have been missed (0.1%, 95% CI 0.05-0.15%).

CONCLUSION

Selective dual testing is expected to achieve a serious beneficial economical outcome and reduce parental anxiety produced by ambiguous cytogenetic findings. However, the percentage of 0.1% undetected clinically significant abnormalities cannot be ignored. A suggestion would include the offering of a choice to the pregnant women, undergoing prenatal screening, by informing them about different approaches and various complications.

[Chromosomal abnormality diagnosis of male infertility by QF-PCR]

To assess the clinical practice of quantitative fluorescence PCR (QF-PCR) in genetic diagnosis of male infertility patients, 78 nonobstructive male infertility patients were pooled for semen routine screening and sexual hormone determination; QF-PCR was applied to detect the polymorphic short tandem repeat (STR) and specific sequence tagged site (STS) of sex chromosomes; routine chromosome G-band was used for karyotype analysis and PCR was used for the detection of AZF microdeletion. Routine screening of semen found 18 azoospermia and 20 oligospermia patients (48.72%). Three patients with 47, XXY, two with 46,XX(SRY+)and one with AZFc microdeletion were detected using QF-PCR technique which were verified by chromosome G-band and PCR. This study suggests that QF-PCR is a comprehensive, rapid and reliable method for detecting abnormal chromosomal regions and microstructures compared with traditional tests and provides a better candidate for diagnosis of male infertility caused by chromosomal anomalies and gene mutation.

Rapid methods for targeted prenatal diagnosis of common chromosome aneuploidies

Improvements in non-invasive screening methods for trisomy 21 (Down syndrome) and other aneuploidies during the first and second trimester of pregnancy have radically changed the indications for prenatal diagnosis over the last decade. Consequently, there was a need for rapid tests for the detection of common chromosome aneuploidies resulting in the development of molecular methods for the rapid, targeted detection of (an)euploidies of the chromosomes 13, 18, 21 and the sex chromosomes. The analysis of large series of prenatal samples has shown that such tests can detect the great majority of chromosome abnormalities in prenatal diagnosis. This resulted in lively discussions on whether conventional karyotyping should remain the standard method for the majority of prenatal cases or can be replaced by rapid tests only. This review gives an overview of different aspects of the three most common tests for rapid, targeted prenatal detection of (an)euploidies, i.e. interphase fluorescence in-situ hybridisation (iFISH), quantitative fluorescent polymerase chain reaction (QF-PCR) and multiplex ligation-dependent probe amplification (MLPA).