Combined QF-PCR and MLPA molecular analysis of miscarriage products: an efficient and robust alternative to karyotype analysis

Genetic testing of products of conception in recurrent pregnancy loss evaluation

Genetic testing of products of conception (POC) has been proposed as a tool to be used in the evaluation of patients with recurrent pregnancy loss (RPL). Following a complete RPL evaluation, POC results may reveal an aneuploidy and provide an explanation for the miscarriage in more than 55% of cases. When the cytogenetic result of the pregnancy loss reveals a euploid pregnancy, management should be directed towards the identification of treatable abnormalities. Furthermore, the results of POC testing might better define a subgroup of patients with unexplained RPL who may benefit from expectant management versus preimplantation genetics (aneuploid unexplained RPL) or investigational therapy (euploid unexplained RPL).

Reducing misdiagnosis caused by maternal cell contamination in genetic testing for early pregnancy loss

The analysis of products of conception (POC) is clinically important to establish the cause of early pregnancy loss. Data from such analyses can lead to specific interventions in subsequent natural or assisted conceptions. The techniques available to examine the chromosomal composition of POC have limitations and can give misleading results when maternal cell contamination (MCC) is overlooked. The aim of this study was to develop a protocol for MCC assessment and to formulate POC material handling, testing, and reporting recommendations. Using array comparative genomic hybridization, we tested 86 POC samples, of which 47 sample pairs (DNA extracted from the POC sample and maternal DNA) were assessed for the presence of MCC. MCC was evaluated using an approach we developed, which exploited the genotyping of 14 STR, AMEL, and SRY loci. POC samples showing the clear presence of villi (63.9%) did not contain any signs of the maternal genome and can therefore be reliably tested using conventional methods. The proportion of 46,XX karyotype in the unselected sample batch was 0.39, which fell to 0.23 in visually good samples and was 0.27 in samples having no signs of contamination upon MCC testing. MCC assessment can rescue visually poor samples from being discarded or wrongly genotyped. We demonstrate here that classification based on visual POC material evaluation and MCC testing leads to predictable and reliable POC genetic testing outcomes. Our formulated recommendations covering POC material collection, transportation, primary and secondary processing, as well as the array of pertinent considerations discussed here, can be implemented by laboratories to improve their POC genetic testing practices. We anticipate our protocol for MCC assessment and recommendations will help reduce the misconception regarding the etiology of miscarried fetuses and foster informed decision-making by clinicians and patients dealing with early pregnancy loss.

Clinical Utility of a High-Resolution Melting Test for Screening Numerical Chromosomal Abnormalities in Recurrent Pregnancy Loss

Recurrent pregnancy loss (RPL) occurs in approximately 5% of clinically identified pregnancies. Determining the cause of RPL is essential. Genetic testing, accompanied by an evidence-based workup, is the well-accepted process for evaluating RPL; however, current genetic tests have limitations in clinical practice. We, thus, developed a high-resolution melting analysis-based test (HRM test) to screen for the most common numerical chromosomal abnormalities present in the products of conception. We examined 765 products-of-conception samples with known karyotypes retrospectively using the HRM test, which showed high technical sensitivity (96.1%) and specificity (96.3%) as well as a high positive predictive value (95.9%) for the screening of chromosomal abnormalities. The cost-effectiveness of four RPL evaluation strategies that employ different genetic tests, karyotyping, chromosomal microarray/next-generation sequencing, the HRM test, and a combination of the HRM test and chromosomal microarray/next-generation sequencing, was then compared. The costs of diagnosing an explained RPL using karyotyping or the HRM test alone were similar. Performance of the HRM screening test before chromosomal microarray/next-generation sequencing analysis improved cost-effectiveness by approximately 30%. Cost-effectiveness was more prominent in the advanced maternal age group. Thus, the HRM test could be used as an initial screening tool, followed by other diagnostic methods to improve the cost-effectiveness of RPL evaluation, or as an alternative genetic test when other methods are unavailable or unaffordable.

Analysis of chromosomes and the T helper 17 and regulatory T cell balance in patients with recurrent spontaneous abortion

The present study investigated the genetic etiology and possible immunological pathogenesis of recurrent spontaneous abortion by analyzing chromosome abnormalities, and the balance between T helper 17 (Th17) and regulatory T (Treg) cells. A total of 54 patients with recurrent spontaneous abortion were selected. The villus and decidual tissues, and peripheral venous blood were collected from each patient. Villus chromosome analysis was performed by high-throughput gene sequencing. Flow cytometry was used to detect Th17 and Treg cells in patients without chromosome abnormalities (n=30) and the control group (normal pregnancy; n=32). Immunoglobulin (IG) combined with human chorionic gonadotropin hormone (HCG) treatment was given to patients without chromosome abnormalities (n=30). Changes in the expression levels of Th17 and Treg cells before and after treatment were compared with patients with successful pregnancy (n=18). Before treatment, compared with the control group, the proportion of Th17 cells in peripheral blood and decidual tissue was increased and the proportion of Treg cells decreased. After treatment, compared with patients before treatment, the proportion of Th17 cells decreased and Treg cells increased, and the Th17 and Treg cells balance was reversed with a biased towards Treg cells. The present results suggested that the Th17 and Treg cell immune imbalance may be an important immune factor in recurrent spontaneous abortion. IG combined with HCG therapy may improve pregnancy outcomes by reversing the imbalance between Th17 and Treg cells.

Early Diagnostics of Freemartinism in Polish Holstein-Friesian Female Calves

Simple Summary

Freemartinism is the most common type of gender developmental disorder, resulting in infertility of heifers from multiple-sex twin pregnancies. The frequency of this syndrome is related to the frequency of multiple pregnancies, the number of which has significantly increased in dairy cattle populations (HF). Therefore, rapid diagnostics is necessary to enable early elimination of heifers with freemartinism from breeding. The aim of the study was to compare and identify the best method for early identification of freemartinism. The use of cytogenetic and molecular methods (PCR, short tandem repeats (STRs), real-time PCR) allowed us to conclude that molecular methods are more effective and guarantee fast and precise diagnosis. An additional advantage of molecular methods is the easy way to collect test material, which can be frozen, unlike blood samples for cytogenetic analysis, which must be fresh and delivered within 24 h to the laboratory, which generates further costs.

Abstract

Freemartinism in females born from heterosexual multiple pregnancies is characterized by the presence of XX/XY cell lines due to the formation of a shared blood system by anastomoses between fetal membranes of co–twins and leads to disturbed development of the reproductive system, including infertility. The aim of this study was to estimate the most precise and effective diagnostic method, especially useful for early identification of freemartinism in young female calves. The cytomolecular evaluation results of 24 Holstein-Friesian heifers from heterosexual twins was verified by molecular techniques: PCR, short tandem repeats (STRs), and relative quantitative PCR. The molecular analyses have been found to be a more efficient testing strategy, with a higher diagnostic success rate than karyotype evaluation. In 21 heifers, leucocyte chimerism determined by the 60, XX/60, XY karyotype was revealed—the proportion of the 60, XY male cell line in individual animals was in the range of 4–66%. In three cases, a normal karyotype 60, XX was identified, which indicates that anastomoses did not occur in 12.5% of studied twins and suggests that these potentially fertile heifers can be qualified for further breeding. The precise and early identification of freemartinism can be the basis for guidelines and selection recommendations concerning the reproductive performance of heifers born from heterosexual multiple pregnancies.

Efficient and cost-effective genetic analysis of products of conception and fetal tissues using a QF-PCR/array CGH strategy; five years of data

BACKGROUND

Traditional testing of miscarriage products involved culture of tissue followed by G-banded chromosome analysis; this approach has a high failure rate, is labour intensive and has a resolution of around 10 Mb. G-banded chromosome analysis has been replaced by molecular techniques in some laboratories; we previously introduced a QF-PCR/MLPA testing strategy in 2007. To improve diagnostic yield and efficiency we have now updated our testing strategy to a more comprehensive QF-PCR assay followed by array CGH. Here we describe the results from the last 5 years of service.

METHODS

Fetal tissue samples and products of conception were tested using QF-PCR which will detect aneuploidy for chromosomes 13, 14, 15, 16, 18, 21, 22, X and Y. Samples that were normal were then tested by aCGH and all imbalance >1Mb and fully penetrant clinically significant imbalance <1Mb was reported.

RESULTS

QF-PCR analysis identified aneuploidy/triploidy in 25.6% of samples. aCGH analysis detected imbalance in a further 9.6% of samples; this included 1.8% with submicroscopic imbalance and 0.5% of uncertain clinical significance. This approach has a failure rate of 1.4%, compared to 30% for G-banded chromosome analysis.

CONCLUSIONS

This efficient QF-PCR/aCGH strategy has a lower failure rate and higher diagnostic yield than karyotype or MLPA strategies; both findings are welcome developments for couples with recurrent miscarriage.

Molecular cytogenetic analysis of early spontaneous abortions conceived from varying assisted reproductive technology procedures

Background

Spontaneous abortion (SA) is the most common complication of pregnancy, and chromosome aberrations are the principal cause of the first trimester abortuses in natural conception (NC) The increasing use of assisted reproductive technology (ART) has raised concern about chromosome abnormalities in ART-initiated pregnancies. Up to date, the literature on the risk of aneuploidy in failed pregnancies among various ART factors remain limited and inconclusive. This study aimed to explore the genetic etiology of pregnancy loss conceived from varying ART procedures.

Results

A total of 560 cases of villus that were successfully collected and performed molecular karyotype analysis were enrolled in present research, including 92 cases of NC, 340 cases of in-vitro fertilization (IVF) and 128 cases of intracytoplasmic sperm injection (ICSI). There was no statistical difference in the distribution of karyotyping results and the aneuploidy rate of each individual chromosome among NC, IVF and ICSI group. Both the total chromosomal abnormality rate and the one chromosome aneuploidy rate were increased with maternal age. Compared with fresh ET abortion group, frozen-thawed embryo transfer (FET) abortion group had elder maternal age (34.68 ± 4.73 years vs. 33.41 ± 4.48 years, P = 0.003) but lower chromosomal aberration rate of abortus (58.33 % vs. 67.50 %, P = 0.040). A slightly higher incidence of chromosome segmental abnormalities was found in FET than in fresh ET abortion (5.26 % vs. 2.08 %, P = 0.066).

Conclusions

Chromosomal abnormality of fetus is the main cause of SA in the first trimester, no matter pregnancies are conceived through NC, IVF or ICSI. ART is a relatively safety treatment, and it does not enhance aneuploidy rate of abortus. The FET is bad for ongonging pregnancy and the aneuploidy rate were increased with maternal age.

Aneusomy detection with Karyolite-Bac on Beads® is a cost-efficient and high throughput strategy in the molecular analyses of the early pregnancy conception losses

Background

Approximately 10–15 % of all clinically recognized pregnancies end in miscarriage, the majority of them occur during the first trimester, underlying the cause of the loss. Genetic analysis of fetal tissues has the potential to provide valuable information and is highly recommended in some cases. Around 3–4 years ago, the gold standard for the analysis was the GTG Kayrotype, is well known that around 50 % of the tissue samples received failed to grow in culture. Different molecular techniques are used to improve the quality and the specificity of the study, intending to circumvent the limits of the Karyotype.

Results

Karyolite-BoBs™ (KL-BoB™) assay is a recent bead-based suspension, low density array technology with consistent results, probed that is an efficient molecular method to detect aneusomies in early pregnancy losses. Fifty samples from abortions were analyzed in order to probe and give more information about the methodology and analyze if KL-BoBs™ is a good and cost-efficient strategy. We detected 32 % of chromosomal abnormalities, in some of the cases more than one aberration was identified, the array CGH validate the observations.

Conclusions

This molecular strategy is a cost-effective sensitive tool in the early pregnancy loss study.

Molecular analysis of products of conception obtained by hysteroembryoscopy from infertile couples

PURPOSE

To analyze the molecular cytogenetic data obtained from products of conception (POC) obtained by selective biopsy of first trimester miscarriages and to estimate the rate of chromosomal anomalies in miscarriages from pregnancies achieved by natural conception (NC) or by assisted reproductive technology (ART) interventions.

METHODS

We used KaryoLite™ BoBs™ (PerkinElmer LAS, Wallac, Turku, Finland) technology to analyze 189 samples from ART or NC pregnancies.

RESULTS

All POC were successfully evaluated. A higher incidence of chromosomal abnormalities was observed in POC after ART using the patient's own oocytes than from NC pregnancies (62.7% vs. 40.6%; p < 0.05). The lowest incidence of chromosomal abnormalities was observed in POCs ART using donor eggs from women younger than 35 years (12.8%). No statistical differences in the percentage of abnormal miscarriages were observed in correlation with sperm concentration: a sperm concentration less than 5 million/mL produced 75% abnormal results and a concentration higher than 5 million/mL produced 51%.

CONCLUSIONS

POC analysis is essential to determine the cause of pregnancy loss. Using culture-independent molecular biology techniques to analyze POCs avoids limitations such as growth failure and reduces the time required for analysis. Selective biopsy of fetal tissue by hysteroembryoscopy avoids the risk of misdiagnosis due to maternal cell contamination. Our results show that maternal age, sperm quality, and ART-assisted pregnancies are risk factors for abnormal gestations.

Effects of subtelomeric copy number variations in miscarriages

PURPOSE

This study was performed on miscarriage samples for chromosome analysis to detect copy number variations (CNVs) related to subtelomeric regions, and with these results we aimed to adapt multiplex ligation-dependent probe amplification (MLPA) method for prenatal diagnosis.

MATERIALS AND METHODS

The cell cultures and DNA isolations were performed on 60 miscarriage samples. For maternal contamination analysis, DNA isolations and quantitative fluorescent polymerase chain reactions were done using peripheric blood of mothers who had miscarriages. We compared short tandem repeat peak profiles of miscarriage samples and mothers. The subtelomeric regions of the chromosomes were assessed using the MLPA method.

RESULTS

Of 43 miscarriage samples, 19 had normal karyotype (44.2%), 10 had numerical abnormalities (23.3%), and 2 had structural abnormalities (4.7%). Subtelomeric 16q duplication was determined in 2 of the 30 miscarriage samples investigated with MLPA method (6.6%).

CONCLUSION

There is no statistically significant difference between two groups (p > 0.05). However, the fact that the 6.6% subtelomeric CNV found in miscarriage samples was not found in controls, showed that further studies are required. We recommend that the miscarriage samples of the couples with recurrent miscarriage should be analyzed in terms of subtelomeric CNV after the exclusion of other clinical reasons.

Bacterial artificial chromosomes (BACs)-on-Beads™ as a diagnostic platform for the rapid aneuploidy screening of products of conception

The aim of the present study was to evaluate the use of KaryoLite™ bacterial artificial chromosomes (BACs)‑on‑Beads™ (BoBs) technology for the rapid screening of products of conception (POC). Validation and prospective studies were carried out on 85 and 95 patient samples, respectively. Validation studies had previously been analyzed using routine culture and G-banded karyotyping. BoBs resulted in an abnormality detection frequency of 27%, with a failure rate of <3%. The time required for processing was significantly lower compared with that of tissue culture. In conclusion, BoBs technology decreased the failure rate, while increasing the analytical sensitivity compared with G-banded karyotype analysis alone. Additionally, significant cost savings may be achieved with regard to the time of processing and analysis of specimens.

Multiplex ligation-dependent probe amplification (MLPA) in tumor diagnostics and prognostics

The increasing knowledge about genetic alterations and molecular biomarkers in cancer initiation and progression opens new possibilities for the treatment of various types of cancer. This requires the inclusion of sensitive, and preferably multiplex, methods for the detection of molecular genetic alterations in the toolbox of classic pathology. Multiplex ligation-dependent probe amplification (MLPA) is a multiplex polymerase chain reaction-based method that can detect changes in the gene copy number status, DNA methylation, and point mutations simultaneously. MLPA probes recognize target sequences of only 50 to 100 nucleotides in length. This makes it possible to use MLPA even on highly fragmented DNA, and allows the detection of small deletions encompassing only a single exon. MLPA is a reliable, cost-effective, and robust method that can be performed using a standard thermocycler and capillary electrophoresis equipment, generating results within 24 hours with a short hands-on working time. Up to 50 different genomic locations can be tested in a single reaction, which can be sufficient to detect those genetic alterations that are of diagnostic and prognostic significance in a certain tumor entity. In the last years, MLPA has been used successfully in tumor diagnostics and in cancer research. This review gives an overview on the collected experience of MLPA applications on tumor DNA, about the advantages but also potential pitfalls and limitations of this technique.

Aneuploidy detection in paraffin embedded tissue from products of conception by mini-STR genotyping

Autosomal trisomy is the most common genetic abnormality observed in pregnancy loss. We designed a panel of mini-short tandem repeats (mini-STRs) for aneuploidy detection in chromosomes 13, 16, 18 and 21 from fresh and formalin fixed, paraffin embedded (FFPE) samples from products of conception (POC). FFPE POCs with trisomy 13 (n = 6), trisomy 18 (n = 6), trisomy 21 (n = 12), 6 euploid for the chromosomes of interest and two trisomy 16 samples from fresh tissue were tested. Concordance between cytogenetics and genotyping was 100% for non-mosaic samples. Mini-STR genotyping is a viable method for targeted aneuploidy detection in low quality DNA samples.

Rapid aneusomy detection in products of conception using the KaryoLite™ BACs-on-Beads™ assay

OBJECTIVE

Chromosome analysis is the traditional method for detecting genetic abnormalities in products of conception, but it is prone to a high failure rate because of the requirement for cell culture. Molecular genetic tests do not require cell culture, but are either more expensive (e.g. chromosomal microarray) or less sensitive than chromosome analysis (e.g. fluorescence in situ hybridization, multiplex ligation mediated amplification). The KaryoLite™ BACs-on-Beads™ (KL-BoBs™) assay is highly multiplexed with low resolution coverage and is designed to detect aneusomy for any chromosome.

METHODS

We retrospectively tested 100 products of conception samples previously characterized by karyotype (n = 90), and/or microarray (n = 61) using KL-BoBs™. We included samples extracted from either cultured or direct specimens from placental villi or fetal somatic tissue, with a variety of chromosomal abnormalities typically identified in our clinical cytogenetics laboratory.

RESULTS

KL-BoBs™ and microarray results were concordant for all cases of aneusomy. On the basis of a review of 3794 consecutive cases in our laboratory, aneusomy accounts for 74.3% of abnormalities detected. Polyploidy and structural abnormalities were not detected by KL-BoBs™.

CONCLUSION

KL-BoBs™ is potentially very useful as a first line test for aneusomy detection because of its lower cost, rapid detection, and ability to generate a molecular karyotype for samples that fail to grow in culture.

QF-PCR: application, overview and review of the literature

Quantitative fluorescent polymerase chain reaction has been in diagnostic use in the UK for over 10 years and has proved to be a cost-effective, robust and accurate rapid prenatal test for common aneuploidies. Specific advantages include detection of triploidy, mosaicism and maternal cell contamination. Its application at our centre is described, with developments including stand-alone testing and improvements in strategies for the preparation and testing of chorionic villus biopsies.

Implementation and experience of an alternative QF-PCR and MLPA diagnostic strategy to detect chromosomal abnormalities in fetal and neonatal pathology samples

Chromosomal abnormalities are a significant cause of pregnancy loss. Solid tissue fetal and neonatal pathology samples are routinely examined by karyotype analysis after cell culture. However, there is a high failure rate, and this approach is expensive and labor intensive. We have therefore evaluated a new molecular strategy involving quantitative fluorescent polymerase chain reaction (QF-PCR) and subtelomere multiplex ligation-dependent probe amplification (MLPA) analysis. A retrospective audit showed that less than 4% of abnormal cases may not be detected by this molecular strategy. We validated this strategy in parallel with cytogenetic analysis on 110 patient samples, which included cases of fetal loss, still birth, neonatal death, termination of pregnancy, recurrent miscarriage, and sudden unexpected death in infancy. This validation showed that 55 of the 57 samples that gave a result for both strategies were concordant. During the 1st year of diagnostic testing, we analyzed 382 samples by the molecular strategy. A 16% abnormality rate was observed. These included trisomies 13, 18, 21, monosomy X, and triploidy detected by QF-PCR (77%), and 23% were other trisomies and subtelomere imbalances detected by MLPA. This strategy had a 92% success rate in contrast to the 20%-30% failure rate observed with cell culture and cytogenetic analysis. We conclude that QF-PCR and subtelomere MLPA is a suitable strategy for analysis of the majority of fetal and neonatal pathology samples, with many advantages over conventional cytogenetic analysis.

Full trisomy 5 in a sample of spontaneous abortion and Arias Stella reaction

BACKGROUND

Historically, 50% of spontaneously expelled abortuses have been thought to be chromosomally abnormal; about 60% are trisomies. In general, trisomy 16 is the most frequent chromosomal abnormality, followed by trisomy 21 and trisomy 22. So far only 1 case of a female fetus with multiple congenital malformations associated with full trisomy 5 has been described.

REPORT

We present a case of de novo full trisomy 5 in a spontaneous abortion sample. A young couple with normal constitutional karyotype experienced the second spontaneous abortion at 9 weeks of gestation, with the cytogenetic formula 47,XX,+5 in all analyzed cells.

CONCLUSIONS

The routine cytogenetic analysis of miscarriages is still an uncommon practice, but it can have a great impact on the management of couples with repeated pregnancy wastage. Besides of the obvious cost benefit for health care, such analysis would help the physician to decide about future patient management, as well as planning the genetic counseling.

Using FISH to increase the yield and accuracy of karyotypes from spontaneous abortion specimens

OBJECTIVE

Cytogenetic analysis of spontaneous abortions is frequently complicated by culture failure and maternal cell contamination (MCC). The objective of the study is to demonstrate that multiplex fluorescence in situ hybridization (FISH) can increase the yield and accuracy of karyotypes from spontaneous abortion specimens.

METHOD

A multiplex interphase FISH probe set was used to analyze two sample sets. (1) Uncultured tissues from 153 abortions samples with a normal 46,XX karyotype and (2) a series of 171 samples that either failed to grow or were contaminated. MCC studies were performed on 70 cultures where both karyotype and FISH indicated a normal female karyotype.

RESULTS

FISH showed 31% (53/171) of the specimens karyotyped as 46,XX were either male or abnormal; 23% (40/118) of these specimens were found to have an abnormal chromosome complement. In specimens with culture failure, FISH showed an abnormal complement in 44.4% (68/153). MCC studies showed 41.49% (29/70) cultures of maternal origin, 45.7% (32/70) fetal, 11.4% (8/70) a maternal/fetal mixture and 1 diploid mole.

CONCLUSION

Results demonstrate the utility of a simple FISH panel in increasing the detection rate of abnormal karyotypes. They also reveal the high frequency of overgrowth of maternal cells in cultured specimens from villi after embryonic loss.

MLPA for confirmation of array CGH results and determination of inheritance

Background

Array CGH has recently been introduced into our laboratory in place of karyotype analysis for patients with suspected genomic imbalance. Results require confirmation to check sample identity, and analysis of parental samples to determine inheritance and thus assess the clinical significance of the abnormality. Here we describe an MLPA-based strategy for the follow-up of abnormal aCGH results.

Results

In the first 17 months of our MLPA-based aCGH follow-up service, 317 different custom MLPA probes for novel aCGH-detected abnormalities were developed for inheritance studies in 164 families. In addition, 110 samples were tested for confirmation of aCGH-detected abnormalities in common syndromic or subtelomeric regions using commercial MLPA kits. Overall, a total of 1215 samples have been tested by MLPA. A total of 72 de novo abnormalities were confirmed.

Conclusions

Confirmation of aCGH-detected abnormalities and inheritance of these abnormalities are essential for accurate diagnosis and interpretation of aCGH results. The development of a new service utilising custom made MLPA probes and commercial MLPA kits for follow-up studies of array CGH results has been found to be efficient and flexible in our laboratory.