Cytogenetic diagnosis of "normal 46,XX" karyotypes in spontaneous abortions frequently may be misleading

Copy number variation sequencing for the products of conception: What is the optimal testing strategy

BACKGROUND

Copy number variation sequencing (CNV-seq) is crucial in prenatal diagnosis, but its limitations in detecting polyploidy, maternal cell contamination (MCC), and uniparental disomy (UPD) restrict its application in the analysis of products of conception (POCs). This study aimed to investigate an optimal genetic testing strategy for POCs in the era of CNV-seq.

METHODS

CNV-seq and quantitative fluorescent polymerase chain reaction (QF-PCR) were performed in all 4,211 spontaneous miscarriage cases. Different testing strategies were compared and the optimal testing strategies were proposed.

RESULTS

Of the 4,211 cases, 2561 (60.82%) exhibited clinically significant chromosomal abnormalities. CNV-seq alone, without QF-PCR, might misdiagnose 311 (7.39%) cases, including 278 polyploidy, 13 UPD, and 20 MCC. In 20 MCC cases identified by QF-PCR, CNV-seq successfully pinpointed the cause of miscarriage in 13 cases. Furthermore, in cases where QF-PCR suggested polyploidy, CNV-seq improved the diagnostic accuracy in 54 (1.28%) hypo/hypertriploidy cases. After comparing four different strategies, the sequential approach (initiating with CNV-seq followed by QF-PCR if necessary) emerged as advantageous, reducing approximately 70% of the cost associated with QF-PCR while maintaining result accuracy.

CONCLUSIONS

We propose an initial CNV-seq followed by QF-PCR if needed-an efficient and cost-effective strategy for the genetic analysis of POCs.

Genetic causes of sporadic and recurrent miscarriage

Approximately 80% of miscarriages happen within the first 12 weeks of gestation. More than half of early losses result from genetic defects, usually presenting as abnormal chromosome numbers or gene rearrangements in the embryo. However, the impact of genetics on pregnancy loss goes well beyond embryonic aneuploidy. For example, the use of big data has recently led to the discovery of specific gene mutations that may be implicated in sporadic and recurrent miscarriages. Further, emerging data suggest that genetic factors play a role in conditions for which there is a causative association with recurrent pregnancy loss. Here, we summarize the evidence on the genetics of miscarriage and provide an overview of the diagnosis and prevention of genetic causes associated with sporadic and recurrent pregnancy loss.

Investigating the "Fetal Side" in Recurrent Pregnancy Loss: Reliability of Cell-Free DNA Testing in Detecting Chromosomal Abnormalities of Miscarriage Tissue

(1) Background: The aim of our study is to evaluate whether cell-free DNA testing can overlap the genetic testing of miscarriage tissue in women with early pregnancy loss (EPL) and length of recurrent pregnancy loss (RPL); (2) Methods: We conducted a prospective cohort study at the Pregnancy Loss Unit of the Fondazione Policlinico Universitario A. Gemelli (IRCCS), Rome, Italy between May 2021 and March 2022. We included women with EPL and length of RPL. Gestational age was >9 weeks + 2 days and <12 weeks + 0 days of gestation corresponding to a crown rump length measurement of >25 and <54 mm. Women underwent both dilation and curettage for the collection of miscarriage tissue and for blood sample collection. Chromosomal microarray analysis (CMA) on miscarriage tissues was performed by oligo-nucleotide- and single nucleotide polymorphisms (SNP)-based comparative genomic hybridization (CGH+SNP). Maternal blood samples were analyzed by Illumina VeriSeq non-invasive prenatal testing (NIPT) to evaluate the cell-free fetal DNA (cfDNA) and the corresponding fetal fraction and the presence of genetic abnormalities; (3) Results: CMA on miscarriage tissues revealed chromosome aneuploidies in 6/10 cases (60%), consisting of trisomy 21 (5 cases) and monosomy X (one case). cfDNA analysis was able to identify all cases of trisomy 21. It failed to detect monosomy X. A large 7p14.1p12.2 deletion concomitant to trisomy 21 was, in one case, detected by cfDNA analysis but it was not confirmed by CMA on miscarriage tissue. (4) Conclusions: cfDNA largely reproduces the chromosomal abnormalities underlying spontaneous miscarriages. However, diagnostic sensitivity of cfDNA analysis is lower with respect to the CMA of miscarriage tissues. In considering the limitations when obtaining biological samples from aborted fetuses suitable for CMA or standard chromosome analysis, cfDNA analysis is a useful, although not exhaustive, tool for the chromosome diagnosis of both early and recurrent pregnancy loss.

Usefulness of combined NGS and QF‐PCR analysis for product of conception karyotyping

Purpose

Since chromosomal abnormalities can be detected in more than half of miscarriages, cytogenetic testing of the product of conception (POC) can provide important information when preparing for a subsequent pregnancy. Conventional karyotyping is the common diagnostic method for a POC but can be problematic due to the need for cell culture.

Methods

We here conducted shallow whole‐genome sequencing (sWGS) using next‐generation sequencing (NGS) for alternative POC cytogenomic analysis. Since female euploidy samples can include 69,XXX triploidy, additional QF‐PCR was performed in these cases.

Results

We here analyzed POC samples from miscarriages in 300 assisted reproductive technology (ART) pregnancies and detected chromosomal abnormalities in 201 instances (67.0%). Autosomal aneuploidy (151 cases, 50.3%) was the most frequent abnormality, consistent with prior conventional karyotyping data. Mosaic aneuploidy was detected in seven cases (2.0%). Notably, the frequency of triploidy was 2.3%, 10‐fold lower than the reported frequency in non‐ART pregnancies. Structural rearrangements were identified in nine samples (3%), but there was no case of segmental mosaicism.

Conclusions

These data suggest that NGS‐based sWGS, with the aid of QF‐PCR, is a viable alternative karyotyping procedure that does not require cell culture. This method could also assist with genetic counseling for couples who undergoes embryo selection based on PGT‐A data.

Detection of Aneuploidies in Products of Conception and Neonatal Deaths in Iranian Patients Using the Multiplex Ligation-Dependent Probe Amplification (MLPA)

Background:

Around 70% of all pregnancies (Including 15% of clinically-recognized ones) are lost due to various fetal or maternal disorders. Chromosomal aneuploidies are among the most common causes of pregnancy loss. Standard chromosome analysis using G-banding technique (Karyotype) is the technique of choice in studying such abnormalities; however, this technique is time-consuming and sensitive, and limited by vulnerabilities such as cell culture failure. The use of molecular cytogenetic techniques, including array-based techniques and Multiplex Ligation-Dependent Probe Amplification (MLPA), has been proposed to overcome the limitations of this method to study the products of conception. This study has been designed to investigate the feasibility of using MLPA technique as a standalone genetic testing, with histopathologic examinations and genetic counseling to detect aneuploidies in products of conception and neonatal deaths.

Methods:

Forty-two verified fetal and neonatal samples were studies and genetic counseling was scheduled for all parents. Histopathologic examinations were carried out on the products of conception, and appropriate fetal tissues were separated for genetic studies. Following DNA extraction and purification, MLPA was carried out to investigate chromosomal aneuploidies.

Results:

Nine samples (21.42%) were diagnosed to be affected with aneuploidy. Detected aneuploidies were trisomy 22 (n=3), trisomy 21(n=1), trisomy 18 (n=2), trisomy 16 (n=1), trisomy 13 (n=1), and monosomy of chromosome X (n=1). The MLPA analysis results were conclusive for all of the fetal samples (Success rate: 100%).

Conclusion:

These results suggest that MLPA, as a standalone genetic testing, is an accurate, rapid, and reliable method in overcoming the limitations of standard cytogenetic techniques in genetic investigation of products of conception.

Genetic analysis of products of conception. Should we abandon classic karyotyping methodology?

OBJECTIVE

To compare the results obtained by the classic and molecular methodology in the analysis of products of conception, the advantages and disadvantages of each method.

METHODS

Retrospective non-randomized analysis of results obtained from product of conception samples submitted to genetic evaluation, from 2012 to 2017. The evaluations were performed using cytogenetics and/or chromosomal microarray analysis or arrays.

RESULTS

Forty samples were analyzed using classic cytogenetics, of which 10% showed no cell growth, 50% had normal results and 40% had abnormalities. Of the 41 cases sent for array analysis it was not possible to obtain results in 7.3%, 39.5% were normal and 60.5% had abnormalities. There was no statistical difference among the results (p=0.89). Most abnormal results were seen till 9 weeks' gestation. The later abnormal miscarriage was seen at 28 weeks' gestation, with karyotype 46,XX,del(15)(q26.2-qter). The results are corroborated by the international literature.

CONCLUSION

Classic cytogenetics and array techniques showed comparable results on the type of alteration observed. Array analysis is preferable to cell culture in delayed abortions, while cytogenetics is more able to show polyploidies. Both have the same growth failure rates when product of conception tissue is not properly collected.

Maternal germline factors associated with aneuploid pregnancy loss: a systematic review

BACKGROUND

Miscarriage describes the spontaneous loss of pregnancy before the threshold of viability; the vast majority occur before 12 weeks of gestation. Miscarriage affects one in four couples and is the most common complication of pregnancy. Chromosomal abnormalities of the embryo are identified in ∼50% of first trimester miscarriages; aneuploidy accounts for 86% of these cases. The majority of trisomic miscarriages are of maternal origin with errors occurring during meiotic division of the oocytes. Chromosome segregation errors in oocytes may be sporadic events secondary to advancing maternal age; however, there is increasing evidence to suggest possible maternal germline contributions to this.

OBJECTIVE AND RATIONALE

The objective of this review was to appraise critically the existing evidence relating to maternal germline factors associated with pregnancy loss secondary to embryo aneuploidy, identify limitations in the current evidence base and establish areas requiring further research.

SEARCH METHODS

The initial literature search was performed in September 2019 and updated in January 2021 using the electronic databases OVID MEDLINE, EMBASE and the Cochrane Library. No time or language restrictions were applied to the searches and only primary research was included. Participants were women who had suffered pregnancy loss secondary to numerical chromosomal abnormalities of the embryo. Study identification and subsequent data extraction were performed by two authors independently. The Newcastle-Ottawa Scale was used to judge the quality of the included studies. The results were synthesized narratively.

OUTCOMES

The literature search identified 2198 titles once duplicates were removed, of which 21 were eligible for inclusion in this systematic review. They reported on maternal germline factors having variable degrees of association with pregnancy loss of aneuploid origin. The Online Mendelian Inheritance in Man (OMIM) gene ontology database was used as a reference to establish the functional role currently attributed to the genes reported. The majority of the cases reported and included were secondary to the inheritance of maternal structural factors such as Robertsonian translocations, deletions and insertions. Germline factors with a plausible role in aneuploid pregnancy loss of maternal origin included skewed X-inactivation and CGG repeats in the fragile X mental retardation (FMR1) gene. Studies that reported the association of single gene mutations with aneuploid pregnancy loss were conflicting. Single gene mutations with an uncertain or no role in aneuploid pregnancy loss included mutations in synaptonemal complex protein 3 (SYCP3), mitotic polo-like kinase 4 (PLK4) and meiotic stromal antigen 3 (STAG3) spindle integrity variants and 5,10-methylenetetrahydrofolate reductase (MTHFR).

WIDER IMPLICATIONS

Identifying maternal genetic factors associated with an increased risk of aneuploidy will expand our understanding of cell division, non-disjunction and miscarriage secondary to embryo aneuploidy. The candidate germline factors identified may be incorporated in a screening panel for women suffering miscarriage of aneuploidy aetiology to facilitate counselling for subsequent pregnancies.

Optimizing the Diagnostic Strategy to Identify Genetic Abnormalities in Miscarriage

INTRODUCTION

The single most common cause of miscarriage is genetic abnormality.

OBJECTIVE

We conducted a prospective cohort study to compare the performance of conventional karyotyping and chromosomal microarray analysis (CMA) using array comparative genomic hybridization (array-CGH) and single nucleotide polymorphism array (SNP-array) to identify genetic abnormalities in miscarriage specimens.

METHODS

A total of 63 miscarriage specimens were included. Conventional karyotyping, array-CGH, and SNP-array were performed and the results compared.

RESULTS

Genetic abnormalities were detected in 31 cases (49.2%) by at least one testing modality. Single autosomal trisomy was the most common defect (71.0%), followed by polyploidy (16.1%), multiple aneuploidy (9.7%), and monosomy X (3.2%). Mosaicisms were identified in four cases and confirmed by fluorescence in situ hybridization (FISH) using appropriate probes. SNP-array had a higher detection rate of genetic abnormalities than array-CGH (93.5 vs. 77.4%), and conventional karyotyping had the lowest detection rate (76.0%). SNP-array enabled the detection of all types of genetic abnormalities, including polyploidy.

CONCLUSIONS

Although conventional karyotyping and FISH are still needed, SNP-array represents the first choice for miscarriage because the technique showed excellent performance in the detection of genetic abnormalities and minimized the probability of testing failure as well as time, costs, and labor.

Karyotype of first clinical miscarriage and prognosis of subsequent pregnancy outcome

RESEARCH QUESTION

Is the karyotype of the first clinical miscarriage in an infertile patient predictive of the outcome of the subsequent pregnancy?

DESIGN

Retrospective cohort study of infertile patients undergoing manual vacuum aspiration with chromosome testing at the time of the first (index) clinical miscarriage with a genetic diagnosis and a subsequent pregnancy. Patients treated at two academic-affiliated fertility centres from 1999 to 2018 were included; those using preimplantation genetic testing for aneuploidy were excluded. Main outcome was live birth in the subsequent pregnancy.

RESULTS

One hundred patients with euploid clinical miscarriage and 151 patients with aneuploid clinical miscarriage in the index pregnancy were included. Patients with euploid clinical miscarriage in the index pregnancy had a live birth rate of 63% in the subsequent pregnancy compared with 68% among patients with aneuploid clinical miscarriage (adjusted odds ratio [aOR] 0.75, 95% CI 0.47-1.39, P = 0.45, logistic regression model adjusting for age, parity, body mass index and mode of conception). In a multinomial logistic regression model with three outcomes (live birth, clinical miscarriage or biochemical miscarriage), euploid clinical miscarriage for the index pregnancy was associated with similar odds of clinical miscarriage in the subsequent pregnancy compared with aneuploid clinical miscarriage for the index pregnancy (32% versus 24%, respectively, aOR 1.49, 95% CI 0.83-2.70, P = 0.19). Euploid clinical miscarriage for the index pregnancy was not associated with likelihood of biochemical miscarriage in the subsequent pregnancy compared with aneuploid clinical miscarriage (5% versus 8%, respectively, aOR 0.46, 95% CI 0.14-1.55, P = 0.21).

CONCLUSION

Prognosis after a first clinical miscarriage among infertile patients is equally favourable among patients with euploid and aneuploid karyotype, and independent of the karyotype of the pregnancy loss.

Identifying the causes of recurrent pregnancy loss in consanguineous couples using whole exome sequencing on the products of miscarriage with no chromosomal abnormalities

Recurrent miscarriages occur in about 5% of couples trying to conceive. In the past decade, the products of miscarriage have been studied using array comparative genomic hybridization (a-CGH). Within the last decade, an association has been proposed between miscarriages and single or multigenic changes, introducing the possibility of detecting other underlying genetic factors by whole exome sequencing (WES). We performed a-CGH on the products of miscarriage from 1625 Iranian women in consanguineous or non-consanguineous marriages. WES was carried out on DNA extracted from the products of miscarriage from 20 Iranian women in consanguineous marriages and with earlier normal genetic testing. Using a-CGH, a statistically significant difference was detected between the frequency of imbalances in related vs. unrelated couples (P < 0.001). WES positively identified relevant alterations in 11 genes in 65% of cases. In 45% of cases, we were able to classify these variants as pathogenic or likely pathogenic, according to the American College of Medical Genetics and Genomics guidelines, while in the remainder, the variants were classified as of unknown significance. To the best of our knowledge, our study is the first to employ WES on the products of miscarriage in consanguineous families with recurrent miscarriages regardless of the presence of fetal abnormalities. We propose that WES can be helpful in making a diagnosis of lethal disorders in consanguineous couples after prior genetic testing.

Clinical utilization of chromosomal microarray analysis for the genetic analysis in subgroups of pregnancy loss

OBJECTIVE

The underlying etiologies of pregnancy loss are heterogeneous and in many cases unexplained. This study was to explore the genetic causes of early and late pregnancy loss using chromosomal microarray analysis (CMA).

METHODS

A cohort of 222 specimens of conceptions underwent genetic analysis using Affymetrix CytoScan 750 K arrays, which includes both SNP markers and copy number markers.

RESULTS

Of the 222-products of conception (POC), the overall detection rate for clinical significantly chromosomal anomalies was 40.54%, including 53 autosomal aneuploidy (23.87%), 16 sex chromosome aneuploidy (7.21%), 5 mutiple aneuploidy (2.25%), 4 triploidy (1.80%), and 12 pathogenic copy number variants (pCNVs) (5.41%). In addition, variants of uncertain significance and loss of heterozygosity were detected in 9 samples and 2 samples, respectively. The detection rates for total chromosomal abnormalities, autosomal aneuploidy, sex chromosome aneuploidy, multiple aneuploidy, and triploidy in specimens of early pregnancy loss was higher than that of late pregnancy loss, while had lower detection rate of pCNVs. Moreover, the detection rate in POC of mothers younger than 35 years was lower than that of advanced maternal age. The detection rate was 40.57% in POC of mothers with adverse pregnancy histories, in which was comparable with that of mothers without adverse pregnancy histories.

CONCLUSIONS

CMA yielded a superior detection rate in early pregnancy loss than that of late pregnancy loss. Moreover, the incidence of chromosome abnormality in cases with advanced maternal age was higher than that of cases with younger maternal age, while adverse pregnancy history seemed not to be the factors affecting the detection rate for chromosomal abnormality in pregnancy loss.

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.

Karyotype evaluation of repeated abortions in primary and secondary recurrent pregnancy loss

PURPOSE

To study the contribution of embryo chromosomal abnormalities in primary and secondary recurrent pregnancy loss (RPL) and to analyze the recurrence of chromosomal constitution in miscarriages from the same couple.

METHODS

Retrospective study of abortion karyotypes in RPL families based on the mother's primary or secondary RPL status (563 embryo specimens, 335 samples from primary, and 228 samples from secondary RPL). RPL was defined as two or more consecutive miscarriages. One hundred eight cases of recurrent embryo/fetal loss in 51 families were analyzed to assess the probability of having the same karyotype pattern (recurrent normal or recurrent abnormal) in both previous and subsequent pregnancy loss. The karyotypes of abortions were established using standard cytogenetic analysis, as well as interphase fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH).

RESULTS

The frequency of aberrations was 43.9% in abortions from primary RPL versus 52.6% in secondary RPL (p = 0.041). Women 35 years of age or older were the main contributors to this difference. The odds ratio of a subsequent abortion having the same karyotype pattern (normal or abnormal) as the previous one was 6.98 (p = 0.0013).

CONCLUSION

The frequency of abnormalities is higher in abortions from the secondary RPL versus primary RPL group, and this difference is due to the relative deficiency of miscarriages with abnormal karyotypes in older women with primary RPL. The probability of having the same karyotype pattern (recurrent normal or recurrent abnormal) in the previous and subsequent abortion is increased significantly compared with chance.

Evaluation of two aneuploidy screening tests for chorionic villus samples: Multiplex ligation-dependent probe amplification and fluorescence in situ hybridization

The vast majority of first-trimester pregnancy losses are the consequence of numerical aberrations in fetal chromosomes, which may involve nearly all chromosomes. Although commercial probes for all chromosomes are available for multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH) analyses, their use has rarely been reported for screening all 24 chromosomes for early fetal demise, especially by FISH. Here, we validated the ability of MLPA and FISH techniques as two low-cost aneuploidy screening methods for 24 chromosomes in 165 chorionic villus samples (CVSs). The results obtained by two methods were compared by the Chi-square test and the Kappa agreement test. Both methods gave conclusive results for all CVSs tested and showed highly consistent results (kappa = 0.890, p < 0.001). There was no statistically significant difference between the aneuploidy rate of the CVSs tested by the two methods (p = 0.180). Most of the samples showed fully concordant molecular karyotyping results (81.21%) between the two analytical methods, 10.91% had incompletely concordant results, and 7.88% had discordant results. The inconsistencies included segmental abnormalities, mosaicism, and polyploidy. Both assays used to screen 24 chromosomes were powerful techniques for detecting aneuploidy in CVSs. In terms of cost-effectiveness and diagnostic accuracy, the combination of subtelomeric (P036, P070) and centromeric (P181) MLPA assays is the better analytic strategy and follow-up analysis by FISH is recommended for MLPA-negative samples.

Chromosomal aberrations in pregnancy and fetal loss: Insight on the effect of consanguinity, review of 1625 cases

Background

Pregnancy loss affects 10%–15% of pregnancies and is caused by several factors, maternal and fetal. Most common cause is chromosomal aneuploidy and has traditionally been detected by karyotyping product of conception and/or fetal tissue. In recent years, array comparative genomic hybridization (a‐CGH) has been used because of its higher detection and lower failure rates.

Methods

DNA was extracted from 1625 products of abortion or fetal tissue. In 1,104 cases both quantitative fluorescent‐polymerase chain reaction (QF‐PCR) and a‐CGH, and in 521 cases only a‐CGH, was performed.

Results

The detection rate using QF‐PCR and a‐CGH is 20% compared to 12.7%, overall, and 15.7%, excluding failed samples, by karyotypes in our center. QF‐PCR and a‐CGH failed in 1.9% of cases, while the failure rate for karyotypes was 20.1%. The difference of detection and failure rates is significant (p‐value < 0.001 and p‐value < 0.001 respectively). Unexpectedly we also found a significant difference in frequency of imbalances in related versus unrelated couples. (χ² = 11.4926, p‐value < 0.001).

Conclusion

It is highly likely that the pregnancy loss in consanguineous couples is caused by other genetic and immune mechanisms. It is plausible that, through the same mechanism by which single gene disorders have a higher prevalence of manifesting disease in consanguineous couples, they can cause lethal genetic disorders leading to pregnancy loss and intra‐uterine fetal death (IUFD) in these couples. Our findings suggest that this is a matter for further study as it will greatly influence the approach to counseling and managing consanguineous couples with pregnancy loss.

Miscarriage chromosome testing: Indications, benefits and methodologies

Rapid advances in genomics have expanded the use of chromosome testing following miscarriage. In addition to conventional cytogenetics, the availability of single nucleotide polymorphism microarray technology and array comparative geneomic hybridization have provided further options for clinicians. This review will cover the indications for testing and the advantages/disadvantages of the various methodologies available.

Implementing a Protocol to Optimize Detection of Chromosome Abnormalities in Cases of Miscarriage or Stillbirth at a Midwestern Teaching Hospital

CONTEXT

Results from chromosome testing after spontaneous abortion (SAB) or intrauterine fetal demise (IUFD) are useful in patient counseling; however, results can be inconclusive when cell cultures for chromosomes are unable to grow from products of conception. Chromosomal microarray analysis (CMA) can analyze DNA from nonviable fetal tissue.

OBJECTIVE

To examine whether establishing a genetic testing protocol for karyotype and CMA on SAB and IUFD tissues increases diagnostic yield.

DESIGN

A retrospective chart review was conducted in cases of SAB or IUFD when karyotyping and/or CMA was requested, comparing two periods: Preprotocol and postprotocol implementation.

MAIN OUTCOME MEASURES

Diagnostic yield was compared by using the number of determinate test results in the preprotocol and postprotocol study periods. A case was considered to have indeterminate results when the final genetic test results reported no fetal tissue or no cell culture growth.

RESULTS

A total of 55 preprotocol and 52 postprotocol patients were analyzed. Diagnostic yield increased from 72.7% to 94.2% after implementation of the genetic testing protocol (p = 0.0004). Indeterminate results occurred more frequently before compared with after implementation of the protocol.

CONCLUSION

A protocol of reflexing to CMA or proceeding directly with CMA gives a higher diagnostic yield in the genetic evaluation of SAB or IUFD. Institutions should consider implementing a genetic testing protocol to improve diagnostic yield. Our study results emphasize the importance of proceeding directly to microarray analysis and give support for current clinical recommendations for genetic testing after fetal demise.

Added value of chromosomal microarray analysis over karyotyping in early pregnancy loss: systematic review and meta-analysis

OBJECTIVE

To estimate the increased test success rate and incremental yield of chromosomal microarray analysis (CMA) over conventional karyotyping in detection of pathogenic copy number variants (CNVs) and variants of unknown significance (VOUS) in early pregnancy loss.

METHOD

This was a systematic review conducted in accordance with PRISMA criteria. All articles identified in PubMed, Ovid MEDLINE and Web of Science, between January 2000 and April 2017, that described CNVs in early pregnancy losses (up to 20 weeks) were included. Risk differences were pooled to estimate the incremental yield of CMA over karyotyping overall, and after stratification. In addition, test success rate, defined as the proportion of informative results, was compared in series in which CMA and karyotyping were performed concurrently.

RESULTS

Twenty-three studies, reporting on 5507 pregnancy losses up to 20 weeks with full data available, met the inclusion criteria for analysis. In the series in which CMA and karyotyping were performed concurrently, CMA showed a significant improvement in success rate, providing informative results in 95% (95% CI, 94-96%) of cases compared with karyotyping in which informative results were provided in 68% (95% CI, 66-70%) of cases. Combined data from reviewed studies revealed that incremental yields of CMA over karyotyping were 2% (95% CI, 1-2%) for pathogenic CNVs and 4% (95% CI, 3-6%) for VOUS. The most common pathogenic CNVs reported were 22q11.21 and 1p36.33 deletion.

CONCLUSION

In comparison with conventional karyotyping, CMA provides a significant increase in test success rate and incremental diagnostic yield in early pregnancy loss. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.

Mosaicism for structural non-centromeric autosomal rearrangement in prenatal diagnoses: evidence for sex-specific selection against chromosomal abnormalities

Background

Mosaicism for chromosome rearrangements is common in preimplantation diagnoses, yet is rare in prenatal diagnoses as well as in other groups of patients referred to cytogenetic testing. Consequently, there is a lack of detailed studies on this kind of mosaicism in all groups of patients. Previous reports have identified a deficit of males among asymptomatic carriers of N/unbalanced Rea. Three mechanisms were proposed for explaining this phenomenon, including a high instability in the early female embryonic development, a male-specific selection against abnormal cells in the early embryo development, or a high intrauterine lethality of male carriers. To address these possibilities, we have performed a meta-analysis of male-to-female ratio (sex ratio, SR) in prenatally diagnosed and in spontaneously aborted carriers of mosaic Rea.

Results

One hundred and twenty one prenatally detected cases of normal cell line/autosome rearrangement mosaicism (N/Rea) with known carriers’ sex were identified from the literature. Carriers of N/unbalanced Rea presented with 38 abnormal and 28 normal/apparently normal outcomes while carriers of N/balanced Rea presented with 24 normal and 3 abnormal outcomes. 58% of carriers of N/unbalanced Rea with an abnormal outcome displayed a high proportion (> 50%) of amniocytes with the abnormality compared to 25% of carriers with normal/apparently normal outcome. More female carriers of N/unbalanced Rea were identified with an abnormal outcome (15 M/23F) in contrast to a notable male predominance (18 M/10F) among those with normal outcome. Additionally, among spontaneously aborted carriers of N/unbalanced Rea, there was a strong female predominance (7 M/23F).

Conclusion

Previous reports have identified a deficit of male among asymptomatic carriers of N/unbalanced Rea. The current data suggests a male-specific selection against chromosomal abnormalities.

Electronic supplementary material

The online version of this article (10.1186/s13039-017-0346-0) contains supplementary material, which is available to authorized users.

Salvage of fetal karyotype information from SNP array data obtained from products of conception with maternal cell contamination

OBJECTIVE

Maternal cell contamination (MCC) is known to increase the risk of misdiagnosis in prenatal diagnosis as well as in diagnostic tests for the products of conception (POC) from miscarriages. We aimed to develop a data correction method to salvage fetal karyotype information from single-nucleotide polymorphism (SNP) array data for POC with MCC when parental genotype data are available.

METHODS

We obtained SNP array data from mixed genomic DNAs of a mother-child pair and used the dataset to assess the accuracy of data correction. We subsequently applied our method to miscarriage specimens with MCC.

RESULTS

We adopted a linear interpolation model as a data correction method and implemented the method in an R package, snpsal. We successfully determined the fetal karyotypes of two miscarriage specimens that were previously undiagnosed due to MCC to be normal in one case and trisomy 16 in the other case using snpsal.

CONCLUSION

The R package, snpsal, developed in this study facilitates rapid and accurate estimation of the fetal karyotype from SNP array data for POC with MCC. © 2017 John Wiley & Sons, Ltd.

The chromosome analysis of the miscarriage tissue. Miscarried embryo/fetal crown rump length (CRL) measurement: A practical use

Objective

To investigate whether miscarried embryo/fetal crown rump length (CRL) measurement may yield a practical application for predicting a conclusive result at the cytogenetic analysis of miscarriage tissue. Our study might help in improving the cytogenetic method, the results of which may be affected by maternal cell contamination (MCC). In particular, we aimed at establishing whether the miscarried embryo/fetal CRL measurement shows accuracy in predicting the possibility of MCC and the scan cut-off value useful to this purpose and, as a result, suggest a multi-step procedure for the genetic ascertainment.

Methods

Women experiencing at least two miscarriages of less than 20 weeks size at the Pregnancy Loss Unit at Fondazione Policlinico A. Gemelli underwent a scan before surgery. The CRL value was recorded. After the dilatation and courettage (D&C) procedure, miscarriage tissue was processed through the proposed multi-step procedure before performing oligo-nucleotide-based and SNP (single nucleotide polymorphisms)-based comparative genomic hybridization (CGH+SNP) microarray analysis.

Results

63 women and 63 miscarriages met the criteria. By using the Receiving Operator Characteristic (ROC) curves, CRL showed an AUC of 0.816 (95%CI:0.703–0.928,p<0.001). A CRL≥24.5 mm cut-off value showed a higher positive likelihood ratio (5.27) but, conversely, a higher negative likelihood ratio (0.64) in predicting the possibility of MCC. Microarray analysis was successful in the totality of cases in which the embryo/fetal origin of miscarriage tissues was proven.

Conclusions

The 24.5 mm CRL value emerges as the most suitable cut-off enabling the identification of cases in which the embryo-fetal component can be isolated in the absence of MCC and the chromosomal array provide informative results.

Comparison of cytogenetics and molecular karyotyping for chromosome testing of miscarriage specimens

OBJECTIVE

To compare chromosome testing of miscarriage specimens between traditional cytogenetic analysis and molecular karyotyping using single nucleotide polymorphism microarrays (SNP) and array comparative genomic hybridization (aCGH).

DESIGN

Prospective blinded cohort study.

SETTING

University-based practice.

PATIENT(S)

Women undergoing dilation and curettage for first-trimester miscarriage between March 2014 and December 2015.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Chromosome analysis from chorionic villi separated equally and submitted for cytogenetics, SNP microarray, and aCGH testing.

RESULT(S)

Sixty samples were analyzed, of which 47 (78%) were chromosomally abnormal. A correct call was defined when a result was concordant with at least one other testing platform. The correct call rate was 85%, 93%, and 85% using cytogenetics, SNP array, and aCGH, respectively. We found a 33% overall discordance rate between results. Discordances were due to maternal cell contamination, balanced chromosome rearrangements, polyploidy, and placental mosaicism. Mosaicism was detected in 18% of all samples. Growth failure occurred in four samples sent to cytogenetics, of which three were chromosomally abnormal by molecular testing.

CONCLUSION(S)

This study demonstrates the many technical limitations of the three testing modalities. Our rates of maternal cell contamination were low, but it is important to note that this is a commonly reported limitation of cytogenetics. Given the similar overall performance of the three testing modalities, providers may choose a method based on individual availability and consideration of limitations as it applies to each clinical scenario. The unexpected high rate of placental mosaicism warrants further investigation.

Utility and limitations of multiplex ligation-dependent probe amplification technique in the detection of cytogenetic abnormalities in products of conception

Background and Introduction: Chromosomal abnormality is found in about half of first-trimester abortions. Karyotype is the gold standard to detect chromosomal abnormalities. Multiplex ligation-dependent probe amplification (MLPA) offers advantage over karyotype in terms of lower failure rate, faster turnaround time, and much higher resolution than conventional karyotyping and found to be 98% concordant with conventional karyotype.

AIM

We performed this study to look for the utility of MLPA in diagnosing chromosomal abnormalities in first-trimester abortions.

MATERIALS AND METHODS

MLPA using subtelomeric SALSA probe sets (P036 and P070) was used to detect cytogenetic abnormalities in products of conception in missed/spontaneous abortions.

RESULTS

A total of ninety abortus samples were analyzed by MLPA. Successful results were provided in (67) 74.4% of the cases while no conclusion could be drawn in 25.6% (23) of the cases. Fifty-five (82.1%) cases were cytogenetically normal and 17.9% (12) had some abnormality. Aneuploidy was detected in 8 (66.7%) cases, 3 (25%) had double-segment imbalance, and one (8.3%) had partial aneuploidy.

CONCLUSION

We suggest that MLPA is a good substitute to traditional karyotype.

Evidence for High Frequency of Chromosomal Mosaicism in Spontaneous Abortions Revealed by Interphase FISH Analysis

Numerical chromosomal imbalances are a common feature of spontaneous abortions. However, the incidence of mosaic forms of chromosomal abnormalities has not been evaluated. We have applied interphase multicolor fluorescence in situ hybridization using original DNA probes for chromosomes 1, 9, 13, 14, 15, 16, 18, 21, 22, X, and Y to study chromosomal abnormalities in 148 specimens of spontaneous abortions. We have detected chromosomal abnormalities in 89/148 (60.1%) of specimens. Among them, aneuploidy was detected in 74 samples (83.1%). In the remaining samples, polyploidy was detected. The mosaic forms of chromosome abnormality, including autosomal and sex chromosomal aneuploidies and polyploidy (31 and 12 cases, respectively), were observed in 43/89 (48.3%) of specimens. The most frequent mosaic form of aneuploidy was related to chromosome X (19 cases). The frequency of mosaic forms of chromosomal abnormalities in samples with male chromosomal complement was 50% (16/32 chromosomally abnormal), and in samples with female chromosomal complement, it was 47.4% (27/57 chromosomally abnormal). The present study demonstrates that the postzygotic or mitotic errors leading to chromosomal mosaicism in spontaneous abortions are more frequent than previously suspected. Chromosomal mosaicsm may contribute significantly to both pregnancy complications and spontaneous fetal loss.

Cytogenetic analysis of spontaneously discharged products of conception by array-based comparative genomic hybridization

Background

Cytogenetic analysis of products of conception (POC) is essential for the management of recurrent pregnancy loss (RPL), but the currently-performed G-banding method is not necessarily applicable to spontaneously discharged POC because of poor quality for culture. We analyzed the karyotypes of 15 spontaneously discharged POC by array-based comparative genomic hybridization (array-CGH).

Results

All specimens were successfully analyzed and 10 cases had abnormal results: gain in copy number (n = 7) and loss in copy number (n = 3). Most of them were estimated to be whole chromosome aneuploidy, whereas one case was compatible with microdeletion. Two cases were suspected to be male diploid contaminated by maternal DNA or triploid because of the unsatisfactory signal patterns on X/Y chromosomes. Two of three cases with normal female DNA pattern were identified to be contaminated with maternal DNA by the additional analysis of short tandem repeats.

Conclusions

Given the potential to analyze non-viable POC specimens, array-CGH is a feasible cytogenetic tool for women, in particular, with a history of RPL who desire non-surgical or expectant management of miscarriages and/or a thorough investigation on the cause for recurrent miscarriage, although it needs to take into account high incidence of maternal contamination in spontaneously discharged POC.

Electronic supplementary material

The online version of this article (doi:10.1186/s40064-016-2594-6) contains supplementary material, which is available to authorized users.

Comprehensive genetic analysis of pregnancy loss by chromosomal microarrays: outcomes, benefits, and challenges

PURPOSE

Chromosomal microarray analysis (CMA) is currently considered first-tier testing in pediatric care and prenatal diagnosis owing to its high diagnostic sensitivity for chromosomal imbalances. The aim of this study was to determine the efficacy and diagnostic power of CMA in both fresh and formalin-fixed paraffin-embedded (FFPE) samples of products of conception (POCs).

METHODS

Over a 44-month period, 8,118 consecutive samples were received by our laboratory for CMA analysis. This included both fresh (76.4%) and FFPE samples (22.4%), most of which were ascertained for recurrent pregnancy loss and/or spontaneous abortion (83%). The majority of samples were evaluated by a whole-genome single-nucleotide polymorphism (SNP)-based array (81.6%); the remaining samples were evaluated by array-comparative genomic hybridization (CGH).

RESULTS

A successful result was obtained in 7,396 of 8,118 (91.1%), with 92.4% of fresh tissue samples and 86.4% of FFPE samples successfully analyzed. Clinically significant abnormalities were identified in 53.7% of specimens (3,975 of 7,396), 94% of which were considered causative.

CONCLUSION

Analysis of POC specimens by karyotyping fails in 20-40% of cases. SNP-based CMA is a robust platform, with successful results obtained in >90% of cases. SNP-based CMA can identify aneuploidy, polyploidy, whole-genome homozygosity, segmental genomic imbalances, and maternal cell contamination, thus maximizing sensitivity and decreasing false-negative results. Understanding the etiology of fetal loss enables clarification of recurrence risk and assists in determining appropriate management for future family planning.Genet Med 19 1, 83-89.

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.

1(st) trimester miscarriage: four decades of study

Miscarriage is a very common occurrence in humans. This paper sets out to present published data on research that has provided increased understanding of pregnancy failure. Clarification of definitions, exploring the range of failures from preclinical to later pregnancy losses, and the scientific tools employed to find information on the losses have been documented. What is now understood, which tools work best, and the associated limitations are all discussed. Early studies used cytogenetic methods and tissue culture to obtain results. Improvements in laboratory tools such as better tissue culture incubators, inverted microscopes, laminar flow hoods, improvements in culture media, all contributed to obtaining more results for patients. These studies demonstrated the significant contribution of unbalanced chromosomal karyotypes to pregnancy failure. Maternal age as a contributing factor in trisomy was clearly demonstrated. First trimester miscarriage exhibits very high cytogenetic abnormality; in contrast to very low rates in later losses. Combining data across all time periods of pregnancy will affect the significance of chromosomal error in the early pregnancy failures. Cytogenetic methods investigate whole genomes, and are considered to represent the standard against which new methods must be validated. New molecular genetic methods provide the opportunity to examine samples without the necessity of tissue culture. Techniques may be site-specific or whole genome. Fluorescent in situ hybridisation (FISH), comparative genomic hybridisation (CGH), array-based CGH, single nucleotide polymorphism (SNP) detection, quantitative polymerase chain reaction (qPCR), and quantitative fluorescent PCR (QF-PCR), have all been utilised. In comparison studies with classical/conventional cytogenetics, each newer method offers advantages and limitations. At the present time, a combined approach using conventional and molecular methods will elucidate the cause of miscarriage for almost all samples. In a clinical setting this would be optimum.

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.

Genetic considerations in recurrent pregnancy loss

Human reproduction is remarkably inefficient; nearly 70% of human conceptions do not survive to live birth. Spontaneous fetal aneuploidy is the most common cause for spontaneous loss, particularly in the first trimester of pregnancy. Although losses owing to de novo fetal aneuploidy occur at similar frequencies among women with sporadic and recurrent losses, some couples with recurrent pregnancy loss have additional associated genetic factors and some have nongenetic etiologies. Genetic testing of the products of conception from couples experiencing two or more losses may aid in defining the underlying etiology and in counseling patients about prognosis in a subsequent pregnancy. Parental karyotyping of couples who have experienced recurrent pregnancy loss (RPL) will detect some couples with an increased likelihood of recurrent fetal aneuploidy; this may direct interventions. The utility of preimplantation genetic analysis in couples with RPL is unproven, but new approaches to this testing show great promise.

Genomic imbalance in products of conception: single-nucleotide polymorphism chromosomal microarray analysis

OBJECTIVE

To report the full cohort of identifiable anomalies, regardless of known clinical significance, in a large-scale cohort of postmiscarriage products-of-conception samples analyzed using a high-resolution single-nucleotide polymorphism (SNP)-based microarray platform. High-resolution chromosomal microarray analysis allows for the identification of visible and submicroscopic cytogenomic imbalances; the specific use of SNPs permits detection of maternal cell contamination, triploidy, and uniparental disomy.

METHODS

Miscarriage specimens were sent to a single laboratory for cytogenomic analysis. Chromosomal microarray analysis was performed using a SNP-based genotyping microarray platform. Results were evaluated at the cytogenetic and microscopic (greater than 10 Mb) and submicroscopic (less than 10 Mb) levels. Maternal cell contamination was assessed using information derived from fetal and maternal SNPs.

RESULTS

Results were obtained on 2,389 of 2,392 specimens (99.9%) that were less than 20 weeks of gestation. Maternal cell contamination was identified in 528 (22.0%) specimens. The remaining 1,861 specimens were considered to be of true fetal origin. Of these, 1,106 (59.4%) showed classical cytogenetic abnormalities: aneuploidy accounted for 945 (85.4%), triploidy for 114 (10.3%), and structural anomalies or tetraploidy for the remaining 47 (4.2%). Of the 755 (40.6%) cases considered normal at the cytogenetic level, SNP chromosomal microarray analysis revealed a clinically significant copy number change or whole-genome uniparental disomy in 12 (1.6%) and three (0.4%) cases, respectively.

CONCLUSION

Chromosomal microarray analysis of products-of-conception specimens yields a high diagnostic return. Using SNPs extends the scope of detectable genomic abnormalities and facilitates reporting "true" fetal results. This supports the use of SNP chromosomal microarray analysis for cytogenomic evaluation of miscarriage specimens when clinically indicated.

LEVEL OF EVIDENCE

III.

Chromosome distribution of early miscarriages with present or absent embryos: female predominance

PURPOSE

The objective of this study is to compare the chromosomal distribution of early miscarriages with or without embryonic poles.

MATERIALS AND METHODS

It was a retrospective study of 223 women who underwent dilation and curettage (D&C) between 1995 and 2013 for early miscarriages. The presence or absence of a fetal pole was evaluated by abdominal or transvaginal ultrasound. Cytogenetic tests of products of conception following culture were determined in both groups.

RESULTS

Of the 223 early miscarriages, 143 had embryos and 80 did not. The abnormality rate differed significantly (61.5 % vs. 46.3 %, p < 0.05), with trisomy 18, 21 and 45X found only in miscarriages with embryos. There were no significant differences between groups in rates of triploidy, tetraploidy, mosaicism, structure and double abnormality. The female abortus rate was higher in miscarriages with or without embryonic poles, as well as in groups with normal and abnormal karyotypes.

CONCLUSIONS

Chromosome distribution differs in miscarriages with or without embryonic poles. The ultrasound findings might offer different direction to determine the causes of early miscarriages. The higher female abortus rate may be associated with early selection.

Prevalence of aneuploidies in products of spontaneous abortion: interest of FISH and MLPA

Spontaneous abortion (SA) is the loss of the conceptus before 22 weeks of gestation when fetal weight is less than 500 g. The genetic etiology accounts for more than two third of SA, and autosomal aneuploidies alone account for up to 70% fetal loss. The aim of this study was to highlight the most common chromosomal causes of fetal loss. In this study, 220 products of abortion and in utero fetal death were analyzed by using FISH (AneuVysion) on interphase nuclei from chorionic villus and by using MLPA (SALSA P036, P070 and P245 kits) on DNA extracted from fetal tissues. The gestational age ranged from the 7th to the 38th week of gestation. Of a total of 151 samples analyzed by using FISH, 10 chromosomal abnormalities were observed: four trisomies 21 (one of them was mosaic), a trisomy 18, a trisomy 13, three triploidies and one monosomy X (Turner). From the additional 69 samples analyzed by using MLPA, two anomalies were found: two monosomies X (Turner). FISH and MLPA are simple, rapid and sensitive tools for the detection of chromosomal aneuploidies. Avoiding the cell culture step necessary for karyotyping, they represent very interesting alternative methods to diagnose genomic disorders in products of abortion in which poor sample quality often leads to cell culture failure.

Miscarriage chromosome testing: utility of comparative genomic hybridization with reflex microsatellite analysis in preserved miscarriage tissue

OBJECTIVE

To assess the utility of comparative genomic hybridization (CGH) and reflex microsatellite analysis (MSA) for chromosome analysis of preserved miscarriage tissue.

DESIGN

Observational study.

SETTING

Academic recurrent pregnancy loss program.

PATIENT(S)

Patients with recurrent early pregnancy loss, defined as two or more miscarriages at <10 weeks, and at least one preserved miscarriage specimen sent for CGH.

INTERVENTION(S)

Preserved miscarriage specimens were sent for CGH. If results were euploid female (46,XX), reflex MSA was performed to assess if the result was of miscarriage or maternal origin.

MAIN OUTCOME MEASURE(S)

Results were recorded as either informative or uninformative. Uninformative results were classified as "CGH failed" or "maternal contamination."

RESULT(S)

Fifty-eight women with 77 miscarriage specimens met the criteria. CGH failed in nine of the preserved miscarriage specimens owing to minimal pregnancy tissue, and two owing to poor-quality DNA. Twenty-two of the 33 specimens reported as 46,XX by CGH were sent for MSA; maternal contamination was confirmed in 23% (5/22). CGH was therefore informative in 79% (61/77) of the specimens; 64% (39/61) were euploid, and 36% (22/61) were noneuploid, with a 46,XX/46,XY ratio of 2.5.

CONCLUSION(S)

CGH with reflex MSA is useful for obtaining chromosome results in preserved miscarriage specimens, although informative results were achieved in only 79% of specimens. Maternal contamination should be assessed after an initial diploid female result.

Reliability of 46,XX results on miscarriage specimens: a review of 1,222 first-trimester miscarriage specimens

OBJECTIVE

To examine the rate of maternal contamination in miscarriage specimens.

DESIGN

Retrospective review of 1,222 miscarriage specimens submitted for chromosome testing with detection of maternal cell contamination (MCC).

SETTING

Referral centers requesting genetic testing of miscarriage specimens at a single reference laboratory.

PATIENT(S)

Women with pregnancy loss who desire complete chromosome analysis of the pregnancy tissue.

INTERVENTION(S)

Analysis of miscarriage specimens using single-nucleotide polymorphism (SNP) microarray technology with bioinformatics program to detect maternal cell contamination.

MAIN OUTCOME MEASURE(S)

Chromosome content of miscarriages and incidence of 46,XX results due to MCC.

RESULT(S)

Of the 1,222 samples analyzed, 592 had numeric chromosomal abnormalities, and 630 were normal 46,XX or 46,XY (456 and 187, respectively). In 269 of the 46,XX specimens, MCC with no embryonic component was found. With the exclusion of maternal 46,XX results, the chromosomal abnormality rate increased from 48% to 62%, and the ratio for XX to XY results dropped from 2.6 to 1.0.

CONCLUSION(S)

Over half of the normal 46,XX results in miscarriage specimens were due to MCC. The use of SNPs in MCC testing allows for precise identification of chromosomal abnormalities in miscarriage as well as MCC, improving the accuracy of products of conception testing.

First-trimester euploid miscarriages analysed by array-CGH

It is estimated that 10-15 % of all clinically recognised pregnancies results in a miscarriage, most of which occur during the first trimester. Large-scale chromosomal abnormalities have been found in up to 50 % of first-trimester spontaneous abortions and, for several decades, standard cytogenetic analysis has been used for their identification. Recent studies have proven that array comparative genomic hybridisation (array-CGH) is a useful tool for the detection of genome imbalances in miscarriages, showing a higher resolution, a significantly higher detection rate and overcoming problems of culture failures, maternal contamination and poor chromosome morphology. In this study, we investigated the possibility that submicroscopic chromosomal changes, not detectable by conventional cytogenetic analysis, exist in euploid miscarriages and could be causative for the spontaneous abortion. We analysed with array-CGH technology 40 foetal tissue samples derived by first-trimester miscarriages with a normal karyotype. A whole-genome microarray with a 100-Kb resolution was used for the analysis. Forty-five copy number variants (CNVs), ranging in size between 120 Kb and 4.3 Mb, were identified in 31 samples (24 gains and 21 losses). Ten samples (10/31, 32 %) have more than one CNV. Thirty-one CNVs (68 %) were defined as common CNVs and 14 were classified as unique. Six genes and five microRNAs contained within these CNVs will be discussed. This study shows that array-CGH is useful for detecting submicroscopic CNVs and identifying candidate genes which could account for euploid miscarriages.

Plasma TNF-α levels are higher in early pregnancy in patients with secondary compared with primary recurrent miscarriage

PROBLEM

Specific pro-inflammatory cytokine profiles in plasma may characterize women with recurrent miscarriage (RM) but the dynamics of the cytokine profiles with progressing pregnancy is largely unknown.

METHOD OF STUDY

Plasma was repeatedly sampled in the first trimester from 47 RM patients. The concentrations of five cytokines including tumour necrosis factor alpha (TNF-α) were measured. TNF-α levels were correlated to carriage of five TNFA promoter polymorphisms.

RESULTS

TNF-α levels increased (P = 0.014) with progressing pregnancy, with higher levels in secondary than primary RM (P = 0.042) but with no significant impact on outcome. Carriage of TNFA -863C and TNFA -1031T was associated with higher TNF-α levels, and the former was found more often in secondary than primary RM (P < 0.02).

CONCLUSION

Plasma TNF-α levels increase during early pregnancy in RM women regardless of outcome, but are higher in secondary than primary RM, which may be partly genetically determined.

Array-based approaches in prenatal diagnosis

The diagnostic benefits of array comparative genomic hybridisation (CGH) have been demonstrated, with this technique now being applied as the first-line test for patients with intellectual disabilities and/or multiple congenital anomalies in numerous laboratories. There are no technical barriers preventing the introduction of array CGH to prenatal diagnosis. The question is rather how this is best implemented, and for whom. The challenges lie in the interpretation of copy number variations, particularly those which exhibit reduced penetrance or variable expression, and how to deal with incidental findings, which are not related to the observed foetal anomalies, or unclassified variants which are currently of uncertain clinical significance. Recently, applications of array technologies to the field of pre-implantation genetic diagnosis have also been demonstrated. It is important to address the ethical questions raised concerning the genome-wide analysis of prenatal samples to ensure the maximum benefit for patients. We provide an overview of the recent developments on the use of array CGH in the prenatal setting, and address the challenges posed.