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

Hematoxylin and Eosin Staining Helps Reduce Maternal Contamination in Short Tandem Repeat Genotyping for Hydatidiform Mole Diagnosis

Short tandem repeat (STR) genotyping provides parental origin information about aneuploidy pregnancy loss and has become the current gold standard for hydatidiform mole diagnosis. STR genotyping diagnostic support most commonly relies on formalin-fixed paraffin-embedded samples, but maternal contamination is one of the most common issues based on traditional unstained sections. To evaluate the influence of hematoxylin and eosin (H&E) staining on DNA quality and STR genotyping, DNA was isolated from unstained, deparaffinized hydrated, and H&E-stained tissue sections (i.e. 3 groups) from each of 6 formalin-fixed paraffin-embedded placentas. The macrodissected view field, DNA quality, and polymerase chain reaction amplification efficiency were compared among groups. STR genotyping analysis was performed in both the test cohort (n = 6) and the validation cohort (n = 149). H&E staining not only did not interfere with molecular DNA testing of formalin-fixed paraffin-embedded tissue but also had a clearer macrodissected field of vision. In the test cohort, H&E-stained sections were the only group that did not exhibit maternal miscellaneous peaks in STR genotyping results. In the validation cohort, 138 (92.62%) cases yielded satisfactory amplification results without maternal contamination. Thus, H&E staining helped to reduce maternal contamination in STR genotyping for hydatidiform mole diagnosis, suggesting that H&E-stained sections can be incorporated into the hydatidiform mole molecular diagnostic workflow.

Clinical application of single nucleotide polymorphism microarray analysis in pregnancy loss in Northwest China

Background: Spontaneous abortion is the most common complication of early pregnancy. In this study, we aim to investigate the clinical application value of genetic diagnosis using single nucleotide polymorphism (SNP) microarray analysis on the products of conception and to characterize the types of genetic abnormalities and their prevalence in pregnancy loss in Northwest China. Methods: Over 48 months, we selected 652 products of conception, which included chorionic villi, fetal tissues, germ cell samples, amniotic fluid samples, cord blood samples, and a cardiac blood sample. We analyzed the distribution of chromosomal abnormalities leading to fetal arrest or abortion using SNP array. The patients were then categorized divided into groups based on maternal age, gestational age, number of miscarriages, and maternal ethnic background. The incidences of various chromosomal abnormalities in each group were compared. Results: Of the 652 cases, 314 (48.16%) exhibited chromosomal abnormalities. These included 286 cases with numerical chromosomal abnormalities, 24 cases with copy number variation, and four cases with loss of heterozygosity. Among them, there were 203 trisomy cases, 55 monosomy cases, and 28 polyploidy cases. In the subgroup analysis, significant differences were found in the frequency of numerical chromosomal abnormalities and copy number variation between the advanced and younger maternal age group as well as between the early and late abortion groups. Furthermore, we identified significant differences in the frequency of numerical chromosomal abnormalities between the first spontaneous abortion and recurrent miscarriage groups. However, there were no significant differences in the frequency of numerical chromosomal abnormalities between the Han and Uighur groups. Conclusion: Our research highlights chromosomal abnormalities as the primary cause of spontaneous abortion, with a higher incidence in early pregnancy and among women of advanced age. The use of SNP array analysis emerges as an effective and reliable technique for chromosome analysis in aborted fetuses. This method offers a comprehensive and dependable genetic investigation into the etiology of miscarriage, establishing itself as a valuable routine selection for genetic analysis in cases of natural abortions.

Polyploidy Phenomenon as a Cause of Early Miscarriages in Abortion Materials

Objectives

Chromosomal abnormalities are an important cause of especially early miscarriages. The aim of this study was to analyze the chromosomal aberrations and determine the frequencies of numerical and structural chromosome abnormalities in spontaneous abortion materials.

Methods

This was a prospective research and ninety two abortion samples obtained from women who had one or more miscarriages were included in the study. Conventional karyotype analysis was performed on each sample to identify possible chromosomal abnormalities.

Results

By karyotype analysis, 11 polyploidy cases, (9 triploids and 2 tetraploids), 8 trisomies (one of which was mosaic), 2 monosomies (monosomy X), 1 isochromosome, 1 Xq deletion, and 4 translocations were detected in abortion materials. Isochromosome and Xq deletion cases were also mosaic. In addition, five polymorphic variants were revealed. We found higher paternal age in polyploidy cases.

Conclusion

The most common anomaly we found in abortion materials was polyploidy. This was followed by aneuploidy (trisomy and monosomy). Polyploidy (triploidy or tetraploidy) emerged as an important cause in cases of spontaneous abortion. Paternal age may be associated with polyploidy especially triploidy.

Using single nucleotide polymorphism array for prenatal diagnosis in a large multicenter study in Southern China

Numerous studies have evaluated the use of single nucleotide polymorphism array (SNP-array) in prenatal diagnostics, but very few have evaluated its application under different risk conditions. Here, SNP-array was used for the retrospective analysis of 8386 pregnancies and the cases were categorized into seven groups. Pathogenic copy number variations (pCNVs) were found in 699 (8.3%, 699/8386) cases. Among the seven different risk factor groups, the non-invasive prenatal testing-positive group had the highest pCNVs rate (35.3%), followed by the abnormal ultrasound structure group (12.8%), and then the chromosomal abnormalities in the couples group (9.5%). Notably the adverse pregnancy history group presented with the lowest pCNVs rate (2.8%). Further evaluation of the 1495 cases with ultrasound abnormalities revealed that the highest pCNV rates were recorded in those cases with multiple system structure abnormalities (22.6%), followed by the groups with skeletal system (11.6%) and urinary system abnormalities (11.2%). A total of 3424 fetuses with ultrasonic soft markers were classified as having one, two, or three ultrasonic soft markers. The different pCNV rates in the three groups were statistically significant. There was little correlation between pCNVs and a previous history of adverse pregnancy outcomes, suggesting that genetic screening under these conditions should be evaluated on a case-by-case basis.

Prevalence of Sex-Related Chromosomal Abnormalities in a Large Cohort of Spanish Purebred Horses

Chromosomal abnormalities are largely associated with fertility impairments in the domestic horse. To date, over 600 cases of individuals carrying abnormal chromosome complements have been reported, making the domestic horse the species with the highest prevalence. However, studies analyzing the prevalence of chromosomal diseases in whole populations are scarce. We, therefore, employed a two-step molecular tool to screen and diagnose chromosomal abnormalities in a large population of 25,237 Pura Raza Español horses. Individuals were first screened using short tandem repeats parentage testing results and phenotypic evaluations. Those animals showing results suggesting chromosomal abnormalities were re-tested using a single nucleotide polymorphism (SNP)-based diagnostic methodology to accurately determine the chromosomal complements. Thirteen individuals showed a positive screening, all of which were diagnosed as chromosomally abnormal, including five 64,XY mares with sex development disorders (DSD) and four cases of blood chimerism (two male/female and two female/female cases). In addition, we detected one Turner and one Klinefelter syndrome and two individuals carrying complex karyotypes. The overall prevalence in the entire population was ~0.05%, with the prevalence of 64,XY DSD and blood chimerism ~0.02% and ~0.016%, respectively. However, the overall results should be taken with caution since the individuals carrying Turner syndrome (in full (63,X) or mosaic (mos 63,X/64,XX) forms) cannot be detected due to limitations in the methodology employed. Finally, the lack of agreement between populational studies performed using karyotyping or molecular methods is discussed. To our knowledge, this is the largest populational study performed evaluating the prevalence of the most common chromosomal abnormalities in the domestic horse.

Patients with Recurrent Pregnancy Loss Have Similar Embryonic Preimplantation Genetic Testing Aneuploidy Rates and In Vitro Fertilization Outcomes to Infertility Patients

Objective

To evaluate aneuploidy rates and in vitro fertilization (IVF)/pregnancy outcomes for patients undergoing IVF and preimplantation genetic testing for aneuploidy (PGT-A) with a recurrent pregnancy loss (RPL) diagnosis compared to infertility diagnoses without RPL.

Design

Retrospective cohort study.

Setting

Academic fertility center.

Patients

Of 372 patients undergoing IVF/PGT-A between January 2016-December 2018, 294 patients were included in the analysis: 56 patients with an RPL diagnosis and 238 with infertility diagnoses without RPL.

Interventions

None.

Main Outcome Measures

The primary outcome measured was the embryonic aneuploidy rate. Secondary outcomes included fertilization and blastulation rates, number of blastocysts biopsied, cycles without euploid blastocysts, and rates of pregnancy losses, clinical pregnancies, and live births after a euploid embryo transfer.

Results

The cohort included 56 patients with RPL and 238 patients without RPL, including data from their first IVF cycle within the time period. Aneuploidy rates were similar between the groups, with a mean of 55% (±31%) in RPL and 54% (±34%) in non-RPL cycles. Similar rates persisted after controlling for age, ovarian reserve, and infertility diagnosis. Fertilization and blastulation rates, as well as cumulative clinical pregnancy, pregnancy loss, and live birth rates after the transfer of at least one euploid embryo were also similar between the two groups.

Conclusions

These results suggest that IVF/PGT-A cycles from patients with an RPL diagnosis have similar IVF and pregnancy outcomes to those of patients with infertility without RPL. This research can help guide counseling for RPL patients considering IVF with PGT-A.

Integrated Workflow for the Label-Free Isolation and Genomic Analysis of Single Circulating Tumor Cells in Pancreatic Cancer

As pancreatic cancer is the third deadliest cancer in the U.S., the ability to study genetic alterations is necessary to provide further insight into potentially targetable regions for cancer treatment. Circulating tumor cells (CTCs) represent an especially aggressive subset of cancer cells, capable of causing metastasis and progressing the disease. Here, we present the Labyrinth-DEPArray pipeline for the isolation and analysis of single CTCs. Established cell lines, patient-derived CTC cell lines and freshly isolated CTCs were recovered and sequenced to reveal single-cell copy number variations (CNVs). The resulting CNV profiles of established cell lines showed concordance with previously reported data and highlight several gains and losses of cancer-related genes such as FGFR3 and GNAS. The novel sequencing of patient-derived CTC cell lines showed gains in chromosome 8q, 10q and 17q across both CTC cell lines. The pipeline was used to process and isolate single cells from a metastatic pancreatic cancer patient revealing a gain of chromosome 1q and a loss of chromosome 5q. Overall, the Labyrinth-DEPArray pipeline offers a validated workflow combining the benefits of antigen-free CTC isolation with single cell genomic analysis.

Research on the Mechanism of Asperosaponin VI for Treating Recurrent Spontaneous Abortion by Bioinformatics Analysis and Experimental Validation

Asperosaponin VI (AS6), as the quality marker of Dipsaci Radix, is verified to exert therapeutic effect on alleviating recurrent spontaneous abortion (RSA). However, due to the lack of relevant research, its molecular mechanism is still unclear. We retrieved targets for AS6 and RSA, and then used their overlapped targets for PPI analysis. In addition, we used GO and KEGG enrichment analyses, and molecular docking to investigate the anti-RSA mechanisms of AS6. Furthermore, we conducted in vitro experiments to validate the predictions of network pharmacology. Results showed that a total of 103 AS6-associated targets and 2084 RSA-associated targets, with 49 targets overlapped. GO enrichment analysis showed 845 significant biological processes like decidualization, while KEGG pathway enrichment analysis revealed 76 significant entries including 18 signaling pathways, which were closely linked to PI3K-Akt, HIF-1, TNF, IL-17, and VEGF signaling pathways, etc. Molecular docking findings verified that AS6 had tight link with the key targets including JUN, CASP3, STAT3, SRC, and PTGS2. Notably, in vitro experiments revealed that AS6 treatment could exert lower expressions of JUN, pro-CASP3, CASP3, STAT3, SRC, and PTGS2 in decidual cells compared with progesterone despite the expressions of STAT3, SRC, and PTGS2 with no significant difference, and mifepristone could interfere with the effects. In general, numerous targets and multiple pathways involve during the process of AS6 treatment against RSA. Moreover, our in vitro research first reported that AS6 may regulate the expressions of key targets (JUN, CASP3, STAT3, SRC, and PTGS2) in decidual cells to promote decidualization, thus treating RSA.

Ultrasound-guided Manual Vacuum Aspiration is an optimal method for obtaining products of conception from early pregnancy loss for cytogenetic testing

OBJECTIVE

The culture failure rate of conventional karyotyping in products of conception evacuated from early pregnancy loss by traditional electrical vacuum aspiration and/or dilation & curettage remains high. We aim to determine whether obtaining products of conception from early pregnancy loss via another evacuation approach, ultrasound-guided manual vacuum aspiration, could decrease the culture failure rate of karyotyping.

METHODS

For patients with early pregnancy loss, ultrasound-guided manual vacuum aspiration (Case group) and traditional electrical vacuum aspiration and/or dilation & curettage (Control group) were applied as surgical methods for pregnancy loss management respectively. The evacuated products of conception were subjected to cytogenetic karyotyping analysis. The primary outcome was the culture failure rate of karyotyping. Secondary outcomes included the chromosomal abnormality spectrum, maternal cell contamination, and complications from the manual vacuum aspiration procedure.

RESULTS

For the case group, 132 products of conception were genetically analyzed by conventional karyotyping. The culture failure rate was significantly lower than that of the control cohort (2.3% vs 7.4%, p = 0.027). 65.2% of cases were abnormal within the detection scope of karyotyping. The euploid female to male ratio was 0.82 (18:22), suggesting a lower likelihood of maternal cell contamination. The efficacy in achieving complete evacuation was 99.6%. There were no significant complications from the procedure.

CONCLUSION

Ultrasound-guided manual vacuum aspiration approach significantly decreased the culture failure rate of karyotyping and decreased maternal cell contamination tendency, enabling a high and accurate cytogenetic diagnosis. It is especially crucial when the cytogenetic analysis is required in the early pregnancy loss clinics.

Key Gene and Functional Pathways Identified in Unexplained Recurrent Spontaneous Abortion Using Targeted RNA Sequencing and Clinical Analysis

Identifying the mechanisms underlying unexplained recurrent spontaneous abortion (URSA) can help develop effective treatments. This study provides novel insights into the biological characteristics and related pathways of differentially expressed genes (DEGs) in URSA. Nineteen patients with URSA and three healthy fertile women with regular menstruation (control group) were recruited. RNA was extracted from the two groups to determine the differential expression of immunoregulatory gene sequences. Gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses were used to identify the biological functions and pathways of the identified DEGs. A protein-protein interaction (PPI) network was constructed using the STRING database. Furthermore, qRT-PCR and ELISA were performed to validate the differential expression of the hub genes. We also explored the regulatory mechanism of Th1/Th2 imbalance. A total of 99 DEGs were identified, comprising 94 upregulated and five downregulated genes. Through GO analysis, nine immune cell function-related clusters were selected, and genes with significant differential expression were primarily enriched in eight immune regulatory functions related to the KEGG signalling pathway. Subsequently, five hub genes (TLR2, CXCL8, IFNG, IL2RA, and ITGAX) were identified using Cytoscape software; qRT-PCR confirmed the differential expression among the hub genes, whereas ELISA revealed a significant difference in extracellular IFN-γ and IL-8 levels. The levels of Th1 (IFN-γ) and the Th1/Th2 ratio were higher in the peripheral blood of URSA patients than in control group patients. These findings suggest that the occurrence of URSA may be associated with the abnormal expression of some specific immunoregulatory genes involved in T-cell activation and differentiation. Among the identified DEGs, IFNG may play a key role in regulating maternal immune response. Although further validation is required, our data provide an important theoretical basis for elucidating the pathogenesis of recurrent spontaneous abortion.

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.

Lower chromosomal abnormality frequencies in miscarried conceptuses from frozen blastocyst transfers in ART

STUDY QUESTION

Are blastocyst culture and cryopreservation in ART associated with chromosomal abnormalities in miscarried products of conception (POC)?

SUMMARY ANSWER

Frozen blastocyst transfer in women aged 35 years or older and frozen embryo transfer (ET) (including both cleavage-stage embryo and blastocyst) in women aged <35 years are associated with decreased frequencies of embryonic chromosomal abnormalities in miscarried POC.

WHAT IS KNOWN ALREADY

Blastocyst culture and embryo cryopreservation have been previously associated with favorable ART treatment outcomes and widely applied in clinical practice. However, the association between these embryo manipulation procedures and embryonic chromosomal abnormalities has not been evaluated to the best of our knowledge.

STUDY DESIGN, SIZE, DURATION

This retrospective study included a total of 720 patients who underwent IVF/ICSI, and the retained POC were obtained. A single-nucleotide polymorphism (SNP)-based chromosomal microarray analysis (CMA) of all miscarried conceptuses was performed.

PARTICIPANTS/MATERIALS, SETTING, METHODS

This study was based on the Clinical Reproductive Medicine Management System/Electronic Medical Record Cohort Database (CCRM/EMRCD) at our center. In total, 720 miscarried POCs were collected from patients undergoing ART (including fresh cleavage-stage ET, fresh blastocyst transfer, frozen cleavage-stage ET and frozen blastocyst transfer), and the incidences and profiles of cytogenetic abnormalities in the miscarried conceptuses were measured via SNP-based CMA.

MAIN RESULTS AND THE ROLE OF CHANCE

The chromosomal abnormality rate in POC varied from 33.7% to 66.7% among the different ET strategies. In the patients aged ≥35 years, frozen blastocyst transfer was significantly associated with a lower incidence of chromosomal aberrations in the POCs (adjusted odds ratio (aOR): 0.171 (95% CI: 0.040-0.738); P = 0.018) than fresh blastocyst transfer. In the patients aged <35 years, frozen ET was significantly associated with a lower incidence of chromosomal aberrations than fresh ET in both cleavage-stage ET cycles and blastocyst transfers cycles (aOR: 0.545 (0.338-0.879), P = 0.013; and aOR: 0.357 (0.175-0.730), P = 0.005, respectively). Trisomy was the most frequent abnormal embryonic karyotype in the different ET strategies, and its frequency significantly differed among strategies (P < 0.05).

LIMITATIONS, REASONS FOR CAUTION

This study was retrospectively designed, and we cannot draw any definite conclusions from our results regarding the adequate safety of embryo cryopreservation in ongoing pregnancy.

WIDER IMPLICATIONS OF THE FINDINGS

To our knowledge, this is the first study assessing the associations of ET strategies with the probability of miscarriage associated with embryonic chromosomal abnormalities. However, the underlying mechanism of these associations is unknown; this study may promote research concerning ET strategies and promote comprehensive consultations and recommendations for patients.

STUDY FUNDING/COMPETING INTEREST(S)

This work was supported by the Natural Science Foundation of China (Grant No.81571409), Science and Technology Research Project of Henan (Grant No. 172102310009) and Medical Science and Technology Research Project of Henan (Grant No. 201701005). The authors declare no competing interests.

TRIAL REGISTRATION NUMBER

N/A.

Diagnostic accuracy and value of chromosomal microarray analysis for chromosomal abnormalities in prenatal detection: A prospective clinical study

Chromosomal microarray analysis (CMA) has emerged as a primary diagnostic tool for the evaluation of developmental delay and structural malformations in children. The aim of this study was to compare the accuracy and value of CMA and karyotyping on diagnosis of chromosomal abnormalities in Fujian province of South China.In the study, 410 clinical samples were collected from pregnant women between March 2015 and December 2016, including 3 villus (0.73%, 3/410), 296 amniotic fluid (72.20%, 296/410), and 111 umbilical cord blood (27.07%, 111/410). All samples were screening for chromosomal abnormalities by both using CMA and karyotyping.The success rate of CMA and karyotyping was 100% (410/410) and 99.27% (407/410), respectively. Sixty-one (14.88%, 61/410) samples were presented with chromosomal abnormalities by using CMA, whereas 47 (11.55%, 47/407) samples were shown with chromosomal abnormalities by using karyotyping. Thirty-one (8.61%, 31/360) samples with normal karyotypes were found to exist chromosomal abnormalities by using CMA. Receiver operating characteristic analysis showed that the area under the curve of karyotyping on the diagnosis of chromosomal abnormalities was 0.90 (95% confidence interval: 0.87-0.93), the sensitivity and specificity was 87.56% and 91.22%, respectively. The area under the curve of CMA on the diagnosis of chromosomal abnormalities was 0.93 (95% confidence interval: 0.90-0.95), with 90.68% sensitivity and 94.40% specificity. Notably, the combination of CMA and karyotyping could improve the diagnosis of chromosomal abnormalities.CMA has a better diagnostic value for screening chromosomal abnormalities, especially for those pregnant women with normal karyotypes. This study has guiding value for prenatal diagnosis in Fujian province of South China.

Cytogenetic Analysis of the Products of Conception After Spontaneous Abortion in the First Trimester

In the present study, we retrospectively recruited 340 patients who underwent spontaneous abortions to investigate chromosomal abnormalities of the conception products in the first trimester. We also performed a relevant analysis of clinical factors. Of these patients, 165 had conception products with chromosomal abnormalities, including 135 aneuploidies, 11 triploidies, 10 complex abnormalities, and 9 segmental aneuploidies. The most common abnormal chromosomes were chromosome 16 in the embryo-transfer group and sex chromosomes in the natural-conception group. The most common abnormal chromosomes in all analyzed maternal age groups were sex chromosomes, 16, and 22. The chromosomal abnormality incidence was related to age and number of spontaneous abortions (both p < 0.05), but not to number of pregnancies, deliveries, induced abortions, or methods of conception (all p > 0.05). The rates of abnormality for chromosomes 12, 15, 20, and 22 increased with age, while the rates for chromosomes 6, 7, 13, and X decreased. In all age groups, aneuploidy was by far the most common abnormality; however, the low-incidence distributions of chromosomal abnormalities were entirely different. Overall, chromosomal aneuploidy was the primary cause of pregnancy loss in the first trimester, and low-frequency abnormalities differed across age subgroups. Chromosomal aberrations were found to be related to maternal age and spontaneous abortion, but not all chromosomal abnormalities increased with age.

Comparative clinical genetic testing in spontaneous miscarriage: Insights from a study in Southern Chinese women

Single nucleotide polymorphism (SNP) array and karyotype analyses were conducted on 441 spontaneous miscarriage placental villous tissues collected from women from southern China. Subsequently, the results from these two analyses were compared to evaluate the best diagnostic strategy for subsequent pre‐pregnancy planning. Here, the success rate of genetic testing using karyotyping and SNP array analysis was 78.46% (346/441) and 100.0% (441/441), respectively. The abnormality rate estimated by both methods was 54.9% (242/441). Three hundred and forty‐six cases were successfully detected via both SNP array and karyotype analyses; the rate of consistent detection was 96.24% (333/346), whereas 13 cases were not consistent. There was no substantial positive correlation between age and genetic abnormalities such as Turner syndrome, structural variation or euploidy state in the different age groups studied. However, the aneuploidy rate was significantly different in each age group. Thus, although SNP array has higher success rate and resolution in genetic abnormality detection, supplementary karyotype analysis is needed for a more accurate revelation of the genetic aetiology of miscarriages. Therefore, this study indicates that simultaneous karyotype and SNP array analyses should be performed for spontaneous miscarriages. Furthermore, miscarriages irrespective of maternal age must be genetically analysed.

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.

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).

Genetics of recurrent pregnancy loss: a review

PURPOSE OF REVIEW

Human reproduction is remarkably inefficient; with pregnancy loss occurring in 10-30% of clinically recognized pregnancies. Of those, 3-5% of couples experience recurrent pregnancy loss (RPL), more than 50% of who never receive an underlying diagnosis. Herein, we review evidence that genetic changes, including pathogenic variant(s) in highly penetrant genes, may provide an explanation for a proportion of couples with pregnancy loss.

RECENT FINDINGS

Genetic abnormalities that may predispose to pregnancy loss include chromosomal aneuploidy, copy number variants, single-gene changes and others. Although previously limited by the need for hypothesis-driven assessment, advancement of various molecular technologies have sheparded in the opportunity to identify molecular cause of highly heterogeneous conditions, including RPL. The identification of causative genetic aberrations associated with RPL demonstrates a promising area of further research.

SUMMARY

The journey of human development from a single-cell zygote to a term infant is complex process. Early research into copy number variants and highly penetrant single-gene changes may provide diagnosis for a proportion of couples with RPL as well as inform genes critical for early human development.

Chromosomal copy number analysis of products of conception by conventional karyotyping and next-generation sequencing

PURPOSE

Chromosomal abnormalities are a major cause of spontaneous abortion, and conventional G-banded karyotyping (G-banding) is mainly utilized for chromosomal analysis. Recently, next-generation sequencing (NGS) has been introduced for chromosomal analysis. Here, we aimed to investigate the applicability and utility of NGS-based chromosomal analysis of products of conception (POC) on chorionic villus samples from spontaneous abortion.

METHODS

The results of chromosomal analysis of 7 chorionic villus samples from spontaneous abortion were compared between conventional G-banding and NGS-based chromosomal copy number analysis. Age dependency and frequency of each chromosomal aneuploidy were evaluated for 279 cases analyzed by NGS.

RESULTS

Excluding two cases (culture failure and maternal cell contamination), the results were consistent between G-banding and NGS. For cases analyzed by NGS, the rate of chromosomal abnormality increased in a maternal age-dependent manner. The frequency of each chromosomal aneuploidy detected by NGS was almost the same as that previously reported. Finally, NGS analysis was possible for difficult cases by G-banding analysis, such as culture failure, maternal cell contamination, long-term storage cases, and low cell number.

CONCLUSIONS

Chromosome analysis using NGS not only obtains comparable results to conventional G-banding, but also can analyze POC more accurately and efficiently.

Analysis of tissue from pregnancy loss and aborted fetus with ultrasound anomaly using subtelomeric MLPA and chromosomal array analysis

OBJECTIVE

To evaluate the incidence and types of chromosomal abnormalities in pregnancy loss and aborted fetuses with anomaly and compare the performance of subtelomeric MLPA and chromosomal microarray analysis (CMA) in these specimens.

METHODS

Samples were collected from spontaneous miscarriages, stillbirths and aborted fetuses with anomaly between January 2015 and April 2019. Chromosomal abnormalities were detected using subtelomeric MLPA and CMA.

RESULTS

Among the 172 miscarriage samples, CMA detected pathogenic chromosomal abnormalities in 88 cases. MLPA could identified all aneuploidies and most pathogenic CNVs, missing all polyploidies; Of the 30 stillbirths, one pathogenic CNV and two VOUS were identified by CMA, all of which were missed from MLPA; Of the 135 aborted fetuses with anomaly, CMA identified pathogenic chromosomal abnormalities in 32 fetuses (23.7%); 18.95% in fetuses with isolated, and 35% in fetuses with multiple anomalies. MLPA can identify all aneuploidies but missing most pathogenic CNVs.

CONCLUSION

Our systematical comparison of subtelomeric MLPA and CMA for chromosomal analysis of tissue from pregnancy loss and aborted fetuses with anomaly is useful for assessing clinical utility of these techniques. MLPA screening, coupled with CMA analysis, is a cost-effective approach to detect chromosomal abnormalities in miscarriage and anomalous fetuses. However, MLPA might not be appropriate for chromosome analysis in stillbirth without structural anomaly; further research with more samples is needed.

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.

Low-pass genome sequencing versus chromosomal microarray analysis: implementation in prenatal diagnosis

PURPOSE

Emerging studies suggest that low-pass genome sequencing (GS) provides additional diagnostic yield of clinically significant copy-number variants (CNVs) compared with chromosomal microarray analysis (CMA). However, a prospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of low-pass GS compared with CMA is warranted.

METHODS

A total of 1023 women undergoing prenatal diagnosis were enrolled. Each sample was subjected to low-pass GS and CMA for CNV analysis in parallel. CNVs were classified according to guidelines of the American College of Medical Genetics and Genomics.

RESULTS

Low-pass GS not only identified all 124 numerical disorders or pathogenic or likely pathogenic (P/LP) CNVs detected by CMA in 121 cases (11.8%, 121/1023), but also defined 17 additional and clinically relevant P/LP CNVs in 17 cases (1.7%, 17/1023). In addition, low-pass GS significantly reduced the technical repeat rate from 4.6% (47/1023) for CMA to 0.5% (5/1023) and required less DNA (50 ng) as input.

CONCLUSION

In the context of prenatal diagnosis, low-pass GS identified additional and clinically significant information with enhanced resolution and increased sensitivity of detecting mosaicism as compared with the CMA platform used. This study provides strong evidence for applying low-pass GS as an alternative prenatal diagnostic test.

Chromosomal copy number variations in products of conception from spontaneous abortion by next-generation sequencing technology

Fetal chromosomal abnormalities are considered to be the main cause of spontaneous abortion (SA). We aimed to determine the differences in the rates and numbers of chromosomal abnormalities between samples from women with a history of one versus more than one SA as well as between samples from first- and second-trimester SAs in women from Northeast China.In total, 1210 products of conception (POCs) from patients with a history of one or more SAs were examined. Of these 1210 samples, 434 were from women with a history of 1 SA, and 776 were from women with a history of more than 1 SA. Additionally, 1071 samples were from the first trimester, 118 were from the second trimester, and 21 were from the third trimester. We identified chromosomal abnormalities by next-generation sequencing (NGS) technology. Among the 1210 POCs in women with SA, 607 (50.17%) had fetal chromosomal abnormalities. There were no significant differences in the rates of chromosomal abnormalities according to the abortion frequency. However, first-trimester SA had a significantly higher percentage of fetal chromosomal abnormalities than second-trimester SA (P < .05). Among 663 chromosomal abnormalities, 633 abnormalities occurred in first-trimester SA; the most frequent karyotype was trisomy 16 (14.38%), followed by monosomy X (13.27%), trisomy 22 (7.90%), and trisomy 15 (5.37%). Thirty abnormalities occurred in second-trimester SA; the most frequent karyotype was trisomy 18 (26.67%), followed by monosomy X (16.67%), trisomy 21 (13.33%), and trisomy 13 (10.00%). No chromosomal abnormalities occurred in the third trimester.These findings indicate the importance of determining the genetic cause of abortion in patients with a history of SA. We also identified a trend suggesting that the percentage of fetal chromosomal abnormalities is significantly higher in first- than second-trimester SA. The detection rate of chromosomal abnormalities in POCs from SA can be increased by NGS, which is beneficial for couples with recurrent miscarriages and offers better genetic counseling in the clinical setting.

Combination of QF-PCR and aCGH is an efficient diagnostic strategy for the detection of chromosome aberrations in recurrent miscarriage

Background

Our aim was to conduct a comprehensive genetic evaluation using the combination of QF‐PCR (quantitative fluorescence polymerase chain reaction) and aCGH (array comparative genomic hybridization) for the detection of the frequency and type of chromosome aberrations in recurrent miscarriage (RM) in the clinical setting.

Methods

This retrospective study was conducted on 73 first‐trimester products of conception (POC) between September 2014 and February 2017. The POCs were collected from 73 women with at least one previous miscarriage and analyzed for chromosomal anomalies using QF‐PCR and aCGH as part of the routine clinical evaluation.

Results

Chromosome aberrations were detected in 52/73 POCs (71.2%), of which 41 (56.2%) were identified by QF‐PCR and an additional 11 (15.1%) by aCGH. Numerical aberrations constituted 92.3% of abnormalities, with trisomies as the most common subtype (72.9%). Causative structural aberrations were found in three samples (5.8%). The frequency of chromosome aberrations was not dependent on the number of previous miscarriages, whereas it significantly increased with advanced maternal age.

Conclusion

Our results confirm that chromosome aberrations are the most common cause of RM and that QF‐PCR and aCGH combination should be included in the routine genetic analysis of POCs of couples with miscarriage.

Inverted duplication, triplication and quintuplication through sequential breakage-fusion-bridge events induced by a terminal deletion at 5p in a case of spontaneous abortion

Background

Integrated chromosome, fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH) analyses have been effective in defining unbalanced chromosomal rearrangements. Discordant chromosome and aCGH results are rarely reported.

Methods

Routine cytogenomic analyses and literature review were performed in the study of a case from products of conception (POC).

Results

Chromosome and FISH analysis revealed a mosaic pattern consisting of a primary aberration of an inverted duplication of 5p and derived secondary and tertiary aberrations from sequential triplication and quintuplication of 5p, respectively. The aCGH analysis detected only a 1.521 Mb terminal deletion at 5p15.33 with no other pathogenic copy number variants in the genome. This mosaic karyotypic pattern likely resulted from chromosome instability induced by sequential breakage‐fusion‐bridge events during in vitro cell culture. A review of literature found heterogeneous distal deletion and inverted duplication of 5p in prenatal and pediatric cases.

Conclusion

This is the first case reported in POC with a unique mosaic pattern and discordant chromosome and aCGH results. Caution should be applied in reporting and interpreting these discordant results and further analysis for underlying mechanism should be considered.

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.

Search for Novel Mutational Targets in Human Endocrine Diseases

The identification of disease-causing genetic variations is an important goal in the field of genetics. Advancements in genetic technology have changed scientific knowledge and made it possible to determine the basic mechanism and pathogenesis of human disorders rapidly. Many endocrine disorders are caused by genetic variations of a single gene or by mixed genetic factors. Various genetic testing methods are currently available, enabling a more precise diagnosis of many endocrine disorders and facilitating the development of a concrete therapeutic plan. In this review article, we discuss genetic testing technologies for genetic endocrine disorders, with relevant examples. We additionally describe our research on implementing genetic analysis strategies to identify novel causal mutations in hypocalcemia-related disorders.

Maternal age, history of miscarriage, and embryonic/fetal size are associated with cytogenetic results of spontaneous early miscarriages

PURPOSE

To clarify the associations of the maternal age, history of miscarriage, and embryonic/fetal size at miscarriage with the frequencies and profiles of cytogenetic abnormalities detected in spontaneous early miscarriages.

METHODS

Miscarriages before 12 weeks of gestation, whose karyotypes were evaluated by G-banding between May 1, 2005, and May 31, 2017, were included in this study. The relationships between their karyotypes and clinical findings were assessed using trend or chi-square/Fisher's exact tests and multivariate logistic analyses.

RESULTS

Three hundred of 364 miscarriage specimens (82.4%) had abnormal karyotypes. An older maternal age was significantly associated with the frequency of abnormal karyotype (p_trend < 0.001), particularly autosomal non-viable and viable trisomies (p_trend 0.001 and 0.025, respectively). Women with ≥ 2 previous miscarriages had a significantly lower possibility of miscarriages with abnormal karyotype than women with < 2 previous miscarriages (adjusted odds ratio [aOR], 0.48; 95% confidence interval [95% CI], 0.27-0.85). Although viable trisomy was observed more frequently in proportion to the increase in embryonic/fetal size at miscarriage (p_trend < 0.001), non-viable trisomy was observed more frequently in miscarriages with an embryonic/fetal size < 10 mm (aOR, 2.41; 95% CI, 1.27-4.58), but less frequently in miscarriages with an embryonic/fetal size ≥ 20 mm (aOR, 0.01; 95% CI, 0.00-0.07) than in anembryonic miscarriages.

CONCLUSIONS

The maternal age, history of miscarriage, and embryonic/fetal size at miscarriage may be independently associated with the frequencies or profiles of cytogenetic abnormalities in early miscarriages.

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.

The Status of Genetic Screening in Recurrent Pregnancy Loss

Recurrent pregnancy loss is often idiopathic, but numerical and structural chromosomal abnormalities constitute an important cause. Numerical chromosomal abnormalities in the conceptus are primarily due to meiotic nondisjunction; the rate and complexity of embryonic aneuploidy are driven by female age. Structural chromosomal abnormalities (balanced translocations or inversions) can lead to unbalanced gametes depending on specific recombination and segregation patterns during meiosis. The attendant reproductive risk depends on the type of rearrangement and its parental origin. Current methods for analysis of products of conception include cytogenetics, array comparative genomic hybridization, and single nucleotide polymorphism microarray; each platform has advantages and disadvantages.