Whole exome sequencing in recurrent early pregnancy loss

Recurrent pregnancy loss: risk factors and predictive modeling approaches

PURPOSE

This review aims to identify and analyze the risk factors associated with recurrent pregnancy loss (RPL) and to evaluate the effectiveness of various predictive models in estimating the risk of RPL. The review also explores recent advancements in machine learning algorithms that can enhance the accuracy of these predictive models. The ultimate goal is to provide a comprehensive understanding of how these tools can aid in the personalized management of women experiencing RPL.

MATERIALS AND METHODS

The review synthesizes current literature on RPL, focusing on various risk factors such as chromosomal abnormalities, autoimmune conditions, hormonal imbalances, and structural uterine anomalies. It also analyzes different predictive models for RPL risk assessment, including genetic screening tools, risk scoring systems that integrate multiple clinical parameters, and machine learning algorithms capable of processing complex datasets. The effectiveness and limitations of these models are critically evaluated to provide insights into their clinical application.

RESULTS

Key risk factors for RPL were identified, including chromosomal abnormalities (e.g. translocations and aneuploidies), autoimmune conditions (e.g. antiphospholipid syndrome), hormonal imbalances (e.g. thyroid dysfunction and luteal phase defects), and structural uterine anomalies (e.g. septate or fibroid-affected uteri). Predictive models such as genetic screening tools and risk scoring systems were shown to be effective in estimating RPL risk. Recent advancements in machine learning algorithms demonstrate potential for enhancing predictive accuracy by analyzing complex datasets, which may lead to improved personalized management strategies.

CONCLUSIONS

The integration of risk factors and predictive modeling offers a promising approach to improving outcomes for women affected by RPL. A comprehensive understanding of these factors and models can aid clinicians and researchers in refining risk assessment and developing targeted interventions. The review underscores the need for further research into specific pathways involved in RPL and the potential of novel treatments aimed at mitigating risk.

Impact of prenatal genomics on clinical genetics practice

Genetic testing for prenatal diagnosis in the pre-genomic era primarily focused on detecting common fetal aneuploidies, using methods that combine maternal factors and imaging findings. The genomic era, ushered in by the emergence of new technologies like chromosomal microarray analysis and next-generation sequencing, has transformed prenatal diagnosis. These new tools enable screening and testing for a broad spectrum of genetic conditions, from chromosomal to monogenic disorders, and significantly enhance diagnostic precision and efficacy. This chapter reviews the transition from traditional karyotyping to comprehensive sequencing-based genomic analyses. We discuss both the clinical utility and the challenges of integrating prenatal exome and genome sequencing into prenatal care and underscore the need for ethical frameworks, improved prenatal phenotypic characterization, and global collaboration to further advance the field.

Revolutionized attitude toward recurrent pregnancy loss and recurrent implantation failure based on precision regenerative medicine

Traditional treatment strategies for recurrent pregnancy loss (RPL) and recurrent implantation failure (RIF) often result in limited success, placing significant emotional and financial burdens on couples. However, novel approaches such as diagnostic gene profiling, cell therapy, stem cell-derived exosome therapy, and pharmacogenomics offer promising, personalized treatments. Combining traditional treatments with precision and regenerative medicine may enhance the efficacy of these approaches and improve pregnancy outcomes. This review explores how integrating these strategies can potentially transform the lives of couples experiencing repeated pregnancy loss or implantation failure, providing hope for improved treatment success. Precision and regenerative medicine represent a new frontier for managing RPL and RIF, offering promising solutions.

Whole exome sequencing identifies a novel mutation in Annexin A4 that is associated with recurrent spontaneous abortion

Background

Recurrent spontaneous abortion (RSA) is a multifactorial disease, the exact causes of which are still unknown. Environmental, maternal, and genetic factors have been shown to contribute to this condition. The aim of this study was to investigate the presence of mutations in the ANXA4 gene in patients with RSA.

Methods

Genomic DNA was extracted from 325 patients with RSA and 941 control women with a normal reproductive history for whole-exome sequencing (WES). The detected variants were annotated and filtered, and the pathogenicity of the variants was predicted through the SIFT online tool, functional enrichment analyses, Sanger sequencing validation, prediction of changes in protein structure, and evolutionary conservation analysis. Furthermore, plasmid construction, Western blotting, RT-qPCR, and cell migration, invasion and adhesion assays were used to detect the effects of ANXA4 mutations on protein function.

Results

An ANXA4 mutation (p.G8D) in 1 of the 325 samples from patients with RSA (RSA-219) was identified through WES. This mutation was not detected in 941 controls or included in public databases. Evolutionary conservation analysis revealed that the amino acid residue affected by the mutation (p.G8D) was highly conserved among 13 vertebrate species, and the SIFT program and structural modeling analysis predicted that this mutation was harmful. Furthermore, functional assays revealed that this mutation could inhibit cell migration, invasion and adhesion.

Conclusion

Our study suggests that an unreported novel ANXA4 mutation (p.G8D) plays an important role in the pathogenesis of RSA and may contribute to the genetic diagnosis of RSA.

Primary cilia abnormalities participate in the occurrence of spontaneous abortion through TGF-β/SMAD2/3 signaling pathway

Spontaneous abortion is the most common complication in early pregnancy, the exact etiology of most cases cannot be determined. Emerging studies suggest that mutations in ciliary genes may be associated with progression of pregnancy loss. However, the involvement of primary cilia on spontaneous abortion and the underlying molecular mechanisms remains poorly understood. We observed the number and length of primary cilia were significantly decreased in decidua of spontaneous abortion in human and lipopolysaccharide (LPS)-induced abortion mice model, accompanied with increased expression of proinflammatory cytokines interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF)-α. The length of primary cilia in human endometrial stromal cell (hESC) was significantly shortened after TNF-α treatment. Knocking down intraflagellar transport 88 (IFT88), involved in cilia formation and maintenance, promoted the expression of TNF-α. There was a reverse regulatory relationship between cilia shortening and TNF-α expression. Further research found that shortened cilia impair decidualization in hESC through transforming growth factor (TGF)-β/SMAD2/3 signaling. Primary cilia were impaired in decidua tissue of spontaneous abortion, which might be mainly caused by inflammatory injury. Primary cilia abnormalities resulted in dysregulation of TGF-β/SMAD2/3 signaling transduction and decidualization impairment, which led to spontaneous abortion.

Discovery of Pathogenic Variants Associated with Idiopathic Recurrent Pregnancy Loss Using Whole-Exome Sequencing

Idiopathic recurrent pregnancy loss (RPL) is defined as at least two pregnancy losses before 20 weeks of gestation. Approximately 5% of pregnant couples experience idiopathic RPL, which is a heterogeneous disease with various causes including hormonal, chromosomal, and intrauterine abnormalities. Although how pregnancy loss occurs is still unknown, numerous biological factors are associated with the incidence of pregnancy loss, including genetic variants. Whole-exome sequencing (WES) was conducted on blood samples from 56 Korean patients with RPL and 40 healthy controls. The WES data were aligned by means of bioinformatic analysis, and the detected variants were annotated using machine learning tools to predict the pathogenicity of protein alterations. Each indicated variant was confirmed using Sanger sequencing. A replication study was also conducted in 112 patients and 114 controls. The Variant Effect Scoring Tool, Combined Annotation Dependent Depletion tool, Sorting Intolerant from Tolerant annotation tool, and various databases detected 10 potential variants previously associated with spontaneous abortion genes in patients by means of a bioinformatic analysis of WES data. Several variants were detected in more than one patient. Interestingly, several of the detected genes were functionally clustered, including some with a secretory function (mucin 4; MUC4; rs200737893 G>A and hyaluronan-binding protein 2; HABP2; rs542838125 G>T), in which growth arrest-specific 2 Like 2 (GAS2L2; rs140842796 C>T) and dynamin 2 (DNM2; rs763894364 G>A) are functionally associated with cell protrusion and the cytoskeleton. ATP Binding Cassette Subfamily C Member 6 (ABCC6) was the only gene with two variants. HABP2 (rs542838125 G>T), MUC4 (rs200737893 G>A), and GAS2L2 (rs140842796 C>T) were detected in only the patient group in the replication study. The combination of WES and machine learning tools is a useful method to detect potential variants associated with RPL. Using bioinformatic tools, we found 10 potential variants in 9 genes. WES data from patients are needed to better understand the causes of RPL.

The Landscape of Point Mutations in Human Protein Coding Genes Leading to Pregnancy Loss

Pregnancy loss is the most frequent complication of a pregnancy which is devastating for affected families and poses a significant challenge for the health care system. Genetic factors are known to play an important role in the etiology of pregnancy loss; however, despite advances in diagnostics, the causes remain unexplained in more than 30% of cases. In this review, we aggregated the results of the decade-long studies into the genetic risk factors of pregnancy loss (including miscarriage, termination for fetal abnormality, and recurrent pregnancy loss) in euploid pregnancies, focusing on the spectrum of point mutations associated with these conditions. We reviewed the evolution of molecular genetics methods used for the genetic research into causes of pregnancy loss, and collected information about 270 individual genetic variants in 196 unique genes reported as genetic cause of pregnancy loss. Among these, variants in 18 genes have been reported by multiple studies, and two or more variants were reported as causing pregnancy loss for 57 genes. Further analysis of the properties of all known pregnancy loss genes showed that they correspond to broadly expressed, highly evolutionary conserved genes involved in crucial cell differentiation and developmental processes and related signaling pathways. Given the features of known genes, we made an effort to construct a list of candidate genes, variants in which may be expected to contribute to pregnancy loss. We believe that our results may be useful for prediction of pregnancy loss risk in couples, as well as for further investigation and revealing genetic etiology of pregnancy loss.

Genetic analysis of chorionic villus tissues in early missed abortions

Chromosomal abnormalities are the most common etiology of early spontaneous miscarriage. However, traditional karyotyping of chorionic villus samples (CVSs) is limited by cell culture and its low resolution. The objective of our study was to investigate the efficiency of molecular karyotyping technology for genetic diagnosis of early missed abortion tissues. Chromosome analysis of 1191 abortion CVSs in early pregnancy was conducted from August 2016 to June 2021; 463 cases were conducted via copy-number variations sequencing (CNV-seq)/quantitative fluorescent-polymerase chain reaction (QF-PCR) and 728 cases were conducted using SNP array. Clinically significant CNVs of CVSs were identified to clarify the cause of miscarriage and to guide the couples' subsequent pregnancies. Among these, 31 cases with significant maternal cell contamination were removed from the study. Among the remaining 1160 samples, 751 cases (64.7%) with genetic abnormalities were identified, of which, 531 (45.8%) were single aneuploidies, 31 (2.7%) were multiple aneuploidies, 50 (4.3%) were polyploidies, 54 (4.7%) were partial aneuploidies, 77 (6.6%) had submicroscopic CNVs (including 25 with clinically significant CNVs and 52 had variants of uncertain significance), and 8 cases (0.7%) were uniparental disomies. Our study suggests that both SNP array and CNV-seq/QF-PCR are reliable, robust, and high-resolution technologies for genetic diagnosis of miscarriage.

Analysis of potential copy-number variations and genes associated with first-trimester missed abortion

Background

Copy number variation sequencing (CNV-seq) was proven to be a highly effective tool in studying of chromosomal copy number variations (CNVs) in prenatal diagnosis and post-natal cases with developmental abnormalities. However, the overall characteristics of missed abortion (MA) CNVs were largely unexplored.

Methods

We retrospectively analyzed the results of CNV-seq in first-trimester MA. The samples included were single pregnancy loss before 13 gestational weeks, and other potential factors affecting embryonic implantation and development had been excluded. Gene ontology and KEGG enrichment analysis was performed on the smallest overlapping regions (SORs) of high-frequency deletion/duplication.

Result

On the basis of strict inclusion and exclusion criteria, only 152 samples were included in our study. 77 (50.7%) samples displayed chromosome number abnormalities, 32 (21%) showed isolated CNVs, and 43 (28.3%) showed no CNVs. A total of 45 CNVs, ranging in size between 300 Kb and 126.56 Mb were identified, comprising 13 segmental aneuploidies CNVs, and 32 submicroscopic CNVs. Among these CNVs, we screened out four SORs (5q31.3, 5p15.33-p15.2, 8p23.3-p23.2, and 8q22.2-24.3), which were potentially associated with first-term MA. 16 genes were identified as potential miscarriage candidate genes through gene-prioritization analysis, including three genes (MYOM2, SDHA and TPPP) critical for embryonic heart or brain development.

Conclusion

We identified some potential candidate CNVs and genes associated with first-trimester MA. 5q31.3 duplications, 5p15.33-p15.2 deletions, 8p23.3-p23.2 deletions and 8p22.2-p24.3 duplications are four potential candidate CNVs. Additionally, MYOM2, SDHA and TPPP are potential genes associated with first-trimester MA.

Chromosomal abnormalities in recurrent pregnancy loss and its association with clinical characteristics

OBJECTIVE

To evaluate the distribution of chromosomal abnormalities in a recurrent pregnancy loss (RPL) cohort and explore the associations between chromosomal abnormalities and clinical characteristics.

METHOD

Over a 5-year period, fresh products of conception (POC) from women with RPL were analyzed by single-nucleotide polymorphism (SNP) array at our hospital. After obtaining the information on clinical characteristics, we investigated the associations between the causative chromosomal abnormalities and clinical characteristics by the chi-squared test or Fisher's exact test and logistic regression.

RESULTS

A total of 2383 cases were enrolled. Overall, 56.9% (1355/2383) were identified with causative chromosomal abnormalities, of which 92.1% (1248/1355) were numerical abnormalities, 7.5% (102/1355) were structural variants, and 0.4% (5/1355) were loss of heterozygosity (LOH). The risk of numerical abnormalities was increased in women with maternal age ≥ 35 years (OR, 1.71; 95% CI, 1.41-2.07), gestational age at pregnancy loss ≤ 12 weeks (OR, 2.78; 95% CI, 1.79-4.33), less number of previous pregnancy losses (twice: OR, 2.32; 95% CI, 1.84-2.94; 3 times: OR, 1.59; 95% CI, 1.23-2.05, respectively), and pregnancy with a female fetus (OR, 1.37; 95% CI, 1.15-1.62). The OR of pregnancy loss with recurrent abnormal CMA was 4.00 (95% CI: 1.87-8.58, P < 0.001) and the adjusted OR was 5.05 (95% CI: 2.00-12.72, P = 0.001). However, the mode of conception was not associated with the incidence of numerical abnormality. No association was noted between structural variants and clinical characteristics.

CONCLUSION

Chromosomal abnormality was the leading cause of RPL. Numerical chromosome abnormality was more likely to occur in cases with advanced maternal age, an earlier gestational age, fewer previous pregnancy losses, and pregnancy with a female fetus.

Etiological identification of recurrent male fatality due to a novel NSDHL gene mutation using trio whole-exome sequencing: A rare case report and literature review

BACKGROUND

Congenital hemidysplasia with ichthyosiform nevus and limb defects (CHILD) syndrome is a rare X-linked dominant, lethal male disorder caused by mutations to the NSDHL (NAD(P)H steroid dehydrogenase-like protein) gene. It primarily exhibits strictly unilateral congenital hemidysplasia with ichthyosiform erythroderma and ipsilateral limb defects in female individuals.

METHODS

A Chinese couple suffering from recurrent spontaneous abortion in male fetuses was enrolled in this study. Chromosomal microarray analysis and whole-exome sequencing were performed for genetic etiological diagnosis.

RESULTS

A 33-year-old pregnant woman with recurrent spontaneous abortion was experiencing her third pregnancy with a male embryo. In this pregnancy, a miscarriage occurred at a gestational age of 10⁺⁶  weeks with no copy number variants. However, a novel mutation c.790-6C>T in the NSDHL gene was observed in the fetus through whole-exome sequencing (WES). Parental verification indicated that the NSDHL gene variant was inherited from the mother. Additionally, the variant in the NSDHL gene was absent in her subsequent pregnancy with a female fetus.

CONCLUSION

In this study, we detected c.790-6C>T, a novel variant in the NSDHL gene that results in recurrent miscarriage in males. Our study may broaden the scope of research on the NSDHL gene in CHILD syndrome and strengthens the application value of WES for the genetic etiological identification of recurrent miscarriage.

Unexplained recurrent pregnancy loss: Novel causes and advanced treatment

In this study, recent research focusing on recurrent pregnancy loss (RPL) are reviewed. Recurrent pregnancy loss is a devastating reproductive health burden that affects about 5% of couples trying to conceive globally. Currently, there are few evidence-based diagnostic and treatment strategies for RPL. More so, the number of unexplained etiology cases in patients with RPL arrives at 50%. Here, we discuss the progress in diagnosis and treatment of unexplained RPL, as well as recommended treatment strategies and controversial etiologies.

A new enrichment approach for candidate gene detection in unexplained recurrent pregnancy loss and implantation failure

Recurrent pregnancy loss (RPL) and implantation failure (RIF) are obstacles to livebirth and multifactorial conditions in which nearly half of the cases remain unexplained, and we aimed to identify maternal candidate gene variants and pathways for RPL and RIF by analyzing whole-exome sequencing (WES) data via a new detailed bioinformatics approach. A retrospective cohort study was applied to 35 women with normal chromosomal configuration diagnosed with unexplained RPL and/or RIF. WES and comprehensive bioinformatics analyses were performed. Published gene expression datasets (n = 46) were investigated for candidate genes. Variant effects on protein structure were analyzed for 12 proteins, and BUB1B was visualized in silico. WES and bioinformatics analyses are effective and applicable for studying URPL and RIF to detect mutations, as we suggest new candidates to explain the etiology. Forty-three variants in 39 genes were detected in 29 women, 7 of them contributing to oligogenic inheritance. These genes were related to implantation, placentation, coagulation, metabolism, immune system, embryological development, cell cycle-associated processes, and ovarian functions. WES, genomic variant analyses, expression data, and protein configuration studies offer new and promising ways to investigate the etiology of URPL and RIF. Discovering etiology-identifying genetic factors can help manage couples' needs and develop personalized therapies and new pharmaceutical products in the future. The classical approach with chromosomal analysis and targeted gene panel testing is insufficient in these cases; the exome data provide a promising way to detect and understand the possible clinical effects of the variant and its alteration on protein structure.

Oxidative stress on vessels at the maternal-fetal interface for female reproductive system disorders: Update

Considerable evidence shows that oxidative stress exists in the pathophysiological process of female reproductive system diseases. At present, there have been many studies on oxidative stress of placenta during pregnancy, especially for preeclampsia. However, studies that directly focus on the effects of oxidative stress on blood vessels at the maternal-fetal interface and their associated possible outcomes are still incomplete and ambiguous. To provide an option for early clinical prediction and therapeutic application of oxidative stress in female reproductive system diseases, this paper briefly describes the composition of the maternal-fetal interface and the molecular mediators produced by oxidative stress, focuses on the sources of oxidative stress and the signaling pathways of oxidative stress at the maternal-fetal interface, expounds the adverse consequences of oxidative stress on blood vessels, and deeply discusses the relationship between oxidative stress and some pregnancy complications and other female reproductive system diseases.

Utility of trio-based prenatal exome sequencing incorporating splice-site and mitochondrial genome assessment in pregnancies with fetal ultrasound anomalies: prospective cohort study

OBJECTIVE

To evaluate the utility of trio-based prenatal exome sequencing (pES), incorporating splice-site and mitochondrial genome assessment, in the prenatal diagnosis of fetuses with ultrasound anomalies and normal copy-number variant sequencing (CNV-seq) results.

METHODS

This was a prospective study of 90 ongoing pregnancies with ultrasound anomalies that underwent trio-based pES after receiving normal CNV-seq results, from September 2020 to November 2021, in a single center in China. By using pES with a panel encompassing exome coding and splicing regions as well as mitochondrial genome for fetuses and parents, we identified the underlying genetic causes of fetal anomalies, incidental fetal findings and parental carrier status. Information on pregnancy outcome and the impact of pES findings on parental decision-making was collected.

RESULTS

Of the 90 pregnancies included, 28 (31.1%) received a diagnostic result that could explain the fetal ultrasound anomalies. The highest diagnostic yield was noted for brain abnormalities (3/6 (50.0%)), followed by hydrops (4/9 (44.4%)) and skeletal abnormalities (13/34 (38.2%)). Collectively, 34 variants of 20 genes were detected in the 28 diagnosed cases, with 55.9% (19/34) occurring de novo. Variants of uncertain significance (VUS) associated with fetal phenotypes were detected in six (6.7%) fetuses. Interestingly, fetal (n = 4) and parental (n = 3) incidental findings (IFs) were detected in seven (7.8%) cases. These included two fetuses carrying a de-novo likely pathogenic (LP) variant of the CIC and FBXO11 genes, respectively, associated with neurodevelopmental disorders, and one fetus with a LP variant in a mitochondrial gene. The remaining fetus presented with unilateral renal dysplasia and was incidentally found to carry a pathogenic PKD1 gene variant resulting in adult-onset polycystic kidney, which was later confirmed to be inherited from the mother. In addition, parental heterozygous variants associated with autosomal recessive diseases were detected in three families, including one with additional fetal diagnostic findings. Diagnostic results or fetal IFs contributed to parental decision-making about termination of the pregnancy in 26 families (26/72 (36.1%)), while negative pES results or identification of VUS encouraged 40 families (40/72 (55.6%)) to continue their pregnancy, which ended in a live birth in all cases.

CONCLUSION

Trio-based pES can provide additional genetic information for pregnancies with fetal ultrasound anomalies without a CNV-seq diagnosis. The incidental findings and parental carrier status reported by trio-based pES with splice-site and mitochondrial genome analysis extend its clinical application, but careful genetic counseling is warranted. © 2022 International Society of Ultrasound in Obstetrics and Gynecology.

Endometrial gland specific progestagen-associated endometrial protein and cilia gene splicing changes in recurrent pregnancy loss

Endometrial glands are essential for fertility, consisting of ciliated and secretory cells that facilitate a suitable uterine environment for embryo implantation. This study sought to determine whether an endometrial gland specific transcriptome and splicing profile are altered in women with recurrent pregnancy loss. Our data provide a comprehensive catalogue of cilia and PAEP gene isoforms and relative exon usage in endometrial glands. We report a previously unannotated endometrial gland cilia transcript GALNT11 and its susceptibility to exon skipping. Key endometrial receptivity gene transcripts are also reported to change in endometrial glands of women with recurrent pregnancy loss. The endometrial gland cilia and PAEP targets identified in this study could be used to identify a perturbed endometrium, isolate causes of recurrent pregnancy loss and develop targeted therapies in personalised medicine.

Functional and pathological role of 15-Lipoxygenase and its metabolites in pregnancy and pregnancy-associated complications

Maternal lipid metabolism status during pregnancy may have pivotal effects on a healthy pregnancy, the progression of labor, and childbirth. Based on evidence, changes in maternal lipid profile and metabolism is related to various alterations in fetal metabolic status, fat mass, birth weight and can result in serious maternal and fetal complications. 15-lipoxygenase accounts as a key enzyme in metabolizing polyunsaturated fatty acids that generate various inflammatory lipid metabolites. The possible involvement of 15- lipoxygenase and its metabolites in the inflammatory process, cell proliferation and death, and immune response has been postulated. The indicative role of the 15- lipoxygenase enzymatic pathway in the implantation process, stages of pregnancy, embryogenesis, organogenesis, progression of labor, pregnancy period, and pregnancy-associated complications is remarkable. Accordingly, this study will review the research conducted on the role of 15- lipoxygenase in different reproductive tissues, and its pathological role in pregnancy-related diseases to provide more insight regarding the emerging role of 15-lipoxygenase in normal pregnancy.

Multiomics Studies Investigating Recurrent Pregnancy Loss: An Effective Tool for Mechanism Exploration

Patients with recurrent pregnancy loss (RPL) account for approximately 1%-5% of women aiming to achieve childbirth. Although studies have shown that RPL is associated with failure of endometrial decidualization, placental dysfunction, and immune microenvironment disorder at the maternal-fetal interface, the exact pathogenesis remains unknown. With the development of high-throughput technology, more studies have focused on the genomics, transcriptomics, proteomics and metabolomics of RPL, and new gene mutations and new biomarkers of RPL have been discovered, providing an opportunity to explore the pathogenesis of RPL from different biological processes. Bioinformatics analyses of these differentially expressed genes, proteins and metabolites also reflect the biological pathways involved in RPL, laying a foundation for further research. In this review, we summarize the findings of omics studies investigating decidual tissue, villous tissue and blood from patients with RPL and identify some possible limitations of current studies.

Impact of parental relatedness on reproductive outcomes among the Old Order Amish of Lancaster County

Genetically isolated populations that arise due to recent bottleneck events have reduced genetic variation reflecting the common set of founders. Increased genetic relatedness among members of isolated populations puts them at increased risk for some recessive disorders that are rare in outbred populations. To assess the burden on reproductive health, we compared frequencies of adverse reproductive outcomes between Amish couples who were both heterozygous carriers of a highly penetrant pathogenic or likely pathogenic variant and noncarrier couples from the same Amish community. In addition, we evaluated whether overall genetic relatedness of parents was associated with reproductive outcomes. Of the 1824 couples included in our study, 11.1% were at risk of producing a child with an autosomal recessive disorder. Carrier couples reported a lower number of miscarriages compared to noncarrier couples (p = 0.02), although the number of stillbirths (p = 0.3), live births (p = 0.9), and number of pregnancies (p = 0.9) did not differ significantly between groups. In contrast, higher overall relatedness between spouses was positively correlated with number of live births (p < 0.0001), pregnancies (p < 0.0001), and stillbirths (p = 0.03), although not with the number of miscarriages (p = 0.4). These results highlight a complex association between relatedness of parents and reproductive health outcomes in this community.

Factors associated with fetal karyotype in spontaneous abortion: a case-case study

Background

Most embryos that spontaneously abort during early pregnancy are found to have chromosomal abnormalities. The purpose of this study is to explore the factors involved in chromosome aberrations during embryogenesis.

Methods

A case-case study was performed to compare the risk factors for spontaneous abortion with and without embryo chromosome aberration. A total of 160 cases of spontaneous abortion were enrolled from a tertiary general hospital in Kunming. KaryoLite BACs-on-Beads (KL-BoBs) and fluorescence in situ hybridization (FISH) were employed to determine chromosomal constitution of abortion chorion villus samples. Maternal serum levels of homocysteine (Hcy) were detected by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Information about clinical background and environmental exposure was collected through a self-designed questionnaire. To identify the inherited chromosomal abnormalities, couples with chromosomal abnormalities in abortus were recalled for karyotyping.

Results

The overall rate of chromosomal abnormalities was 62.5% (100/160, KL-BoBs combined with FISH) including 51.9% (83/160) aneuploidies, 6.3% (10/160) polyploidies, and 4.4% (7/160) structural abnormalities. Only one case of structural abnormality was found to be inherited from maternal balanced translocation. Compared to abortus with normal karyotype, abortus with abnormal karyotype showed a positive association with parental age and elevated maternal serum homocysteine (Hcy) level, but negative association with previous miscarriage and perceived noise.

Conclusions

Embryonic chromosomal aberrations accounted for the majority of spontaneous abortion cases. A combination of internal and external factors may induce spontaneous abortion through fetal chromosomal aberrations or other pathogenic mechanisms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12884-022-04491-8.

Prioritization of putatively detrimental variants in euploid miscarriages

Miscarriage is the spontaneous termination of a pregnancy before 24 weeks of gestation. We studied the genome of euploid miscarried embryos from mothers in the range of healthy adult individuals to understand genetic susceptibility to miscarriage not caused by chromosomal aneuploidies. We developed GP , a pipeline that we used to prioritize 439 unique variants in 399 genes, including genes known to be associated with miscarriages. Among the prioritized genes we found STAG2 coding for the cohesin complex subunit, for which inactivation in mouse is lethal, and TLE4 a target of Notch and Wnt, physically interacting with a region on chromosome 9 associated to miscarriages.

Exome-Sequencing Identifies Novel Genes Associated with Recurrent Pregnancy Loss in a Chinese Cohort

Recurrent pregnancy loss (RPL) is a common reproductive problem affecting around 5% of couples worldwide. At present, about half of RPL cases remained unexplained. Previous studies have suggested an important role for genetic determinants in the etiology of RPL. Here, we performed whole-exome sequencing (WES) analysis on 100 unrelated Han Chinese women with a history of two or more spontaneous abortions. We identified 6736 rare deleterious nonsynonymous variants across all patients. To focus on possible candidate genes, we generated a list of 95 highly relevant genes that were functionally associated with miscarriage according to human and mouse model studies, and found 35 heterozygous variants of 28 RPL-associated genes in 32 patients. Four genes (FOXA2, FGA, F13A1, and KHDC3L) were identified as being strong candidates. The FOXA2 nonsense variant was for the first time reported here in women with RPL. FOXA2 knockdown in HEK-293T cells significantly diminished the mRNA and protein expression levels of LIF, a pivotal factor for maternal receptivity and blastocyst implantation. The other genes, with 29 variants, were involved in angiogenesis, the immune response and inflammation, cell growth and proliferation, which are functionally important processes for implantation and pregnancy. Our study identified several potential causal genetic variants in women with RPL by WES, highlighting the important role of genes controlling coagulation, confirming the pathogenic role of KHDC3L and identifying FOXA2 as a newly identified causal gene in women with RPL.

A Systematic Review to Guide Future Efforts in the Determination of Genetic Causes of Pregnancy Loss

Background: Pregnancy loss is the most common obstetric complication occurring in almost 30% of conceptions overall and in 12–14% of clinically recognized pregnancies. Pregnancy loss has strong genetic underpinnings, and despite this consensus, our understanding of its genetic causes remains limited. We conducted a systematic review of genetic factors in pregnancy loss to identify strategies to guide future research.

Methods: To synthesize data from population-based association studies on genetics of pregnancy loss, we searched PubMed for relevant articles published between 01/01/2000-01/01/2020. We excluded review articles, case studies, studies with limited sample sizes to detect associations (N &lt; 4), descriptive studies, commentaries, and studies with non-genetic etiologies. Studies were classified based on developmental periods in gestation to synthesize data across various developmental epochs.

Results: Our search yielded 580 potential titles with 107 (18%) eligible after title/abstract review. Of these, 54 (50%) were selected for systematic review after full-text review. These studies examined either early pregnancy loss (n = 9 [17%]), pregnancy loss &gt;20 weeks' gestation (n = 10 [18%]), recurrent pregnancy loss (n = 32 [59%]), unclassified pregnancy loss (n = 3 [4%]) as their primary outcomes. Multiple genetic pathways that are essential for embryonic/fetal survival as well as human development were identified.

Conclusion: Several genetic pathways may play a role in pregnancy loss across developmental periods in gestation. Systematic evaluation of pregnancy loss across developmental epochs, utilizing whole genome sequencing in families may further elucidate causal genetic mechanisms and identify other pathways critical for embryonic/fetal survival.

Embryonic lethal genetic variants and chromosomally normal pregnancy loss

OBJECTIVE

To examine whether rare damaging genetic variants are associated with chromosomally normal pregnancy loss and estimate the magnitude of the association.

DESIGN

Case-control.

SETTING

Cases were derived from a consecutive series of karyotyped losses at one New Jersey hospital. Controls were derived from the National Database for Autism Research.

PATIENT(S)

Cases comprised 19 chromosomally normal loss conceptus-parent trios. Controls comprised 547 unaffected siblings of autism case-parent trios.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

The rate of damaging variants in the exome (loss of function and missense-damaging) and the proportions of probands with at least one such variant among cases vs. controls.

RESULTS

The proportions of probands with at least one rare damaging variant were 36.8% among cases and 22.9% among controls (odds ratio, 2.0; 99% confidence interval, 0.5-7.3). No case had a variant in a known fetal anomaly gene. The proportion with variants in possibly embryonic lethal genes increased in case probands (odds ratio, 14.5; 99% confidence interval, 1.5-89.7); variants occurred in BAZ1A, FBN2, and TIMP2.

CONCLUSION(S)

Rare genetic variants in the conceptus may be a cause of chromosomally normal pregnancy loss. A larger sample is needed to estimate the magnitude of the association with precision and identify relevant biologic pathways.

Changes in the level of fetoplacental complex hormones in pregnant women with miscarriage

The purpose of the study was TO analyze the fetoplacental complex hormone levels and changes in their dynamics in pregnant women with miscarriage and the impact of these features on the subsequent course of pregnancy. Hormone levels were determined at different stages of gestation in 50 healthy women with a physiological course of pregnancy (control group) and 50 pregnant women with a history of miscarriage (main group). The women of the main group had a significantly slower rate of increase in hormones and a lag in quantitative indicators than the control group. The estradiol level indicators were 4.1 times (76.0%) and 2.89 times (65.5%) lower in women with miscarriage in the embryonic and late fetal period, respectively, compared to healthy women. Indicators of the level of placental lactogen and chorionic gonadotropin in the embryonic period in women with miscarriage were lower by 39.1% and 50.9%, respectively, compared to healthy women. In the late fetal period, the level of these hormones was lower by 72.9% and 35.4%, respectively. In the embryonic and late fetal periods, progesterone levels were lower by 67.4% and 68.4%, respectively, compared to the control group. The data obtained are evidence of a pronounced hormonal abnormality of the placenta, and hence a marker of fetoplacental dysfunction, which on the background of miscarriage develops at the early stages and continues to progress with the course of pregnancy.

Molecular autopsy by proxy in preconception counseling

Monogenic diseases that result in early pregnancy loss or neonatal death are genetically and phenotypically highly variable. This often poses significant challenges in arriving at a molecular diagnosis for reproductive planning. Molecular autopsy by proxy (MABP) refers to the genetic testing of relatives of deceased individuals to deduce the cause of death. Here, we specifically tested couples who lost one or more children/pregnancies with no available DNA. We developed our testing strategy using whole exome sequencing data from 83 consanguineous Saudi couples. We detected the shared carrier state of 50 pathogenic variants/likely pathogenic variants in 43 families and of 28 variants of uncertain significance in 24 families. Negative results were seen in 16 couples after variant reclassification. In 10 families, the risk of more than one genetic disease was documented. Secondary findings were seen in 10 families: either genetic variants with potential clinical consequences for the tested individual or a female carrier for X‐linked conditions. This couple‐based approach has enabled molecularly informed genetic counseling for 52% (43/83 families). Given the predominance of autosomal recessive causes of pregnancy and child death in consanguineous populations, MABP can be a helpful approach to consanguineous couples who seek counseling but lack molecular data on their deceased offspring.

Screening of Candidate Pathogenic Genes for Spontaneous Abortion using Whole Exome Sequencing

BACKGROUND

Spontaneous abortion is a common disease in obstetrics and reproduction.

OBJECTIVE

This study aimed to screen candidate pathogenic genes for spontaneous abortion using whole-exome sequencing.

METHODS

Genomic DNA was extracted from abortion tissues of spontaneous abortion patients and sequenced using the Illumina HiSeq2500 high-throughput sequencing platform. Whole exome sequencing was performed to select harmful mutations, including SNP and insertion and deletion sites, associated with spontaneous abortion. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and gene fusion analyses were performed. MUC3A and PDE4DIP were two novel mutation genes that were screened and verified by PCR in abortion tissues of patients.

RESULTS

A total of 83,633 SNPs and 13,635 Indel mutations were detected, of which 29172 SNPs and 3093 Indels were screened as harmful mutations. The 7 GO-BP, 4 GO-CC, 9 GO-MF progress, and 3 KEGG pathways were enriched in GO and KEGG pathway analyses. A total of 746 gene fusion mutations were obtained, involving 492 genes. MUC3A and PDE4DIP were used for PCR verification because of their high number of mutation sites in all samples.

CONCLUSION

There are extensive SNPs and Indel mutations in the genome of spontaneous abortion tissues, and the effect of these gene mutations on spontaneous abortion needs further experimental verification.

Exploration of the potential roles of m6A regulators in the uterus in pregnancy and infertility

Infertility is a prevalent female reproductive disease worldwide. Currently, there are many unknown etiologies of infertility. N6-methyladenosine (m6A) is the most prevalent modification of eukaryotic mRNA. This study intended to investigate the implications of m6A regulators in the uterus for pregnancy and infertility. Pregnant ICR mice on days (D) 0, 4, 6, 10, and 15 were used to monitor m6A methylation in the uterus by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and then m6A methylation regulators were detected by real-time quantitative PCR (qPCR), western blot and immunohistochemistry (IHC). We found that m6A levels increased and that m6A regulators were expressed differently in the uterus during pregnancy. Then, we acquired expression data from endometrial tissue from women with infertility and recurrent pregnancy loss from the Gene Expression Omnibus (GEO) database. The expression of m6A regulators in infertility was significantly dysregulated according to the data mining technique. Specifically, the mRNA levels of METTL16 (p = 0.0147) and WTAP (p = 0.028) were lower and those of ALKBH5 (p = 0.0432) and IGF2BP2 (p = 0.0016) were higher in the endometrium of infertile patients. Meanwhile, many immunity-related pathways are abnormal in infertility, such as cytokine-cytokine receptor interactions, natural killer cell-mediated cytotoxicity and leukocyte transendothelial migration. In conclusion, we found that the m6A levels in the uterus increased as pregnancy progressed, and these regulators were dysregulated in the endometrium of infertility patients. These results suggest that m6A methylation may be very important in the establishment of implantation and maintenance of pregnancy and may become a new direction for research on infertility.

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.

Study on pathogenic genes of dwarfism disease by next-generation sequencing

BACKGROUND

There are many factors that lead to dwarfism, and the mechanism has not yet been elucidated. Next-generation sequencing may identify candidate-related gene mutations, which may clarify the molecular cause.

AIM

To analyze genetic variation by using a constructed panel related to dwarfism by utilizing next-generation sequencing platform sequencing analysis to screen candidate-related gene mutations.

METHODS

Physical and laboratory characteristics, including clinical examination, growth hormone drug challenge test, serum insulin-like growth factor-1 (IGF-1), IGF binding protein 3, other related tests, imaging examination, and chromosome karyotyping, were analyzed. Next-generation sequencing was performed to analyze pathogenicity variability.

RESULTS

In the 39 dwarfism patients, 10 had pathogenicity variability. Gene variation was found in the OBSL1, SLC26A2, PTPN11, COL27AI, HDAC6, CUL7, FGFR3, DYNC2H1, GH1, and ATP7B genes. Of the 10 patients with pathogenicity variability, the related physical characteristics included double breast development and growth hormone deficiency, enuresis and indirect inguinal hernia on the left, two finger distance of 70.2 cm, head circumference of 49.2 cm, ischium/lower body length of 1.8 cm, weak limb muscles, and partial growth hormone deficiency. After 6 mo of growth hormone therapy, the concentrations of IGF-1 and IGF binding protein 3 increased from 215.2 ± 170.3 to 285.0 ± 166.0 and 3.9 ± 1.4 to 4.2 ± 1.1, respectively.

CONCLUSION

OBSL1, SLC26A2, PTPN11, COL27AI, HDAC6, CUL7, FGFR3, DYNC2H1, GH1, and ATP7B genes may be related to the incidence of dwarfism, and more research needs to be performed to elucidate the mechanism.

Selected genetic causes of miscarriages

Approximately 15–25% of pregnancies end in spontaneous abortion, which is an expulsion from the mother body of the fetus weighing less than 500 g or before the 20th week of gestation. Determining abortions etiology is difficult due to its multifactorial character. Chromosomal abnormalities cause 38.6–80% of miscarriages. The largest group (93%) of chromosomal aberrations found in miscarried fetuses are numerical changes – aneuploidies and polyploidies. Much rarer (7%) are unbalanced structural aberrations, which can arise de novo or can be inherited from a carrier parent. In couples with spontaneous abortions, reciprocal chromosomal translocations (RCT) occur the most frequently, next are Robertsonian translocations and inversions. More complex chromosome abnormalities, e.g. double aneuploidies are found in 3.8% of fetuses. Another group of causes responsible for abortions are monogenic diseases of embryo or fetus resulting from autosomal dominant, autosomal recessive or X-linked mutations. Among mutations which may contribute to pregnancy loss are factor V Leiden gene mutations (c.1601G>A, earlier 1691G>A) and prothrombin gene mutation (c.97G>A, earlier 20210G>A). The research on mutations in candidate genes, eg.: ALOX15, CR1, CYP1A1, CYP17, CYP2D6, FOXP3, HLA-G, IL-6, KHDC3L, NLRP7, NOS3, PLK4, SYCP3, TLR3, TNF, TP53 and VEGFA is still ongoing.

KH domain containing 3 like (KHDC3L) frame-shift mutation causes both recurrent pregnancy loss and hydatidiform mole

OBJECTIVE

Recurrent pregnancy loss (RPL) is a common infertility-related complication that affects approximately 1-3 % of women worldwide. Known causes of etiology are found in approximately half the cases but the other half remain unexplained. It is estimated that several thousands of genes contribute to reproductive success in mammals and the genetic causes of RPL cannot be fully addressed through targeted genetic tests. In recent years, massive parallel sequencing technologies has helped discovering many causal mutations in hereditary diseases such as RPL.

STUDY DESIGN

Using whole-exome sequencing (WES), we studied a large multiplex consanguineous family with multiple cases of RPL and hydatidiform moles (HM). In addition, targeted Sanger sequencing was applied to 40 additional non-related individuals with RPL.

RESULTS

The use of WES permitted to identify the pathogenic variant in KHDC3L (c.322_325delGACT) in related who experienced RPL with or without HM. Sanger sequencing confirmed the segregation of the mutation throughout the pedigree and permitted to establish this variant as the genetic cause responsible for RPL and HM in this family.

CONCLUSION

KHDC3L is well established as a susceptibility gene for HM but we confirmed here that KHDC3L deleterious variants can also induce RPL. In addition, we observed a genotype-phenotype correlation, demonstrating that women with a truncating KHDC3L homozygous variant could not sustain a pregnancy and often had pregnancy losses mainly due to HM while those with the same heterozygous variant could have children but often endured RPL with no HM.

Whole exome sequencing, a hypothesis-free approach to investigate recurrent early miscarriage

RESEARCH QUESTION

Are there genetic determinants shared by unrelated women with unexplained recurrent early miscarriage (REM)?

DESIGN

Thirty REM cases and 30 controls were selected with extreme phenotype among women from Eastern Brittany (France), previously enrolled in an incident case-control study on thrombophilic mutations. Cases and controls were selected based on the number of early miscarriages or live births, respectively. Peripheral blood was collected for DNA extraction at initial visit. The burden of low-frequency variants in the coding part of the genes was compared using whole exome sequencing (WES).

RESULTS

Cases had 3 to 17 early miscarriages (20 cases: ≥5 previous losses). Controls had 1 to 4 live births (20 controls: ≥3 previous live births) and no miscarriages. WES data were available for 29 cases and 30 controls. A total of 209,387 variants were found (mean variant per patient: 59,073.05) with no difference between groups (P = 0.68). The top five most significantly associated genes were ABCA4, NFAM1, TCN2, AL078585.1 and EPS15. Previous studies suggest the involvement of vitamin B12 deficiency in REM. TCN2 encodes for vitamin B12 transporter into cells. Therefore, holotranscobalamin (active vitamin B12) was measured for both cases and controls (81.2 ± 32.1 versus 92.9 ± 34.3 pmol/l, respectively, P = 0.186). Five cases but no controls were below 50 pmol/l (P = 0.052).

CONCLUSIONS

This study highlights four new genes of interest in REM, some of which belong to known networks of genes involved in embryonic development (clathrin-mediated endocytosis and ciliary pathway). The study also confirms the involvement of TCN2 (vitamin B12 pathway) in the early first trimester of pregnancy.

A case–control study identifying the frequency and spectrum of chromosomal anomalies and variants in a cohort of 1000 couples with a known history of recurrent pregnancy loss in the Eastern region of India

Background:

Recurrent pregnancy loss (RPL) is a common occurrence that affects up to 15% of couples in their reproductive years. In both males and females with RPL and infertility, chromosomal abnormalities play a significant impact.

Aim:

The study was designed to examine the involvement of chromosomal anomalies and the frequency of certain chromosomal variants persistent among couples experiencing RPL.

Setting and Design:

This case–control study was conducted on 1000 couples from January 2015 to September 2020 in the state of Odisha, India, strictly adhering to principles of Helsinki Declaration (1975). The study was performed at the School of Biotechnology, KIIT University in collaboration with inDNA Life Sciences Private Limited.

Materials and Methods:

A cohort of 1148 individuals with a history of RPL were selected for the study and they were screened with respect to fertile controls for the presence of any chromosomal anomaly using G-banding, nucleolar organizing region (NOR)-banding and fluorescence in situ hybridisation wherever necessary.

Statistical Analysis:

The connection between distinct polymorphic variations and the occurrence of RPL was assessed using Fisher's exact test. Significant was defined as a P ≤ 0.005.

Results:

One hundred and thirty-four individuals were found to harbor chromosomal anomalies. This study elucidates that along with balanced chromosomal translocations, the involvement of polymorphic variants also plays a significant role in cases of RPL.

Conclusion:

The cumulative occurrence of chromosomal anomalies and variants across our cohort of 1148 individuals indicates that the chromosomal assessment of all couples experiencing RPL must be performed by all the clinicians. This study aids us in identifying chromosomal polymorphisms as major players of RPL in addition to novel chromosomal translocations.

Analysis of Chromosomal Copy Number in First-Trimester Pregnancy Loss Using Next-Generation Sequencing

Embryonic chromosomal abnormality is one of the significant causative factors of early pregnancy loss. Our goal was to evaluate the clinical utility of next-generation sequencing (NGS) technology in identifying chromosomal anomalies associated with first-trimester pregnancy loss. In addition, we attempted to provide fertility guidance to couples anticipating a successful pregnancy. A total of 1,010 miscarriage specimens were collected between March 2016 and January 2019 from women who suffered first-trimester pregnancy loss. Total DNA was isolated from products of conception, and NGS analysis was carried out. We detected a total of 634 cases of chromosomal variants. Among the 634 cases, 462 (72.9%) displayed numerical variants including 383 (60.4%) aneuploidies, 44 (6.9%) polyploidies, and 34 (5.5%) mosaicisms. The other 172 (27.1%) cases showed structural variants including 19 (3.0%) benign copy number variations (CNVs), 52 (8.2%) pathogenic CNVs, and 101 (16%) variants of unknown significance (VOUS) CNVs. When maternal age was ≥ 35 years, the sporadic abortion (SA) group showed an increased frequency of chromosomal variants in comparison with the recurrent miscarriage (RM) group (90/121 vs. 64/104). It was evident that the groups with advanced maternal age had a sharply increased frequency of aneuploidy, whatever the frequency of pregnancy loss (71/121 vs. 155/432, 49/104 vs. 108/349). Our data suggest that NGS could be used for the successful detection of genetic anomalies in pregnancy loss. We recommend that fetal chromosome analysis be offered routinely for all pregnancy losses, regardless of their frequency.

Genetic Variants Contributing to Early Recurrent Pregnancy Loss Etiology Identified by Sequencing Approaches

Recurrent pregnancy loss (RPL) affects up to 5% of couples. It is believed that genetic factors contribute to the disease's etiology and pathophysiology. Hundreds of genes represent coherent RPL candidates due to mammalian implantation's inherent complexity. Sanger sequencing (direct sequencing) of candidate genes has identified potential RPL causative genes (and variants), including those regulating embryo implantation and pregnancy maintenance. Although this approach is a reliable technique, the simultaneous analysis of large genomic regions is challenging. Next-generation sequencing (NGS) technology has thus emerged as a useful alternative for determining genetic variants and transcriptomic disturbances contributing to monogenic and polygenic diseases pathogenesis. However, interpreting results remains challenging as NGS experiments provide an enormous amount of complex data. The molecular aspects of specific diseases must be fully understood for accurate interpretation of NGS data. This review was thus aimed at describing (for the first time) the most relevant studies involving Sanger and NGS sequencing, leading to the description of variants related to RPL pathogenesis. Successful RPL-related NGS initiatives (including RNAseq-based studies) and future challenges are discussed. We consider that the information given here should be useful for clinicians, scientists, and students to enable a better understanding of RPL etiology. It may also provide a basis for the development of diagnostic/prognostic approaches contributing toward translational medicine.

Genome Sequencing Explores Complexity of Chromosomal Abnormalities in Recurrent Miscarriage

Recurrent miscarriage (RM) affects millions of couples globally, and half of them have no demonstrated etiology. Genome sequencing (GS) is an enhanced and novel cytogenetic tool to define the contribution of chromosomal abnormalities in human diseases. In this study we evaluated its utility in RM-affected couples. We performed low-pass GS retrospectively for 1,090 RM-affected couples, all of whom had routine chromosome analysis. A customized sequencing and interpretation pipeline was developed to identify chromosomal rearrangements and deletions/duplications with confirmation by fluorescence in situ hybridization, chromosomal microarray analysis, and PCR studies. Low-pass GS yielded results in 1,077 of 1,090 couples (98.8%) and detected 127 chromosomal abnormalities in 11.7% (126/1,077) of couples; both members of one couple were identified with inversions. Of the 126 couples, 39.7% (50/126) had received former diagnostic results by karyotyping characteristic of normal human male or female karyotypes. Low-pass GS revealed additional chromosomal abnormalities in 50 (4.0%) couples, including eight with balanced translocations and 42 inversions. Follow-up studies of these couples showed a higher miscarriage/fetal-anomaly rate of 5/10 (50%) compared to 21/93 (22.6%) in couples with normal GS, resulting in a relative risk of 2.2 (95% confidence interval, 1.1 to 4.6). In these couples, this protocol significantly increased the diagnostic yield of chromosomal abnormalities per couple (11.7%) in comparison to chromosome analysis (8.0%, chi-square test p = 0.000751). In summary, low-pass GS identified underlying chromosomal aberrations in 1 in 9 RM-affected couples, enabling identification of a subgroup of couples with increased risk of subsequent miscarriage who would benefit from a personalized intervention.

Genetic diagnosis in first or second trimester pregnancy loss using exome sequencing: a systematic review of human essential genes

PURPOSE

Non-aneuploid recurrent pregnancy loss (RPL) affects approximately 100,000 pregnancies worldwide annually. Exome sequencing (ES) may help uncover the genetic etiology of RPL and, more generally, pregnancy loss as a whole. Previous studies have attempted to predict the genes that, when disrupted, may cause human embryonic lethality. However, predictions by these early studies rarely point to the same genes. Case reports of pathogenic variants identified in RPL cases offer another clue. We evaluated known genetic etiologies of RPL identified by ES.

METHODS

We gathered primary research articles from PubMed and Embase involving case reports of RPL reporting variants identified by ES. Two authors independently reviewed all articles for eligibility and extracted data based on predetermined criteria. Preliminary and amended analysis isolated 380 articles; 15 met all inclusion criteria.

RESULTS

These 15 articles described 74 families with 279 reported RPLs with 34 candidate pathogenic variants in 19 genes (NOP14, FOXP3, APAF1, CASP9, CHRNA1, NLRP5, MMP10, FGA, FLT1, EPAS1, IDO2, STIL, DYNC2H1, IFT122, PADI6, CAPS, MUSK, NLRP2, NLRP7) and 26 variants of unknown significance in 25 genes. These genes cluster in four essential pathways: (1) gene expression, (2) embryonic development, (3) mitosis and cell cycle progression, and (4) inflammation and immunity.

CONCLUSIONS

For future studies of RPL, we recommend trio-based ES in cases with normal parental karyotypes. In vitro fertilization with preimplantation genetic diagnosis can be pursued if causative variants are found. Utilization of other sequencing technologies in concert with ES should improve understanding of the causes of early embryonic lethality in humans.

Potential genetic causes of miscarriage in euploid pregnancies: a systematic review

BACKGROUND

Approximately 50% of pregnancy losses are caused by chromosomal abnormalities, such as aneuploidy. The remainder has an apparent euploid karyotype, but it is plausible that there are cases of pregnancy loss with other genetic aberrations that are not currently routinely detected. Studies investigating the use of exome sequencing and chromosomal microarrays in structurally abnormal pregnancies and developmental disorders have demonstrated their clinical application and/or potential utility in these groups of patients. Similarly, there have been several studies that have sought to identify genes that are potentially causative of, or associated with, spontaneous pregnancy loss, but the evidence has not yet been synthesized.

OBJECTIVE AND RATIONALE

The objective was to identify studies that have recorded monogenic genetic contributions to pregnancy loss in euploid pregnancies, establish evidence for genetic causes of pregnancy loss, identify the limitations of current evidence, and make recommendations for future studies. This evidence is important in considering additional research into Mendelian causes of pregnancy loss and appropriate genetic investigations for couples experiencing recurrent pregnancy loss.

SEARCH METHODS

A systematic review was conducted in MEDLINE (1946 to May 2018) and Embase (1974 to May 2018). The search terms ‘spontaneous abortion’, ‘miscarriage’, ‘pregnancy loss’, or ‘lethal’ were used to identify pregnancy loss terms. These were combined with search terms to identify the genetic contribution including ‘exome’, ‘human genome’, ‘sequencing analysis’, ‘sequencing’, ‘copy number variation’, ‘single-nucleotide polymorphism’, ‘microarray analysis’, and ‘comparative genomic hybridization’. Studies were limited to pregnancy loss up to 20 weeks in humans and excluded if the genetic content included genes that are not lethal in utero, PGD studies, infertility studies, expression studies, aneuploidy with no recurrence risk, methodologies where there is no clinical relevance, and complex genetic studies. The quality of the studies was assessed using a modified version of the Newcastle–Ottawa scale.

OUTCOMES

A total of 50 studies were identified and categorized into three themes: whole-exome sequencing studies; copy number variation studies; and other studies related to pregnancy loss including recurrent molar pregnancies, epigenetics, and mitochondrial DNA aberrations. Putatively causative variants were found in a range of genes, including CHRNA1 (cholinergic receptor, nicotinic, alpha polypeptide 1), DYNC2H1 (dynein, cytoplasmic 2, heavy chain 1), and RYR1 (ryanodine receptor 1), which were identified in multiple studies. Copy number variants were also identified to have a causal or associated link with recurrent miscarriage.

WIDER IMPLICATIONS

Identification of genes that are causative of or predisposing to pregnancy loss will be of significant individual patient impact with respect to counselling and treatment. In addition, knowledge of specific genes that contribute to pregnancy loss could also be of importance in designing a diagnostic sequencing panel for patients with recurrent pregnancy loss and also in understanding the biological pathways that can cause pregnancy loss.

Next generation sequencing in recurrent pregnancy loss-approaches and outcomes

Next generation sequencing (NGS) has revolutionized the diagnosis of postnatal genetic diseases, but so far has been used less frequently to study reproductive disorders. Here we provide an overview of approaches and outcomes of genome sequencing for identifying causes of recurrent pregnancy loss (RPL). This includes exome sequencing to look for pathogenic sequence changes in the whole exome or in a preselected list of genes considered important for early embryonic development and pregnancy maintenance, as well as low coverage whole genome sequencing useful for identifying cryptic balanced chromosome rearrangements and copy number variants (CNVs) in couples with RPL and miscarriages. For the purpose of this review only studies with at least 2 pregnancy losses were included with NGS performed on complete families, or only on miscarriages, couples or females with RPL. Overall, mutations in candidate genes responsible for recurrent embryonic/fetal loss were found in up to 60% of cases, opening the door for possible identification of affected future pregnancies at the preimplantation stage. Recurrence of specific mutations or affected genes in different studies was rare (e.g.DYNC2H1, KIF14, RYR1 and GLE1) however genes involved in cell division, cilia function or fetal movement were frequently identified as candidates, the later possibly reflecting the fact that a large number of studied cases had features of fetal akinesia deformation sequence (FADS). Genome sequencing of the couple and miscarriages is most informative, as it allows analysis of the individual mutations as well as their collective burden on the genome and biological processes. However genome sequencing of the couple with RPL with follow up of candidate parental mutations in miscarriages appears to be a promising avenue when miscarriage DNA amounts or quality are suboptimal for whole genome studies. In the future, increasing the number of studied families, establishment of a database cataloguing CNVs and mutations found in early pregnancy loss as well as their functional assessment in miscarriage cells and parental reproductive tissues is needed for improved understanding of their role in adverse pregnancy outcome.

Genetic Variants Contributing to Early Recurrent Pregnancy Loss Etiology Identified by Sequencing Approaches

Recurrent pregnancy loss (RPL) affects up to 5% of couples. It is believed that genetic factors contribute to the disease's etiology and pathophysiology. Hundreds of genes represent coherent RPL candidates due to mammalian implantation's inherent complexity. Sanger sequencing (direct sequencing) of candidate genes has identified potential RPL causative genes (and variants), including those regulating embryo implantation and pregnancy maintenance. Although this approach is a reliable technique, the simultaneous analysis of large genomic regions is challenging. Next-generation sequencing (NGS) technology has thus emerged as a useful alternative for determining genetic variants and transcriptomic disturbances contributing to monogenic and polygenic diseases pathogenesis. However, interpreting results remains challenging as NGS experiments provide an enormous amount of complex data. The molecular aspects of specific diseases must be fully understood for accurate interpretation of NGS data. This review was thus aimed at describing (for the first time) the most relevant studies involving Sanger and NGS sequencing, leading to the description of variants related to RPL pathogenesis. Successful RPL-related NGS initiatives (including RNAseq-based studies) and future challenges are discussed. We consider that the information given here should be useful for clinicians, scientists, and students to enable a better understanding of RPL etiology. It may also provide a basis for the development of diagnostic/prognostic approaches contributing toward translational medicine.

Cytogenetic and genetic investigation of miscarriage cases in Eastern China

Objective: Recurrent miscarriage (RM) affects about 5% of pregnancies. Etiology of 30-50% RM cases remains unknown. Advanced highly sensitive detection and analysis methods may help solve some of the cases.Methods: Products of conception from 1155 RM cases were analyzed using classic karyotyping. Some cases without abnormal findings were subjected to next generation DNA sequencing (NGS) and chromosome copy number variation (CNV) analysis.Results: Classic karyotyping identified abnormalities in 56.62% of the cases. Of the103 specimens analyzed using NGS, 39 (37.86%) were found to carry "pathogenic" CNVs. Recurrent microdeletions and microduplications were identified, and some with unique distribution patterns.Conclusion: NGS CNV analysis is a highly sensitive and flexible method for detecting genetic abnormalities in RM cases.

A survey of undetected, clinically relevant chromosome abnormalities when replacing postnatal karyotyping by Whole Genome Sequencing

Whole genome sequencing (WGS) holds the potential to identify pathogenic gene mutations, copy number variation, uniparental disomy and structural rearrangements in a single genetic test. With its high diagnostic yield and decreasing costs, the question arises whether WGS can serve as a single test for all referrals to diagnostic genome laboratories ("one test fits all"). Here, we provide an estimate for the proportion of clinically relevant aberrations identified by light microscopy in postnatal referrals that would go undetected by WGS. To this end, we compiled the clinically relevant abnormal findings for each of the different referral categories in our laboratory during the period 2006-2015. We assumed that WGS would be performed on 300-500 bp DNA fragments with 150-bp paired sequence reads, and that the mean genome coverage is 30x, corresponding to current practice. For the detection of chromosomal mosaicism we set minimum thresholds of 10% for monosomy and 20% for trisomy. Based on the literature we assumed that balanced Robertsonian translocations and ∼9% of other, balanced chromosome rearrangements would not be detectable because of breakpoints in sequences of repetitive DNA. Based on our analysis of all 14,957 referrals, including 1455 abnormal cases, we show that at least 8.1% of these abnormalities would escape detection (corresponding to 0.79% of all referrals). The highest rate occurs in referrals of premature ovarian failure, as 73.3% of abnormalities would not be identified because of the frequent occurrence of low-level sex chromosome mosaicism. Among referrals of recurrent miscarriage, 25.6% of abnormalities would go undetected, mainly because of a high proportion of balanced Robertsonian translocations. In referrals of mental retardation (with or without multiple congenital anomalies) the abnormality would be missed in only 0.35% of referrals. These include cases without imbalances of unique DNA sequences but of clinical relevance, as for example, r(20) epilepsy syndrome. The expected shift to large-scale implementation of WGS ("one test fits most") as initial genetic test will be beneficial to patients and their families, since a cause for the clinical phenotype can be identified in more cases by a single genetic test at an early phase in the diagnostic process. However, a niche for genome analysis by light microscopy will remain. For example, in referrals of newborns with a suspicion of Down syndrome, karyotyping is not only a cost-effective method for providing a quick diagnosis, but also discriminates between trisomy 21 and a Robertsonian translocation involving chromosome 21. Thus, when replacing karyotyping by WGS, one must be aware of the rates and spectra of undetected abnormalities. In addition, it is equally important that requirements for cytogenetic follow-up studies are recognized.

Association study of the three functional polymorphisms (TAS2R46G>A, OR4C16G>A, and OR4X1A>T) with recurrent pregnancy loss

This study was purposed to investigate whether genetic polymorphisms in the function of stop-gain are associated with a fetal or placental development play roles and a development of idiopathic recurrent pregnancy loss (RPL) in Korean females. Three stop-gain polymorphisms were selected using next-generation sequencing screening, which allows for the rigorous examination and discovery of previously uncharacterized stop-gain genes and stop-gain expression profiles. Accordingly, we investigated the association of stop-gain polymorphisms in Korean women with RPL. Three functional polymorphisms in the TAS2R46G>A (rs2708381), OR4C16G>A (rs1459101), and OR4X1A>T (rs10838851) genes were genotyped using polymerase chain reaction (PCR)-restriction fragment length polymorphism assays and real-time PCR analysis. We determined that the OR4C16G>A polymorphism was associated with idiopathic RPL in Korean women (Adjusted odds ratio [AOR] 1.782; 95% confidence interval [CI] 1.004-3.163; P = 0.048, and AOR 1.766; 95% CI 1.020-3.059; P = 0.042). In addition, the prevalence of RPL was increased in women with the OR4C16GA + AA genotype and blood coagulation measures of prothrombin time (PT) > 10.4 s (AOR 8.292; 95% CI 2.744-25.054). We suggest that the OR4C16G>A polymorphism might serve as a clinically useful biomarker for the development, prevention, and prognosis of RPL.