Chromosomal Copy Number Variation Analysis in Pregnancy Products from Recurrent and Sporadic Miscarriage Using Next-Generation Sequencing

The chromosomal characteristics of spontaneous abortion and its potential associated copy number variants and genes

PURPOSE

This study aimed to investigate the correlation between chromosomal abnormalities in spontaneous abortion with clinical features and seek copy number variations (CNVs) and genes that might be connected to spontaneous abortion.

METHODS

Over 7 years, we used CNV-seq and STR analysis to study POCs, comparing chromosomal abnormalities with clinical features and identifying critical CNVs and genes associated with spontaneous abortion.

RESULTS

Total chromosomal variants in the POCs were identified in 66.8% (2169/3247) of all cases, which included 45.2% (1467/3247) numerical abnormalities and 21.6% (702/3247) copy number variants (CNVs). Chromosome number abnormalities, especially aneuploidy abnormalities, were more pronounced in the group of mothers aged ≥ 35 years, the early miscarriage group, and the chorionic villi group. We further analyzed 212 pathogenic and likely pathogenic CNVs in 146 POCs as well as identified 8 statistically significant SORs through comparison with both a healthy population and a group of non-spontaneously aborted fetuses. Our analysis suggests that these CNVs may play a crucial role in spontaneous abortion. Furthermore, by utilizing the RVIS score and MGI database, we identified 86 genes associated with spontaneous abortion, with particular emphasis on PARP6, ISLR, ULK3, FGFRL1, TBC1D14, SCRIB, and PLEC.

CONCLUSION

We found variability in chromosomal abnormalities across clinical features, identifying eight crucial copy number variations (CNVs) and multiple key genes that may be linked to spontaneous abortion. This research enhances the comprehension of genetic factors contributing to spontaneous abortion.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Identification of chromosomal abnormalities in miscarriages by CNV-Seq

OBJECTIVE

The primary object of this study is to analyze chromosomal abnormalities in miscarriages detected by copy number variants sequencing (CNV-Seq), establish potential pathways or genes related to miscarriages, and provide guidance for birth health in the following pregnancies.

METHODS

This study enrolled 580 miscarriage cases with paired clinical information and chromosomal detection results analyzed by CNV-Seq. Further bioinformatic analyses were performed on validated pathogenic CNVs (pCNVs).

RESULTS

Of 580 miscarriage cases, three were excluded as maternal cell contamination, 357 cases showed abnormal chromosomal results, and the remaining 220 were normal, with a positive detection rate of 61.87% (357/577). In the 357 miscarriage cases, 470 variants were discovered, of which 65.32% (307/470) were pathogenic. Among all variants detected, 251 were numerical chromosomal abnormalities, and 219 were structural abnormalities. With advanced maternal age, the proportion of numerical abnormalities increased, but the proportion of structural abnormalities decreased. Kyoto Encyclopedia of Genes and Genomes pathway and gene ontology analysis revealed that eleven pathways and 636 biological processes were enriched in pCNVs region genes. Protein-protein interaction analysis of 226 dosage-sensitive genes showed that TP53, CTNNB1, UBE3A, EP300, SOX2, ATM, and MECP2 might be significant in the development of miscarriages.

CONCLUSION

Our study provides evidence that chromosomal abnormalities contribute to miscarriages, and emphasizes the significance of microdeletions or duplications in causing miscarriages apart from numerical abnormalities. Essential genes found in pCNVs regions may account for miscarriages which need further validation.

Homocysteine increases uterine artery blood flow resistance in women with pregnancy loss

OBJECTIVE

Uterine arterial blood flow is an important factor in embryonic development. Increased uterine artery blood flow resistance may be related to vascular damage. Homocysteine (HCY) can induce injury of endothelial through various pathways. Therefore, we investigate the association between serum HCY levels and uterine artery blood flow in the non-pregnant state in women who have experienced pregnancy loss (PL).

METHODS

364 women eligible for PL were included in the study. The detection of HCY was completed by the Laboratory of Lanzhou University Second Hospital. We divided the patients into three groups: Low-HCY (HCY<10 umol/L, n = 144), Medium-HCY (HCY 10∼15 umol/L, n = 174) and High-HCY (HCY>15 umol/L, n = 46). The patients were subjected to vaginal color Doppler ultrasonography to measure bilateral uterine artery resistance index (RI), pulsatility index (PI) and peak systolic velocity/end diastolic velocity (S/D).

RESULT

Among 364 women, the right uterine artery RI in L-HCY, M-HCY, and H-HCY groups were 0.78±0.08, 0.79±0.07 and 0.81±0.07, respectively (P = 0.04). The left uterine artery RI in L-HCY, M-HCY, and H-HCY groups were 0.78±0.08, 0.81±0.07 and 0.81±0.07, respectively (P = 0.01). The right uterine artery RI level and the left uterine artery RI was significantly associated with HCY level (r = 0.103, P = 0.050; r = 0.104, P = 0.047, respectively). Of these, 177 women experienced their next pregnancy, and 33 patients experienced PL again. The pregnancy rate in l-HCY, M-HCY, and HHCY groups were 47.92% (69/144), 49.43% (86/174) and 47.83% (22/46), respectively (P = 0.95). In next pregnancy, the PL rate in l-HCY, M-HCY, and HHCY groups were 8.70% (6/69), 22.58% (22/86) and 22.73% (5/22), respectively (P = 0.03).

CONCLUSION

HCY can increase the uterine artery resistance in the non-pregnant state and is associated with the abortion rate of next pregnancy.

Risk Factors of Pregnancy Failure in Infertile Patients Undergoing Assisted Reproductive Technology

Background

Infertile couples need to use assisted reproductive technology (ART) to give birth. However, pregnancy failure after ART is not uncommon. At present, the results of studies on the causes of pregnancy failure after ART are inconsistent.

Methods

A retrospective cohort study involving 715 embryo transfer cycles was conducted at the Reproductive Medicine Center of Meizhou People's Hospital, from December 2015 to June 2022. According to the pregnancy, they were divided into clinical pregnancy group and pregnancy failure group. The relationship between demographic characteristics and pregnancy status between the two groups was analyzed.

Results

The pregnancy failure rate after ART was 49.7% (355/715). There were statistically significant distribution differences of maternal age, paternal age, COH protocols, and number of embryos transferred between clinical pregnancy and pregnancy failure groups (all P<0.01). Multiple logistic regression analysis shows that high maternal age (>35 years old vs ≤35 years old: OR 2.173, 95% CI: 1.386-3.407, P=0.001), and GnRH-a short protocol (GnRH-a short protocol vs GnRH-a long protocol: OR 2.139, 95% CI: 1.127-4.058, P=0.020) may increase risk of pregnancy failure in ART pregnancies, while two embryos transferred (two embryos transferred vs one embryo transferred: OR 0.563, 95% CI: 0.377-0.839, P=0.005) may reduce risk of pregnancy failure. In addition, high maternal age, GnRH antagonist protocol, and GnRH-a short protocol may increase risk of implantation failure, while two embryos transferred may reduce risk of implantation failure. And high maternal age may increase risk of biochemical pregnancy.

Conclusion

The risk of pregnancy failure increased in ART cycles with maternal age >35 years old and GnRH-a short protocol, while reduced with two embryos transferred.