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Analysis of prenatal diagnosis and pregnancy outcomes for rare autosomal trisomies detected by non-invasive prenatal testing in 33,079 cases

BMC Medical Genomics volume 18, Article number: 29 (2025) Cite this article

Abstract

Background

Non-invasive prenatal testing is widely used for screening common fetal aneuploidy disorders such as trisomy 21, trisomy 18, and trisomy 13. However, its ability to detect rare autosomal trisomies has introduced a new layer of complexity and clinical uncertainty.

Methods

A retrospective analysis was conducted on the prenatal diagnostic results and pregnancy outcomes of cases identified as high-risk for rare autosomal trisomies through non-invasive prenatal testing at the reproductive medicine center, Renmin hospital, Hubei university of medicine, from 2015 to 2023.

Results

66 cases identified as high-risk for rare autosomeal trisomies, yielding a detection rate of 0.20% (66/33,079). 7 declined amniocentesis, while the others underwent the procedure. Prenatal diagnostic procedures did not confirm the presence of the corresponding rare autosomal trisomy in any of these cases. Among the 66 cases of rare autosomal trisomies (RATs), 5 cases were lost to follow-up, and 1 case underwent termination of pregnancy (TOP) for personal reasons, leaving 60 cases with valid pregnancy outcomes. Of these 60 valid outcomes, 50 (83.33%) resulted in full-term births, while 10 (16.67%) experienced adverse pregnancy outcomes.

Conclusion

Prenatal diagnosis for high-risk rare autosomal trisomies typically reveals a normal karyotype with no detectable chromosomal abnormalities, and most cases can achieve full-term pregnancy outcomes. However, adverse pregnancy outcomes such as preterm birth, fetal demise, placental abnormalities, and intrauterine growth restriction are common and should be given clinical attention and consideration.

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Introduction

Lo et al. first identified fetal free DNA in maternal plasma and serum in 1997, establishing the foundation for using fetal free DNA in the diagnosis of genetic disorders [1, 2]. Non-invasive prenatal testing (NIPT) is an advanced technique that analyzes fetal aneuploidy disorders by detecting fetal free DNA in maternal plasma [2, 3]. It primarily screens for the more common chromosomal abnormalities, including trisomy 21, trisomy 18, and trisomy 13. The scope of NIPT-plus has been extended to detect chromosomal microdeletions and microduplications, demonstrating its potential to serve as a first-line prenatal screening method [4,5,6].

Currently, NIPT commonly uses low-depth whole-genome sequencing technology, enabling the reliable detection of aneuploidies in autosomes beyond chromosomes 13, 18, and 21. Trisomies in these other autosomes, also called rare autosomal trisomies, are often associated with recurrent miscarriages before the 12th week of pregnancy [7]. In fact, some pregnant women beyond 12 weeks of gestation who undergo non-invasive prenatal screening may receive supplemental reports regarding rare autosomal trisomies, which presents new challenges for clinical counseling.

Fetal free DNA in the maternal peripheral blood mainly originates from apoptotic placental cells, and the results of NIPT reflect the chromosomal status of the placenta [8]. Confined placental mosaicism (CPM) refers to the presence of chromosomal abnormalities in the placenta but not in the fetus. When confined placental mosaicism occurs, the results of non-invasive prenatal screening may not match those of amniocentesis [9]. Rare autosomal trisomies detected through noninvasive prenatal screening may indicate (mosaic) fetal trisomy or confined placental mosaicism, both of which can be linked to a higher risk of adverse perinatal outcomes.

Currently, reporting RATs detected by NIPT is controversial, there are limited evidence-based guidelines on managing RATs detected by NIPT, and there is a lack of effective clinical reports on RATs detected by NIPT and subsequent invasive testing [10, 11]. This study aims to analyze the prenatal diagnosis results and pregnancy outcomes of pregnant women identified as high-risk for rare autosomal trisomies through non-invasive prenatal testing, providing reference insights for genetic counseling and obstetric management of high-risk cases involving rare autosomal trisomies.

Materials and methods

Inclusion and exclusion criteria of the patients

Over a 55-month period (August 2018 to December 2023), 33,079 pregnant women were enrolled at the Reproductive Medicine Center, Renmin Hospital, Hubei University of Medicine, to undergo NIPT using next-generation sequencing (NGS). Eligibility criteria included singleton or twin pregnancies with no structural abnormalities detected by ultrasound, and a gestational age of at least 12 weeks at the time of sample collection. The exclusion criteria adhered to Chinese government regulations and included the following: chromosomal abnormalities in either parent of the fetus, stem cell therapy, a history of organ transplantation, immunotherapy within the past month, or allogeneic blood transfusion within the past year.

Non-invasive prenatal testing

Maternal peripheral blood samples (5 mL) were collected in Cell-Free DNA Storage Tube (CWBIO) and preserved as whole blood at room temperature for 96 h until DNA extraction. The blood samples were processed using a two-step centrifugation method (first at 1,600 × g for 10 min, followed by 16,000 × g for 10 min at 4 °C) to separate the plasma. Maternal plasma (200 µL) was used for cffDNA extraction, followed by end repair and adaptor ligation, and then DNA was amplified using PCR. All these procedures were automated using the BGISP-100 (BGI, Shenzhen, China). After pooling, the double-stranded DNA was thermally denatured into single strands, followed by the addition of cyclic buffer and ligase to generate DNA circles through cyclization. These DNA circles were then used to create DNA Nanoballs™ via rolling circle replication. The Nanoballs™ were subsequently loaded onto chips and sequenced using the BGISEQ-500 platform (BGI). Sequencing involved single-end reads with a length of 35 bp and a minimum of 4–6 million reads. Algorithms developed by BGI-Shenzhen were used to detect chromosomal aneuploidy [5].

Genetic analysis of amniotic fluid cells.

Amniocentesis was conducted between 18 and 20 weeks of gestation. Amniotic fluid cells were cultured and subjected to G-banding following standard procedures, achieving a resolution of 320–400 bands. Chromosomal copy number variation analysis was carried out using low-depth whole-genome sequencing on the BGISeq-500 platform. Sequencing involved single-end reads with a length of 35 bp and a minimum of 18 million reads. QC and copy number variation (CNV) detection were performed using previously established methods [12]. Briefly, uniquely aligned reads were categorized into adjustable sliding windows, each 50 kb in length with 5-kb increments, based on their mapped locations (GRCh37/hg19). The coverage for each window was determined by the number of reads and underwent a two-step bias correction process.

Results

Frequency of RATs detected by NIPT

There were 66 RATs identified from the 33,079 NIPT samples. The most frequently detected trisomy involved chromosome 7 (n = 17), followed by chromosome 3 (n = 8) and chromosome 16 (n = 7). The range and frequency of the affected chromosomes are illustrated in Fig. 1. Notably, trisomies of chromosomes 1, 4, 11, 17, and 19 were not detected.

Fig. 1
figure 1

Rare autosomal trisomy case frequency

Full size image

Prenatal diagnosis of RATs

Among the 66 pregnant women identified as high-risk for RATs, 7 declined amniocentesis, while the others underwent the procedure. Chromosomal karyotyping and CNV analysis of amniotic fluid cells did not detect any RATs. Interestingly, one case reported high risk for trisomy 5, but karyotype analysis of the amniotic fluid cells revealed 47, XXY.

Pregnancy outcomes of RATs

Among the 66 cases of RATs, 5 were lost to follow-up, and 1 case underwent TOP for personal reasons, leaving 60 cases with valid pregnancy outcomes. Of these 60 valid cases, 50 (83.33%) resulted in full-term births, while 10 (16.67%) experienced adverse pregnancy outcomes: 4 cases of preterm birth, 2 cases of miscarriage, 1 case of TOP due to fetal abnormalities caused by a placental vascular tumor, 1 case of TOP due to slow fetal development, 1 case of TOP due to bilateral renal pelvis dilation combined with a globular placenta, and 1 case of TOP following a diagnosis of chromosomal abnormality (47,XXY), as shown in Table 1.

Table 1 Clinical outcome data for each RAT case
Full size table

Discussion

The so-called fetal cell-free DNA in maternal circulation actually originates from apoptotic trophoblast cells [13]. Detection of RATs by NIPT indicates that the placenta may be trisomic or a mosaic trisomy [14]. Most fetuses with rare trisomies do not survive beyond 12 weeks of gestation [15]. Therefore, RATs detected by NIPT after 12 weeks are most likely indicative of placental mosaicism, with little correlation to fetal trisomy [11, 14]. In this study, no RATs or low-level mosaicism were found in the subsequent prenatal diagnoses of detected RATs, indirectly supporting this conclusion.

The presence of trisomic cell lines in the placenta can disrupt normal placental development and function by altering gene dosage, potentially resulting in intrauterine growth restriction, gestational hypertension, preterm birth, and miscarriage [16,17,18]. We followed up on 60 pregnant women identified as high-risk for RATs, 50 of whom had normal full-term live births, while 10 experienced adverse pregnancy outcomes. Among the adverse outcomes, there were 4 cases of preterm birth, 2 miscarriages, 1 case of intrauterine growth restriction leading to TOP, 1 case of fetal abnormality due to placental hemangioma leading to TOP, 1 case of hydronephrosis combined with a globular placenta leading to TOP, and 1 case of a diagnosed chromosomal abnormality (47, XXY) resulting in TOP. The 4 preterm births were linked to trisomies 3, 7, 15, and 16, while the 2 miscarriages were associated with trisomies 16 and 20. Placental abnormalities were found in cases involving trisomies 7 and 9, and the case of intrauterine growth restriction was related to trisomy 16. Overall, trisomy 16 was the most frequently associated with adverse pregnancy outcomes.

According to reports, most RATs have a low likelihood of fetal mosaicism, and the results of conventional amniocentesis are usually normal [11]. Although the amniocentesis results for the pregnant women at high risk for RATs in our study were all normal, these results lacked detection of uniparental disomy (UPD). The primary mechanism of UPD formation is trisomy rescue, where one of the extra chromosomes in a trisomic embryo is lost, restoring a disomic state [19, 20]. If chromosomes 7, 11, 14, 15, or 20 are involved, maternal UPD can lead to a phenotype. Paternal UPD is associated with phenotypes linked to chromosomes 6, 11, 14, 15, and 20 [21]. In our report, RATs involved all five of these chromosomes except chromosome 11. Therefore, prenatal diagnosis of trisomies involving chromosomes related to UPD should include genetic testing for UPD.

Conclusion

In summary, amniocentesis results for RATs are generally normal, but adverse pregnancy outcomes such as preterm birth, miscarriage, and intrauterine growth restriction can still occur, highlighting the need for enhanced prenatal management. For RATs involving chromosomes associated with UPD, genetic testing for UPD is needed to considered in prenatal diagnosis after obtaining informed consent. More studies should be performed to clarify pregnancy outcomes in cases of RATs.

Data availability

The datasets generated and/or analysed during the current study are not applicable to any public data repository mandates, as this study does not involve protein sequences, DNA or RNA sequences, genetic polymorphisms, macromolecular structures, or microarray data. All the data generated or analyzed during this study are available from the corresponding author by reasonable request.

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Acknowledgements

NA.

Funding

The present study was funded by the Talent Research Starting Foundation (2016QDJZR09), Hubei University of Medicine (2016).

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Author notes

  1. Xu Yan and Kai Ding contributed equally to this work.

Authors and Affiliations

  1. Reproductive Medicine Center, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China

    Xu Yan, Kai Ding, Xin Zhang, Shuai Zhang, Haiying Peng & Ying Zhang

  2. Biomedical Engineering College, Hubei University of Medicine, Shiyan, 442000, China

    Xu Yan, Kai Ding, Shuai Zhang, Haiying Peng & Ying Zhang

  3. Hubei Clinical Research Center for Reproductive Medicine, Shiyan, 442000, China

    Xu Yan, Kai Ding, Xin Zhang, Shuai Zhang, Haiying Peng & Ying Zhang

  4. Shiyan Key Laboratory of Reproduction and Genetics, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China

    Xu Yan, Kai Ding, Xin Zhang, Shuai Zhang, Haiying Peng & Ying Zhang

  5. Hubei Key Laboratory of Embryonic Stem Cell Research, Shiyan, 442000, China

    Xu Yan, Kai Ding, Xin Zhang, Shuai Zhang, Haiying Peng & Ying Zhang

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Contributions

YX and ZY designed the study. DK analyzed and interpreted the data and wrote the manuscript. ZX, PHY and ZS collected clinical data. All authors have read and approved the final version of the manuscript.

Corresponding author

Correspondence to Ying Zhang.

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Ethics approval and consent to participate

The study was approved by the Ethical Committee of Renmin Hospital, Hubei University of Medicine. Informed consent was provided by all patients or by the parents of the patients. The patients were informed of the diagnostic tests and genetic analysis before operations in accordance with the Declaration of Helsinki. Written informed consents to participate were obtained from participants. All methods were carried out in accordance with relevant guidelines and regulations. This study was carried out in compliance with the ARRIVE guidelines.

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The authors declare no competing interests.

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Yan, X., Ding, K., Zhang, X. et al. Analysis of prenatal diagnosis and pregnancy outcomes for rare autosomal trisomies detected by non-invasive prenatal testing in 33,079 cases. BMC Med Genomics 18, 29 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12920-025-02099-3

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BMC Medical Genomics

ISSN: 1755-8794

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