Clinical application of expanded carrier screening based on next-generation sequencing in the Chinese population

Abstract

Objective

Expanded carrier screening (ECS) enables proactive identification of at-risk couples (ARCs) and individuals, facilitating informed reproductive decision-making through genetic counseling. This study evaluates the clinical utility of ECS among the population in Anhui Province, China, where its implementation remains understudied. Retrospectively analysis of genetic testing results assessed the carrier frequencies for targeted diseases, identified prevalent pathogenic genes and variants, and ARCs detection rate alongside associated reproductive choices and pregnancy outcomes.

Methods

In this single-center retrospective study (June 2020–October 2023), 2,530 reproductive-aged individuals (486 couples; 1,558 individuals) underwent next-generation sequencing (NGS)-based ECS using a customized panel targeting 152 recessive monogenic disorders. Carrier rates, pathogenic variants, ARC detection, and subsequent reproductive outcomes were analyzed.

Results

Overall, 38.50% (974/2,530) of participants carried ≥ 1 pathogenic/likely pathogenic (P/LP) variant. The most prevalent autosomal recessive (AR) disorders included DFNB4 (3.08%), DFNB1A (2.81%), Wilson disease (2.57%), Krabbe disease (2.37%), and phenylketonuria (2.13%). Duchenne muscular dystrophy (DMD, 0.28%) was the most common X-linked (XL) disorder. Twenty ARCs (4.12%, 20/486) were identified, including sixteen pregnant couples. Among these, 56.25% (9/16) opted for invasive prenatal diagnosis, confirming eight unaffected fetuses with healthy live births and one twin pregnancy requiring selective termination of an affected fetus. Five pregnant ARCs declined prenatal diagnosis, four of whom delivered healthy infants, while one pregnancy was terminated due to structural anomalies. Of three non-pregnant ARCs, two pursued preimplantation genetic testing for monogenic disorders (PGT-M), resulting in one healthy birth.

Conclusion

Our study demonstrated that the ECS for reproductive-age individuals can identify couples and individuals at risk of conceiving a child with a recessive genetic disorder and support reproductive choices through the provision of genetic counseling to reduce the likelihood of offspring with congenital anomalies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00404-025-08100-9.

What does this study add to the clinical work

What is already known about this topic?

It is possible to reduce the risk of having a child with monogenic diseases by expanded carrier screening (ECS) during pregnancy or early in the pregnancy. The clinical utility of ECS has not been fully evaluated.

What does this study add?

38.50% of the population carries at least one recessive monogenic disorder, and through genetic counselling, maximizes the benefits of reproductive autonomy of 4.12% at-risk couples (ARCs).

Introduction

Monogenic diseases are one of the important causes of birth defects, primarily arising from pathogenic variants in single genes. These disorders follow distinct inheritance patterns: autosomal recessive conditions (e.g., hereditary deafness, spinal muscular atrophy [SMA], and thalassemia) require biallelic mutations, while X-linked recessive disorders such as Duchenne muscular dystrophy (DMD) manifest in males through hemizygosity of a single pathogenic allele on the X chromosome. The OMIM database documents more than 6800 distinct monogenic diseases (https://www.omim.org/statistics/entry). According to data from the Clinical Genomic Database (CGD) [1], over 2,000 of these are recessive disorders, including autosomal recessive (AR) and X-linked (XL) recessive disorders, which represent a significant disease burden. Each individual may carry 2–5 recessive disease-causing genes, and single-gene mutations resulting in genetic disorders account for approximately 20% of child deaths and 10% of pediatric hospitalizations [2]. Most monogenic diseases have severe consequences, such as fatality, disability, or deformity. Effective treatment methods are either unavailable or costly, imposing a significant burden on families and society while diminishing the quality of family life [3]. Most monogenic diseases occur in offspring whose parents appear phenotypically normal but carry recessive disease-causing gene mutations. For instance, couples who both carry the P/LP variants in the same AR gene or the female carrying the variants in XL gene, that is, at-risk couples (ARCs), face an increased risk of having children with monogenic diseases. It is estimated that 2% ~ 4% of reproductive-aged couples without family history belong to ARCs who are at risk of having children with some recessive genetic disease [4], and most recessive monogenic disorders have no detectable prenatal phenotype in the uterus, making them undetectable by routine prenatal screening. Therefore, there is an urgent need to develop effective screening patterns for monogenic diseases. Thus, if genetic testing is performed on both partners prior to conception or in early pregnancy to ascertain their carrier status, followed by genetic counseling and guidance regarding reproductive options, it is possible to mitigate the risk of transmitting such diseases during pregnancy through a process known as carrier screening.

Carrier screening initially focused on the identification of specific diseases in high-risk populations, starting with screening for individual ethnicity-specific or disease types such as sickle cell disease (SCD), Tay–Sachs disease (TSD), cystic fibrosis (CF), and SMA [5–7]. With the rapid advancement of high-throughput sequencing technology, carrier screening has evolved from screening for a single disease to multiple diseases, and from specific high-risk ethnic group screening to general population screening across all races. Consequently, the expanded carrier screening (ECS) was formally proposed by the American College of Medical Genetics and Genomics (ACMG) [8], utilizing NGS methods to simultaneously identify multiple recessive single-gene disorders, thereby significantly enhancing screening efficiency. The objective of ECS is to identify carriers of single-gene inherited mutations and identify ARCs, and provide information on potential genetic disorders and reproductive risks for future offspring. This allows for informed reproductive decisions to be made before or during pregnancy, including the utilization of PGT-M or invasive prenatal diagnosis, to prevent the birth of children with defects.

Since 2013, international professional associations such as the ACMG and the American College of Obstetricians and Gynecologists (ACOG) have continuously issued multiple guidelines or statements [9–13] to provide guidance and support for the clinical implementation of ECS. This has enabled simultaneous screening for over 100 monogenic diseases, with the target population being couples who are pregnant or planning to become pregnant. However, it is imperative to note that the current disease selection criteria have been established primarily based on demographic and clinical characteristics of U.S. and European populations. Given the substantial heterogeneity in disease prevalence and distribution patterns across different ethnic groups, these criteria may lack sufficient generalizability to Chinese population cohorts. Although there have been many studies on the application of ECS in the Chinese population [14–16], ECS has yet to be standardized for clinical implementation in China. The domestic clinical popularization work of ECS has not yet established a standardized framework, encompassing the target population, disease selection, economic cost, screening strategy, and genetic counseling. This study of genetic screening of childbearing age individuals aims to understand the carrier status of 152 recessive monogenic disorders in the population of Fuyang area, and to assess their reproductive risk, and to effectively reduce the occurrence of birth defects.

Materials and methods

Study population

A retrospective analysis was conducted on the results of ECS for 152 recessive monogenic diseases at the prenatal diagnosis center of Fuyang People’s Hospital from June 2020 to October 2023. The screening targeted couples or individuals with normal phenotypes during family planning or early pregnancy. Basic clinical information, including age, gender, pregnancy status, gestational age, and history of genetic diseases, were collected from the subjects.

ECS panel

An ECS panel comprising 152 recessive monogenic (AR and XL) diseases associated with 144 genes was used in this study (Table S1). The selection of single-gene disorders adhered to recommended guidelines established by the ACMG, ACOG, the National Society of Genetic Counselors (NSGC), the Perinatal Quality Foundation (PQF), and the Society for Maternal–Fetal Medicine (SMFM), as well as the expert consensus on carrier screening issued in China. These guidelines encompassed considerations for prenatal diagnosis as well as establishing an effective clinical correlation between mutations and disease severity. These diseases are classified into the following disease systems: metabolism, neurological and musculoskeletal, followed by skin, blood, immune system, endocrine, digestive, urinary, respiratory, ocular auditory multi-systems, etc. The mode of inheritance of these genes was predominantly AR (n = 142), with a smaller proportion being XL (n = 10).

Genomic sequencing and data analysis

3–5 mL of peripheral blood of the subjects was collected for ECS, and genomic DNA was extracted from peripheral blood using DNeasy Blood and Tissue kit (QIAQEN). The library construction and hybridization capture kit (BGI, China) was utilized for targeted regions capture, enrichment, elution, following the manufacturer’s protocol. The DNA was sequenced on BGISEQ-2000 (BGI, China) platform. The data were off-loaded and analyzed subsequently. First, raw reads obtained after sequencing are assessed for quality, and low quality or adapter reads are removed. Subsequently, the high-quality data is aligned to the human reference genome (GRCh37/hg19) using Burrows Wheeler Aligner (BWA) software. Repetitions caused by PCR amplification are removed using Picard. Single nucleotide variants (SNVs) and insertions and deletions (Indels) were queried using GATK software and Samtools software, respectively. Then a comparison with various databases is performed to annotate and identify mutations found. The utilized databases include dbSNP, HapMap, dbNSFP, HGMD, and the 1,000 Genomes Project.

Variant interpretations and validation

The classification and interpretation of variants were performed according to the standards and guidelines recommended by ACMG [17]. All the identified variants were classified into five categories: pathogenic, likely pathogenic, uncertain significance, likely benign, and benign. Finally, positive mutations in this ECS panel, namely known as pathogenic and likely pathogenic mutations, were reported. Sanger sequencing was employed to SNVs validation, while quantitative polymerase chain reaction (qPCR) or multiplex ligation-dependent probe amplification (MLPA) were used for the validation of copy number variants (CNVs). In addition, gene deletion variants associated with thalassemia were validated using gap-PCR.

Statistics

The statistical analysis aimed to identify the carrier rate of target genetic diseases, disease types, P/LP gene types, and carrier rate of ARCs in the detection samples. Data were expressed as numbers and percentages (%). The data were presented using SPSS version 17.0.

Results

Population demographics

The study included a total of 2530 participants for screening, comprising 1558 individuals (with 1431 females and 127 males) and 486 couples. The age of the participants ranged from 18 to 54 years, with a median age of 30 years. A total of 1563 female participants were pregnant, and the gestational age is shown in Table 1.

Table 1.

Demographics of the study participants

Demographics	N	Percentage (%)
Total	2530
Couples	486	38.42
Singulars	1558	61.58
Participants’ age (years)
≤ 24	301	11.90
25–29	913	36.09
30–34	839	33.16
35–39	361	14.27
≥ 40	116	4.58
Pregnancy status of female
Not pregnancy	354	18.47a
Pregnancy (weeks)	1563	81.53a
≤ 12	240	15.36b
12 ~ 16	952	60.91b
16 ~ 20	345	22.07b
20 ~ 24	22	1.41b
> 24	4	0.25b
Gravidity
0	196	10.22a
1	1205	62.86a
≥ 2	464	24.21a
NA	52	2.71a
Parity
0	1589	82.89a
1	221	11.53a
≥ 2	55	2.87a
NA	52	2.71a

^aPercentage of 1917 female participants

^bPercentage of 1563 pregnancy female participants

Disease carrier frequencies

A total of 2,530 individuals underwent the ECS for 152 recessive monogenic diseases, resulting in the identification of 38.50% (974/2530) carriers with at least one P/LP variant of these diseases. Among these carriers, 776 (30.67%, 776/2530) were found to be carriers of 1 disease, 173 were found to be carriers of 2 diseases (6.84%, 173/2530), and 24 were carriers of 3 diseases (1.06%, 24/2530). In addition, one individual was found to carry P/LP variants of four diseases (0.04%, 1/2530), while no individuals carried five or more diseases. On average, each individual harbored an average of 1.09 P/LP variants.

A total of 126 (82.89%, 126/152) target recessive monogenic diseases involving 120 genes were identified in 2,530 subjects. The carrier frequencies of the top ten disorders identified through the screening are summarized in Table 2. Six diseases with a carrier frequency greater than 2.00% were identified, with the most common being autosomal recessive deafness 4 (DFNB4) with a carrier rate of 3.08% (78/2530). The remaining diseases, in descending order of carrier frequency, included autosomal recessive deafness 1A (DFNB1A), Wilson disease, Krabbe disease, phenylketonuria, and methylmalonic acidemia (MMA) (cblC type). The carrier rates for these conditions were 2.81% (71/2530), 2.57% (65/2530), 2.37% (60/2530), 2.13% (54/2530), and 2.09% (53/2530), respectively. Two X-linked genetic diseases, namely Duchenne muscular dystrophy (DMD) and hemophilia B, with carrier rates of 0.28% (7/2530) and 0.04% (1/2530), respectively, were detected in this study, as shown in Table 3.

Table 2.

Top ten AR diseases detected by ECS panel with the highest carrier rate

Disease	Gene	N	Carrier frequency (%)	Most common variation
DFNB4	SLC26A4	78	3.08	c.919-2A > G
DFNB1A	GJB2	71	2.81	c.235del (p.Leu79Cysfs*3)
Wilson disease	ATP7B	65	2.57	c.2333G > T (p.Arg778Leu)
Krabbe disease	GALC	60	2.37	c.1901 T > C (p.Leu634Ser)
PKU	PAH	54	2.13	c.728G > A (p.Arg243Gln)
MMA, cblC type	MMACHC	53	2.09	c.609G > A (p.Trp203*)
SMA	SMN1	43	1.70	Exon7 Del
α-Thalassemia	HBA1、HBA2	36	1.42	− α3.7
PCD	SLC22A5	32	1.26	c.1400C > G (p.Ser467Cys)
Sitosterolemia	ABCG5、ABCG8	29	1.15	ABCG5: c.1336C > T (p.Arg446*)

DFNB4 autosomal recessive deafness 4, with enlarged vestibular aqueduct, DFNB1A autosomal recessive deafness 1A, PKU phenylketonuria, MMA methylmalonic aciduria and homocystinuria, SMA spinal muscular atrophy, PCD primary carnitine deficiency, DMD Duchenne muscular dystrophy, Del deletion

Table 3.

XL diseases with the highest carrier rate in the study population

Disease	Gene	N	Variation
DMD	DMD	1	Exon51_52 Del
		1	Exon14_17 Dup
		1	Exon28_29 Del
		1	Exon43_44 Del
		1	Exon48_49 Del
		1	Exon48_51 Del
		1	c.7555G > A (p.Asp2519Asn)
Hemophilia B	F9	1	c.479G > A (p.Gly160Glu)

Del deletion, Dup duplication

ARCs

In this study, a total of 20 ARCs were identified, among which 12 couples were found to be carriers of P/LP variants associated with the same AR disease, and the most prevalent was MMA, accounting for 4 ARCs. This was followed by two couples with DFNB1A and another two couples with DFNB4. The remaining couples were carriers of hypophosphatasia, SMA, phenylketonuria, and Krabbe disease, respectively. In addition, among the 20 ARCs, there were 8 female subjects who carried P/LP variants related to XL diseases. Specifically, seven of them were carriers of DMD, while the remaining one was a carrier of hemophilia B. After the ECS, genetic counseling was conducted for ARCs. There four ARCs were not pregnant at the time of ECS, two families were scheduled to undergo PGT-M to assist pregnancy. After follow-up, one of the families had given birth to a normal boy by combining assisted reproduction technology (ART) with PGT-M. One of non-pregnant ARCs had no pregnancy plan for the time being, and the other couple planned to have a natural pregnancy, and subsequently gave birth to a healthy girl, the result of prenatal diagnosis showed that the fetus did not carry the disease-causing variant. Among the 16 pairs of pregnant ARCs, 56.25% (9/16) opted for invasive prenatal diagnosis to confirm whether the fetus was affected. The results of prenatal diagnosis revealed that five fetuses were carriers of target diseases only, while three fetuses did not carry any P/LP variants associated with the target disease. Close follow-up for pregnancy outcomes of pregnant ARCs were conducted, a total of eight fetuses were delivered alive and healthy. In addition, a twin pregnancy provides another example, wherein one fetus was identified as an affected baby through prenatal diagnosis and underwent a fetal reduction accordingly, and the other fetus was delivered without abnormality. The other five pregnant ARCs declined prenatal diagnosis. Four of them gave birth to full-term babies with no abnormality, while one was still in the pregnancy during the follow-up. There are also two cases of pregnant ARCs who did not undergo prenatal diagnosis, one case underwent induced abortion subsequently due to fetal omphalocele and the unshown fetal nasal bone through ultrasound examination in the second trimester, and the other experienced spontaneous abortion at 19w + 3 (Table 4).

Table 4.

Genetic variants, prenatal diagnosis, pregnancy decision-making and outcomes in ARCs

No	Disease	Gene	Inheritance pattern	Gender	Variants	Prenatal diagnosis	Pregnancy decision-making and outcomes
1	DMD	DMD	XL	Female	Exon14_17 Dup	Fetus did not carry the disease-causing variant	Term infant, male, normal
2	DMD	DMD	XL	Female	c.7555G > A (p.Asp2519Asn)	Reject	Term infant, female, normal
3	DMD	DMD	XL	Female	Exon43_44 Del	–	Unpregnant and plan to PGT-M
4	DMD	DMD	XL	Female	Exon28_29 Del	ND	TOP due to fetal structural abnormalities
5	DMD	DMD	XL	Female	Exon51_52 Del	Fetus was a carrier of the disease	Term infant, female, normal
6	DMD	DMD	XL	Female	Exon48_51 Del	Fetus was a carrier of the disease	Term infant, female, normal
7	DMD	DMD	XL	Female	Exon48_49 Del	Fetus did not carry the disease-causing variant	Term infant, female, normal
8	Hemophilia B	F9	XL	Female	c.479G > A (p.Gly160Glu)	ND	Spontaneous abortion occurred at 19 weeks of pregnancy
9	MUT-Related MMA	MMUT	AR	Female	c.1677-1G > A	Fetus was a carrier of the disease	Term infant, male, normal
				Male	c.914 T > C (p.Leu305Ser)
10	MUT-Related MMA	MMUT	AR	Female	c.1208G > A (p.Arg403Gln)	–	Birth of a normal boy through PGT-M
				Male	c.1106G > A (p.Arg369His)
11	MUT-Related MMA	MMUT	AR	Female	c.2179C > T (p.Arg727*)	–	No pregnancy plan
				Male	c.1677-1G > A
12	DFNB1A	GJB2	AR	Female	c.235del (p.Leu79Cysfs*3)	Reject	Term infant, female, normal
				Male	c.235del (p.Leu79Cysfs*3)
13	DFNB1A	GJB2	AR	Female	c.49_50del (p.Ser17Hisfs*30)	Reject	Keep pregnancy
				Male	c.235del (p.Leu79Cysfs*3)
14	DFNB4	SLC26A4	AR	Female	c.919-2A > G	Reject	term infant, normal
				Male	c.919-2A > G
15	DFNB4	SLC26A4	AR	Female	c.919-2A > G	Fetus did not carry the disease-causing variant	Term infant, female, normal
				Male	c.665G > T (p.Gly222Val)
16*	Hypophosphatasia, infantile/ childhood	ALPL	AR	Female	c.88C > T (p.Arg30*)	Fetus did not carry the disease-causing variant	Term infant, female, normal
				Male	c.1091_1092insGCAG (p.Ser364Argfs*42)
17	MMA, cblC type	MMACHC	AR	Female	c.609G > A (p.Trp203*)	Fetus was a carrier of the disease	Term infant, male, normal
				Male	c.80A > G (p.Gln27Arg)
18	SMA	SMN1	AR	Female	Exon7 Del	Reject	Term infant, female, normal
				Male	Exon7 Del
19	PKU	PAH	AR	Female	c.992 T > C (p.Phe331Ser)	Fetus was a carrier of the disease	Term infant, male, normal
				Male	c.1174 T > A (p.Phe392Ile)
20	Krabbe disease	GALC	AR	Female	c.461C > A (p.Pro154His)	Fraternal twins, one fetus was affected and the other was unaffected	TOP for the fetus with genetic abnormalities, the other unaffected one was born healthy
				Male	c.1901 T > C (p.Leu634Ser)

PGT-M preimplantation genetic testing for monogenic/single-gene disorders, ND not done, TOP termination of pregnancy

*The family was not pregnant at the time of testing, and a prenatal diagnosis was performed after a natural pregnancy through follow-up

Discussion

In this retrospective study, we assessed the clinical utility of an NGS-based ECS panel of 152 disorders in 2530 participants.

Overall, 38.50% (974/2,530) of participants carried ≥ 1 pathogenic/likely pathogenic (P/LP) variant. The most prevalent autosomal recessive (AR) disorders were DFNB4 (3.08%), DFNB1A (2.81%), Wilson disease (2.57%), Krabbe disease (2.37%), phenylketonuria (2.13%), and MMA (2.09%). Duchenne muscular dystrophy (DMD, 0.28%) was the most common X-linked (XL) disorder. Regional and global comparisons highlight significant ethnic variability. Carrier rates in China range from 27.49% (11-disease panel, n = 20,952) [16] to 43.27% (n = 3,737) [18], contrasting with higher rates in U.S. (78%, n = 131 women) [19] and Vietnamese (63.6%, n = 540 genes) [21] cohorts. These disparities reflect differences in panel size and population genetics, with expanded panels correlating positively with carrier detection [22].

The incidence rate of DFNB4 is marginally higher than that reported in other studies [18, 23]. The predominant mutation observed in the P and LP variants of the SLC26A4 gene associated with DFNB4 is c.919-2A > G (37/79, 46.84%). Studies have demonstrated that this mutation is present in 15.23% of deaf patients and 74.8% of patients with large vestibular aqueduct. DFNB1A disease related to the GJB2 gene was the secondary common hereditary deafness disorder in this study. However, the variant GJB2 c.109G > A (p.Val37Ile) was not included in this screening due to its characteristic of exhibiting significant clinical phenotype variation and uncertain penetrance [24]. The carrier rate of DFNB1A disease observed in this study is comparable to the carrier rate (2.62%) reported in a study conducted in southwest China [18] after excluding the Val37Ile variant, but it is higher than rates reported in other studies [16]. In this study, c.235delC(p.Leu79Cysfs*3) was identified as the most prevalent pathogenic mutations in GJB2, accounting for 67.61% (48/71) of cases. These findings are consistent with the results of previous study on hereditary hearing loss conducted by Tsukada et al. [25] in Japan and one ECS study conducted in Thailand [20]. However, there are variations in carrier rates among different ethnic populations. The prevalence of genetically related hearing loss is higher in Asian populations, overall. The prevalence of Wilson disease, a systemic multisystem disorder caused by pathogenic mutations in ATP7B gene, ranges from 1/2600 to 1/30,000 individuals worldwide. In this study, the reported carrier rate (2.57%) exceeded the maximum carrier frequency documented in the OMIM database. Specifically, carriers were found to account for 2.89% and 3.3% of individuals in southwest China [18] and Vietnam [21], respectively. The carrying rate of Krabbe disease (GALC) reported by Chan et al. was 1/48 (2.1%) [26], while the recently published ECS study of Chinese Han population calculated that the carrier rate was 1.8% [27], and varied greatly in different regions. Furthermore, this study identified other relatively prevalent genetic metabolic disorders, such as phenylketonuria (PAH) and MMA (MMACHC), which exhibit a higher prevalence in China compared to other regions [18] and are less frequently observed in other countries. Overall, the prevalence of recessive monogenic diseases varies significantly among different ethnic groups [19, 28]. The presence of specific pathogenic variants among individuals of different ethnicities underscores the importance of designing ethnicity-based carrier screening programs and enhances the global repertoire of disease-causing gene panel.

This study identified a total of 20 pairs of ARCs (4.12%). MMA and DMD were the most prevalent AR disorders (n = 4 couples) and XL recessive diseases (n = 7 women), respectively. The detection rate and specific types of ARCs were found to be influenced by various factors including screening methods, the specific diseases screened for, and the number of couples included in the study. Reported detection rates for ARCs varied from 0.21% to 16.9% [16, 18, 19, 29]. Genetic counseling and management for ARCs were conducted to provide effective reproductive decision support for reducing the risk of single-gene disease in offspring. According to the consensus and research findings, it is recommended that couples consider PGT-M and targeted prenatal diagnosis before pregnancy or prenatal diagnosis after natural conception to mitigate fertility risks. The management of pregnant ARCs necessitates additional specific genetic counseling, and the decision regarding prenatal or neonatal diagnosis should be based on factors such as disease prognosis severity, postnatal treatment efficacy, and overall disease management. If the results of prenatal diagnosis indicate that the fetus is at high risk of being a patient, the decision to terminate pregnancy can be made according to the prognosis and treatment of the disease, or perform targeted diagnostic evaluation and preparatory measures for postnatal treatment [12, 30]. In this study, two non-pregnant ARCs were scheduled to take PGT-M after genetic counseling. In 2018, a study at the Center for Medical Reproduction carried out ECS in combination with preimplantation genetic diagnosis (PGD) to help obtain a healthy newborn [31]. An ESC study of people seeking ART and the general population successfully followed 15 ARCs who changed their reproductive plans through PGT-M and preimplantation genetic testing for aneuploidy (PGT-A), and three of these couples had already achieved a successful pregnancy resulting in an unaffected baby [32]. The invasive prenatal diagnosis was conducted on 56.25% (9/16) pregnant ARCs to confirm the presence of fetal disease. Following confirmation through prenatal diagnosis and subsequent clinical intervention, all fetuses remained alive and exhibited good health during the follow-up.

In our study, among 20 high-risk couples, 25% (5 couples) declined prenatal diagnosis, with follow-up data indicating live births reported as healthy in four cases and one ongoing pregnancy. The primary reasons for refusal included prohibitive costs of prenatal testing and concerns about miscarriage risks. This finding is consistent with the broader literature, which indicates that 23.4–47.4% of at-risk couples (ARCs) choose not to pursue interventions [18, 20, 27, 34–36]. This decision is influenced by multiple factors. Disparities in the perception of disease severity play a significant role; for instance, some consider treatable conditions such as late-onset hearing loss an acceptable risk. Uncertainties regarding variant penetrance and clinical expressivity also contribute to this decision. As an example, for the GJB2 c.109G > A variant, only a portion of homozygous or compound heterozygous carriers experience delayed hearing loss [18, 35]. Religious and ethical considerations are additional determining factors. Some ARCs object to procedures like pregnancy termination or gender selection for X-linked disorders [20]. Technical and psychological barriers are also prevalent. Distrust of invasive procedures or reproductive technologies often leads couples to forgo interventions. Financial constraints are another significant obstacle; for example, individuals with FMR1 full mutations may decline preimplantation genetic testing for monogenic diseases (PGT-M) due to high costs [36]. Psychosocial burdens, including the fear of familial discrimination, can also impact decision-making. This was evident in two spouses of SMN1 carriers who declined screening [36]. Moreover, the late identification of risks, particularly at 29 gestational weeks or later, further complicates the decision-making process for ARCs [35].

To address the multifaceted challenges inherent in this research area, the subsequent studies can encompass three interrelated dimensions: longitudinal monitoring, qualitative exploration, and educational optimization. First, it is necessary to conduct long-term prospective studies to systematically monitor the reproductive outcomes and psychological adjustment trajectories of the research participants. This longitudinal research approach will provide crucial insights into the long-term impacts of reproductive decisions. Second, qualitative research methods, such as in-depth structured interviews, should be adopted to elucidate the complex motivational factors underlying reproductive choices. These qualitative data will supplement the quantitative research findings, enabling us to have a more nuanced understanding of the decision-making process. Third, pre-screening educational materials should be optimized to ensure that patients can obtain clear, evidence-based information regarding disease prognoses and the associated risk–benefit profiles of existing interventions. To further strengthen the research framework, several methodological improvement measures are proposed. These include the development of standardized genetic counseling protocols, the establishment of systematic follow-up procedures, the extension of the screening period to the preconception and early pregnancy stages, and the exploration of alternative non-invasive diagnostic methods. Overall, these initiatives aim to overcome the existing barriers in reproductive health care, enhance the effectiveness of risk communication, and ultimately enable couples to make informed decisions regarding their reproductive health issues.

In addition, this study involving 1558 cases of individual screening suggests that 315 women and 43 men carry at least one AR disease. This population can be categorized as having a potential risk of transmitting recessive single-gene diseases to their offspring. Understanding the complexity and preventability of monogenic disorders will help to increase the willingness of their partners to further carry out ESC [33].

In conclusion, this study conducted a screening of 152 recessive monogenic diseases in a general population of childbearing age (2530 individuals) in this region, identifying the diseases with a high carrier rate. These findings provide valuable insights for clinical ECS in China and offer comprehensive genetic counseling to ARCs. Moreover, it offers reproductive options for families at risk of having offspring with genetic disorders, including techniques such as PGT-M before conception or prenatal diagnosis during pregnancy to prevent the birth of children with defects.

Supplementary Information

Below is the link to the electronic supplementary material.

Abbreviations

ECS

Expanded carrier screening

NGS

Next-generation sequencing

ARCs

At-risk couples

PGT-M

Preimplantation genetic testing for monogenic disorders

PGD

Preimplantation genetic diagnosis

PGT-A

Preimplantation genetic testing for aneuploidy

CGD

Clinical genomic database

AR

Autosomal recessive

SNVs

Single nucleotide variants

CNVs

Copy number variants

VUS

Variants of unknown clinical significance

QPCR

Quantitative polymerase chain reaction

MLPA

Multiplex ligation-dependent probe amplification

Author contributions

JL, JC and CM conducted the conception, data analysis and initial manuscript drafting. LM, JZ and CW participated in the data collection and interpretation. SL and JL involved in revising the manuscript critically for important intellectual content. YW played a prominent role in the conception, design, clinical and genomic supervision of the study. All authors reviewed and approved the final manuscript.

Funding

This work was supported by the Key Research and Development Program of Fuyang City (Major Project) (No: FYZDYF2023LCYX025).

Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request. The data are not publicly available due to privacy or ethical restrictions.

Declarations

Conflict of interest

The authors declare no competing interests.

Ethical approval and consent to participate

The study was approved by the Ethics Committee of the Fuyang People’s Hospital (No. [2023]6). The study was carried out in accordance with the declaration of Helsinki. Written informed consent was obtained from all participants.