Gene-environment interactions in birth defect etiology: Challenges and opportunities

Whole-genome sequencing analysis in fetal structural anomalies: novel phenotype-genotype discoveries

OBJECTIVES

The identification of structural variants and single-nucleotide variants is essential in finding molecular etiologies of monogenic genetic disorders. Whole-genome sequencing (WGS) is becoming more widespread in genetic disease diagnosis. However, data on its clinical utility remain limited in prenatal practice. We aimed to expand our understanding of implementing WGS in the genetic diagnosis of fetal structural anomalies.

METHODS

We employed trio WGS with a minimum coverage of 40× on the MGI DNBSEQ-T7 platform in a cohort of 17 fetuses presenting with aberrations detected by ultrasound, but uninformative findings of standard chromosomal microarray analysis (CMA) and exome sequencing (ES).

RESULTS

Causative genetic variants were identified in two families, with an increased diagnostic yield of 11.8% (2/17). Both were exon-level copy-number variants of small size (3.03 kb and 5.16 kb) and beyond the detection thresholds of CMA and ES. Moreover, to the best of our knowledge, we have described the first prenatal instance of the association of FGF8 with holoprosencephaly and facial deformities.

CONCLUSIONS

Our analysis demonstrates the clinical value of WGS in the diagnosis of the underlying etiology of fetuses with structural abnormalities, when routine genetic tests have failed to provide a diagnosis. Additionally, the novel variants and new fetal manifestations have expanded the mutational and phenotypic spectrums of BBS9 and FGF8. © 2023 International Society of Ultrasound in Obstetrics and Gynecology.

Multivariate logistic regression analysis of risk factors for birth defects: a study from population-based surveillance data

OBJECTIVE

To explore risk factors for birth defects (including a broad range of specific defects).

METHODS

Data were derived from the Population-based Birth Defects Surveillance System in Hunan Province, China, 2014-2020. The surveillance population included all live births, stillbirths, infant deaths, and legal termination of pregnancy between 28 weeks gestation and 42 days postpartum. The prevalence of birth defects (number of birth defects per 1000 infants) and its 95% confidence interval (CI) were calculated. Multivariate logistic regression analysis (method: Forward, Wald, α = 0.05) and adjusted odds ratios (ORs) were used to identify risk factors for birth defects. We used the presence or absence of birth defects (or specific defects) as the dependent variable, and eight variables (sex, residence, number of births, paternal age, maternal age, number of pregnancies, parity, and maternal household registration) were entered as independent variables in multivariate logistic regression analysis.

RESULTS

Our study included 143,118 infants, and 2984 birth defects were identified, with a prevalence of 20.85% (95%CI: 20.10-21.60). Multivariate logistic regression analyses showed that seven variables (except for parity) were associated with birth defects (or specific defects). There were five factors associated with the overall birth defects. The risk factors included males (OR = 1.49, 95%CI: 1.39-1.61), multiple births (OR = 1.44, 95%CI: 1.18-1.76), paternal age < 20 (OR = 2.20, 95%CI: 1.19-4.09) or 20-24 (OR = 1.66, 95%CI: 1.42-1.94), maternal age 30-34 (OR = 1.16, 95%CI: 1.04-1.29) or > = 35 (OR = 1.56, 95%CI: 1.33-1.81), and maternal non-local household registration (OR = 2.96, 95%CI: 2.39-3.67). Some factors were associated with the specific defects. Males were risk factors for congenital metabolic disorders (OR = 3.86, 95%CI: 3.15-4.72), congenital limb defects (OR = 1.34, 95%CI: 1.14-1.58), and congenital kidney and urinary defects (OR = 2.35, 95%CI: 1.65-3.34). Rural areas were risk factors for congenital metabolic disorders (OR = 1.21, 95%CI: 1.01-1.44). Multiple births were risk factors for congenital heart defects (OR = 2.09, 95%CI: 1.55-2.82), congenital kidney and urinary defects (OR = 2.14, 95%CI: 1.05-4.37), and cleft lip and/or palate (OR = 2.85, 95%CI: 1.32-6.15). Paternal age < 20 was the risk factor for congenital limb defects (OR = 3.27, 95%CI: 1.10-9.71), 20-24 was the risk factor for congenital heart defects (OR = 1.64, 95%CI: 1.24-2.17), congenital metabolic disorders (OR = 1.56, 95%CI: 1.11-2.21), congenital limb defects (OR = 1.61, 95%CI: 1.14-2.29), and congenital ear defects (OR = 2.13, 95%CI: 1.17-3.89). Maternal age < 20 was the risk factor for cleft lip and/or palate (OR = 3.14, 95%CI: 1.24-7.95), 30-34 was the risk factor for congenital limb defects (OR = 1.37, 95%CI: 1.09-1.73), >=35 was the risk factor for congenital heart defects (OR = 1.51, 95%CI: 1.14-1.99), congenital limb defects (OR = 1.98, 95%CI: 1.41-2.78), and congenital ear defects (OR = 1.82, 95%CI: 1.06-3.10). Number of pregnancies = 2 was the risk factor for congenital nervous system defects (OR = 2.27, 95%CI: 1.19-4.32), >=4 was the risk factor for chromosomal abnormalities (OR = 2.03, 95%CI: 1.06-3.88) and congenital nervous system defects (OR = 3.03, 95%CI: 1.23-7.47). Maternal non-local household registration was the risk factor for congenital heart defects (OR = 3.57, 95%CI: 2.54-5.03), congenital metabolic disorders (OR = 1.89, 95%CI: 1.06-3.37), congenital limb defects (OR = 2.94, 95%CI: 1.86-4.66), and congenital ear defects (OR = 3.26, 95%CI: 1.60-6.65).

CONCLUSION

In summary, several risk factors were associated with birth defects (including a broad range of specific defects). One risk factor may be associated with several defects, and one defect may be associated with several risk factors. Future studies should examine the mechanisms. Our findings have significant public health implications as some factors are modifiable or avoidable, such as promoting childbirths at the appropriate age, improving the medical and socio-economic conditions of non-local household registration residents, and devoting more resources to some specific defects in high-risk groups, which may help reducing birth defects in China.

The detection efficacy of noninvasive prenatal genetic testing (NIPT) for sex chromosome abnormalities and copy number variation and its differentiation in pregnant women of different ages

Objective

To analyze the efficacy of noninvasive prenatal genetic testing (NIPT) in detecting fetal sex chromosome abnormalities and copy number variation (CNV), compare the efficacy between NIPT and serological screening alone, and further analyze the fetal sex chromosome abnormalities and CNV differentiation in pregnant women of different ages, so as to provide a reference for the prevention and control of fetal birth defects.

Methods

Clinical data from 22,692 pregnant women admitted to our hospital from January 2013 to December 2022 were retrospectively analyzed. All participants underwent serological screening and NIPT screening to compare fetal chromosomal abnormalities between the two screening modalities. 145 women whose fetus were diagnosed as sex chromosome abnormalities and 36 women whose fetus were diagnosed as CNV abnormalities based on NIPT screening were selected for prenatal diagnosis by amniocentesis or karyotyping. Taking prenatal diagnosis as the standard, the four-grid table method was used to detect the positive predictive value of NIPT screening for fetal sex chromosomal abnormalities and CNV. According to the age, pregnant women were divided into 18-30 years old (n = 9844), 31-35 years old (n = 7612), >35 years old (n = 5236), and then the detection rates of sexual fetal chromosomal abnormalities, CNV and total chromosomal abnormalities were compared in pregnant women.

Results

Among the 22,692 pregnant women in this study, the high-risk proportion of serologic screening with 4.38% was higher than that of NIPT screening with 1.93% (P < 0.05). Among the 145 women with fetal sex chromosome abnormalities screened by NIPT, 122 cases of fetal sex chromosome abnormalities were diagnosed prenatally, including 45, X/47, XXX/47, XYY/47, XXY. The positive predictive values of NIPT screening were 25.00%, 58.82%, 85.71%, and 85.71%, respectively, with an overall predictive value of 44.26%. The positive predictive value of fetal sex chromosome abnormalities in NIPT screening was higher than that of serological screening (P < 0.05). Among the 36 pregnant women with fetal CNV, NIPT screening showed that CNVs≤10 Mb and CNVs>10 Mb were 33.33% and 66.67%, respectively. There were 12 cases of prenatal diagnosis of fetal CNV, among which the NIPT-screened positive predictive values of fetal copy number deletion, duplicate, deletion and duplicate were 50.00%, 57.14% and 100.00%, respectively, with an overall predictive value of 58.33%. The positive predictive value of CNV in NIPT screening was higher than that of serological screening without statistically significant difference (P > 0.05). The results of NIPT screening showed that the detection rate of fetal sex chromosome abnormalities and total abnormalities of pregnant women over 35 years of age was significantly higher than that of pregnant women aged 18-30 and 31-35 years (P < 0.05).

Conclusion

NIPT screening could greatly improve the detection efficacy of fetal sex chromosome abnormalities, CNV and other chromosome abnormalities, and decline the false positive rate. However, the positive predictive value of NIPT screening was relatively low, and further prenatal testing and genetic counseling are still required. In addition, NIPT screening for fetal sex chromosome abnormalities, and the detection rate of total abnormalities in pregnant women older than 35 years old were increased significantly, and pregnancy at an advanced age may be one of the risk factors for fetal chromosomal abnormalities.

Update from a cohort study for birth defects in Hunan Province, China, 2010-2020

To define the relationship between sex, residence, maternal age, and a broad range of birth defects by conducting a comprehensive cross-analysis based on up-to-date data. Data were obtained from the Birth Defects Surveillance System in Hunan Province, China, 2010-2020. Prevalences of birth defects (number of cases per 10,000 fetuses (births and deaths at 28 weeks of gestation and beyond)) with 95% confidence intervals (CI) were calculated by sex, residence, maternal age, year, and 23 specific defects. Cross-analysis of sex, residence, and maternal age was conducted, and crude odds ratios (ORs) were calculated to examine the association of each maternal characteristic with birth defects. A total of 1,619,376 fetuses and 30,596 birth defects were identified. The prevalence of birth defects was 188.94/10,000 (95% CI 186.82-191.05). Birth defects were more frequent in males than females (210.46 vs. 163.03/10,000, OR = 1.30, 95% CI 1.27-1.33), in urban areas than in rural areas (223.61 vs. 162.90/10,000, OR = 1.38, 95% CI 1.35-1.41), and in mothers ≥ 35 than mothers 25-29 (206.35 vs. 187.79/10,000, OR = 1.10, 95% CI 1.06-1.14). Cross-analysis showed that the prevalence of birth defects was higher in urban females than in rural males (194.53 vs. 182.25/10,000), the difference in prevalence between males and females was more significant for maternal age < 20 compared to other age groups (OR = 1.64, 95% CI 1.37-1.95), and the prevalence difference between urban and rural areas is more significant for maternal age 25-34 compared to other age groups (OR = 1.49, 95% CI 1.43-1.57). Cleft palates were more frequent in males, and nine specific defects were more frequent in females. Five specific defects were more frequent in rural areas, and eight were more frequent in urban areas. Compared to mothers 25-29, five specific defects were more frequent in mothers < 20, seven specific defects were more frequent in mothers 20-24, two specific defects were more frequent in mothers 30-34, and ten specific defects were more frequent in mothers ≥ 35. Our data indicate that sex, residence, and maternal age differences in the prevalences of birth defects and most specific defects are common. We have found some new epidemiological characteristics of birth defects using cross-analysis, such as residence is the determining factor for the prevalence of birth defects, the difference in prevalence between males and females was more significant for maternal age < 20 compared to other age groups, the prevalence difference between urban and rural areas is more significant for maternal age 25-34 compared to other age groups. And differences in the epidemiological characteristics of some specific defects from previous studies. Future studies should examine mechanisms. Our findings contributed to clinical counseling and advancing research on the risk factors for birth defects.

Diagnosis, treatment, and research status of rare diseases related to birth defects

Rare diseases are diseases that occur at low prevalence, and most of them are chronic and serious diseases that are often life-threatening. Currently, there is no unified definition for rare diseases. The diagnosis, treatment, and research of rare diseases have become the focus of medicine and biopharmacology, as well as the breakthrough point of clinical and basic research. Birth defects are the hard-hit area of rare diseases and the frontiers of its research. Since most of these defects have a genetic basis, early screening and diagnosis have important scientific value and social significance for the prevention and control of such diseases. At present, there is no effective treatment for most rare diseases, but progress in prenatal diagnosis and screening can prevent the occurrence of diseases and help prevent and treat rare diseases. This article discusses the progress in genetic-related birth defects and rare diseases.