Genomic architecture of fetal central nervous system anomalies using whole-genome sequencing

Abstract

Structural anomalies of the central nervous system (CNS) are one of the most common fetal anomalies found during prenatal imaging. However, the genomic architecture of prenatal imaging phenotypes has not yet been systematically studied in a large cohort. Patients diagnosed with fetal CNS anomalies were identified from medical records and images. Fetal samples were subjected to low-pass and deep whole-genome sequencing (WGS) for aneuploid, copy number variation (CNV), single-nucleotide variant (SNV, including insertions/deletions (indels)), and small CNV identification. The clinical significance of variants was interpreted based on a candidate gene list constructed from ultrasound phenotypes. In total, 162 fetuses with 11 common CNS anomalies were enrolled in this study. Primary diagnosis was achieved in 62 cases, with an overall diagnostic rate of 38.3%. Causative variants included 18 aneuploids, 17 CNVs, three small CNVs, and 24 SNVs. Among the 24 SNVs, 15 were novel mutations not reported previously. Furthermore, 29 key genes of diagnostic variants and critical genes of pathogenic CNVs were identified, including five recurrent genes: i.e., TUBA1A, KAT6B, CC2D2A, PDHA1, and NF1. Diagnostic variants were present in 34 (70.8%) out of 48 fetuses with both CNS and non-CNS malformations, and in 28 (24.6%) out of 114 fetuses with CNS anomalies only. Hypoplasia of the cerebellum (including the cerebellar vermis) and holoprosencephaly had the highest primary diagnosis yields (>70%), while only four (11.8%) out of 34 neural tube defects achieved genetic diagnosis. Compared with the control group, rare singleton loss-of-function variants (SLoFVs) were significantly accumulated in the patient cohort.

Fig. 1. Diagnostic yields of WGS in different types of CNS anomalies and distribution of diagnostic variants.

Bars indicate case numbers (left y-axis) and the dashed line shows the diagnostic rate (%) (right y-axis). Cases were repeatedly counted if more than one sonographic feature was presented. Isolated brain anomalies only included aplasia of the corpus callosum, arachnoid cyst, and ventriculomegaly, as other CNS anomalies are usually complex and involve several anatomical structures of the brain. ACC aplasia of corpus callosum.

Fig. 2. Critical genes identified in diagnosed cases and gene-related inheritance patterns.

a Frequency of genes with diagnostic variants or critical genes in diagnostic CNVs. b Percentage of inheritance modes of diseases associated with genes in (a), AR autosomal recessive, AD autosomal dominant, XLD X-linked dominant.

Fig. 3. Accumulation of rare singleton deleterious variants in fetal CNS cohort.

Distribution of rare singleton deleterious missense variants of a MAF = 0; b MAF ≤ 0.01. Accumulation of rare SLoFVs of c MAF = 0, with median of 8 in cases (solid line) and 6 in controls (dashed line) with P = 1.7 × 10⁻⁹ by two-sided Wilcoxon test and d MAF ≤ 0.01, with median of 13.5 in cases and 9 in controls with P = 2.2 × 10⁻¹⁶ by two-sided Wilcoxon test. SLoFVs singleton loss-of-function variants.

Fig. 4. Prenatal imaging of two typical cases, P221 (top row) and P796 (bottom row).

Sonographic hyperechoic lesions in a cerebral lateral ventricles and b brain parenchyma indicated by arrows. c Hypointensity lesions revealed by T2-weighted MRI in cerebral lateral ventricles indicated by arrows. d Large space-occupying lesion in left ventricle shown by d sonography. Widths of the cerebral ventricle of P796 were 0.84 cm on left (e) and 1.04 cm on right (f) shown by sonography. g Coronal and h sagittal view of T2 MRI showing abnormal cortical gyration indicated by arrows.