Detection and characterization of mutational landscape of neurodevelopmental disorders from long read whole genome DNA sequencing

Abstract

Background: Neurodevelopmental disorders (NDDs) are a group of rare disorders that manifest very early in life and are characterized by cognitive, linguistic, behavioral, and motor impairments that negatively impact personal, social, academic, and occupational functioning. The genetic underpinning of neurodevelopmental disorders (NDDs) in diverse ethnic populations, especially those with high rates of consanguinity, remains largely unexplored. Here, we aim to elucidate genomic insight from 576 clinically well-phenotype and highly consanguineous (16%) NDD cohorts by different genotyping technologies such as chromosomal microarray (CMA), Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS). Methods: The cohort comprised 576 participants with one or more NDDs (male-to-female ratio 2.1:1, N=390 males, and 186 females) among whom 98.26% (566/576) were under 18 years old. In this study, participants underwent either CMA (N=247) or WES (N=127) and long read WGS (N=10) or a combination (both WES and CMA; N=202). We have thoroughly reviewed the clinical records of all participants and applied the human phenotype ontology (HPO) to characterize the individuals’ phenotype systematically. Rare variants’ pathogenicity were classified according to the guidelines of the American College of Medical Genetics and Genomics (ACMG). Deep clinical multi-variate data was coupled with rare variants for stratification analysis. Candidate gene identification was done by applying gene constraint metrics (i.e. pLI and "critical-exon" Genes (CEGs)) to the population data. Results: Genetic diagnosis rates were 17% (42/576) with CMA, 29.92% (38/576) with WES, and 37.13% (75/576) with combined. A greater percentage of females had pathogenic variants compared to males (p<1.79×10-6). Notably, children of consanguineous parents showed a significantly higher diagnostic yield (p<0.01) compared to those from non-consanguineous parents. On comparing diagnostic yield across tests, WES was significantly better (p<2.96×10-4) at identifying causative variants in the children of consanguineous parents (63.64%, 14/22) than CMA (13.79%, 4/29). Moreover, the yield was significantly higher for certain HPO clinical categories, including abnormal facial shape (p<3.8×10-10), GDD (p<1.32×10-9), seizure v (p<2.01×10-7), hypotonia (p<2.36×10-5) and microcephaly (p<8.17×10-4). From CMA data, we have identified 18 CEGs from focal CNV (<1Mb). Of the 18, PSMC3 was found as a candidate gene for Autism Spectrum Disorder (ASD). Moreover, we got a 2.1Mb duplication disrupting the KMT2B gene associated with intellectual disability. CMA analysis also revealed 10 variable length copy number variants (CNVs) on the 15q11-q13 imprinted locus in 10 participants. Neurodevelopmental disorders such as Angelman syndrome (AS), Prader-Willi syndrome (PWS), and 15q11-q13 duplication syndrome (Dup15q) are the 3 outcomes of genetic variations in this imprinted region. Our extensive phenotypic observations of 10 participants, revealed a range of clinical characteristics that overlap and are specific to PWS, AS, and Dup15q syndrome. Among the WES-identified pathogenic variants, 36.19% (38/105) were novel, implicating 35 unique genes. Besides primary findings, we also found 312 pathogenic variants as incidental finding in 60.8% (200/329) of participants. Of these, 25.5% (84/329) participants are at risk of having another secondary disease besides NDDs and 35.3% (116/329) were carriers of secondary recessive diseases.; 3.3% (11/329) were in one of the ACMG actionable genes (ATP7B, GAA, PMS2, SDHB and BRCA1). Long-read sequencing of seizure participants unresolved by combined test identified expanded FMR1 trinucleotide repeats. Additionally, we identified two recurrent X-linked variants in the G6PD in 3.65% (12/329) of NDD participants. These variants were absent in large population control cohorts and cohorts comprising neurodevelopmental and neuropsychiatric populations of European descendants, indicating a possible associated risk factor potentially resulting from ancient genetic drift. Conclusion: This study unveils unique clinical and genomic insights from a consanguinity-rich Bangladeshi NDD cohort that have implications for clinical genetic testing in developing nations. They underscore the need for tailored approaches considering the specific diagnostic yields of different methods and the potential for ethnic specificity in genetic risk factors, as exemplified by G6PD variants. The collection of such data is not only essential for understanding the genetic underpinnings of NDDs but also for informing strategies in precision medicine, ultimately leading to more effective interventions and management of these complex disorders. vi