High Throughput Sequencing Detection And Genetic Analysis Of 90 Children With Developmental Delay

Objective:Genetic testing and analysis of 90 children with developmental delay were performed to use low depth whole genome sequencing technology(CNV-seq)based on high-throughput sequencing.Karyotype analysis results and corresponding clinical phenotypes were used as a reference to explore the correlation between pathogenic chromosomal copy number variations(CNVs)and clinical phenotypes of developmental disorder diseases,to screen the possible pathogenic candidate genes,and to find pathogenic CNVs at relatively high frequency to clarify the pathogenic cause.Whole exome sequencing(WES)was performed in some affected children with negative CNV-seq results to search for possible disease causing loci.To explore the related genetic mechanisms in children with developmental delay and provide theoretical guidance for Gene diagnosis and genetic counselling.Methods:Clinical data(including basic information,clinical phenotypes,genetic data,etc.)were collected from children who were diagnosed with developmental delay and who had undergone karyotyping at the Shanxi children’s Hospital(Shanxi maternal and child health hospital)from 2017 to 2019.Patient peripheral blood was collected for CNV-seq and the results were analyzed for pathogenicity.The results of CNV-seq were annotated using databases such as Clin Var,Decipher,OMIM,and DGV,pathogenicity of CNVs was assessed according to the ACMG,and relevant reported literature was retrieved through the Pub Med database.Whole exome sequencing(WES)was performed in a subset of affected children with negative CNV-seq results,and the results were analyzed biochemically through the National Human Genetic Resource Sharing Service Platform,in combination with clinical phenotypes,to clarify the pathogenicity of variants in affected children.Results:CNV-seq detected 90 children with developmental delay,and relatively high frequencies of pathogenic CNVs were chromosomes 7,8,and 22.Pathogenic or likely pathogenic CNVs were detected in 18 cases,and the positive CNV-seq detection rate was20%(18/90).Of these,pathogenicity was adjudicated by ACMG analysis,with 15 cases of pathogenic CNVs and 3 cases of likely pathogenic CNVs.A total of 72 patients had negative CNV-seq results,including 32 cases with variants of unknown significance(VOUS),35 cases with normal results,and 5 cases with polymorphic CNVs.Karyotyping clearly suggested a developmental disorder in 4 patients and a possible disease associated in 1 patient,all of which were confirmed by CNV-seq.After whole exome sequencing(WES)of 10 of these children with negative CNV-seq results,one patient with Wiedemann-Steiner syndrome due to a de novo nonsense variant in the KMT2 A gene was detected among those with normal results for genomic copy number variants(CNVs).Conclusion:This study confirms CNVs as an important cause of developmental delay in children and that microdeletions / microduplications larger than 1 MB have a higher probability of pathogenicity.Relatively high frequencies of pathogenic CNVs were chromosomes 7,8,and 22,and most of the microdeletion / duplication segments detected were known to be strongly associated with developmental delay disorders and candidate genes that were likely to be pathogenic were screened.CNV-seq is the first-line test for the diagnosis of this group of disorders.Compared with conventional karyotyping,CNV-seq is a higher throughput sequencing based and more efficient genetic test that detects most disorders caused by chromosomal microdeletions / microduplications.It can explain the associated clinical phenotype.In combination with whole exome sequencing(WES),testing of affected children with negative CNV-seq results should lead to timely identification of some disorders associated with developmental disabilities and their possible disease causing loci.Establishing correlations between different genomic CNVs,gene variants,and patient phenotypes will provide genetic insights into disease diagnosis and re-fertility.