Genome sequencing(GS) has been applied in the diagnosis of global developmental delay(GDD)/intellectual disability(ID). However, the performance in those with inconclusive results from chromosomal microarray analysis(CMA) and exome sequencing(ES) is unknown. We recruited 100 pediatric GDD/ID patients from multiple sites in China from February 2018 to August 2020 for GS. Patients have received at least one genomic diagnostic test prior to enrollment. Reanalysis of CMA/ES data was performed. The yield of GS was calculated and explanations for missed diagnoses by CMA/ES were investigated. Clinical utility was assessed by interviewing the parents by phone. The overall diagnostic yield of GS was 23%. Seven families could have been solved with reanalysis of ES data. 13 families were missed by previous CMA/ES due to improper method. Three remained unsolved after ES reanalysis due to allele dropout, complex variants missed by ES, and a CNV in untranslated regions. Follow-up of the diagnosed families revealed that nine families experienced changes in clinical management, including identification of targeted treatments, cessation of unnecessary treatment, and considerations for family planning. GS demonstrated high diagnostic yield and clinical utility in this cohort of undiagnosed GDD/ID patients, detecting a wide range of variant types of different sizes in a single workflow.

This is the first study describing a cohort of Mainland China patients broaden the clinical and molecular spectrum of Phelan-McDermid syndrome (PMS) or 22q13 deletion syndrome. A total of 30 Mainland China patients were clinically and genetically evaluated. We discover that nineteen patients with 22q13.3 deletions, one patient with terminal deletions and duplications, one patient with duplications, and nine patients with SHANK3 mutations were included. Six novel heterozygous variants, c.3838_3839insGG, c.3088delC, c.3526G>T, c.3372dupC, c.3120delC and c.3942delC, were firstly reported. Besides, we demonstrated speech delay, DD/ID, ASD, hypotonia and hyperactivity were prominent clinical features. Since most reported cases used to genotype-phenotype analyses are caused by 22q13 deletions usually encompassing many genes including SHANK3, we performed genotype-phenotype analysis, and found hypotonia was 100% of cases with loss of SHANK3 alone and there was no significant difference between loss of SHANK3 alone and deletions encompass more than SHANK3 gene regarding hypotonia, DD/ID, ASD, increased pain tolerance, gait abnormalities, impulsiveness, repetitive behaviors, regression and nonstop crying which are high frequency in loss of SHANK3 alone group. This analysis improves the understanding that SHANK3 haploinsufficiency is a major contributor to the neurological phenotypes of PMS and also responsible for other important phenotypes such as hypotonia.