Detecting The Genetic Etiologies Of Short Stature By Genome Technologies

Short stature is defined as height that is two standard deviations below the mean height for age,sex and region(less than the 3rd percentile).It is the most common reason for pediatric hopsital visit for developmental concerns.Genetic factors play a major role in determining the height of an individual.At present,clinical evaluation for short stature is limited to height measurements,routine laboratory and radiological examinations.Genetic testing for single gene disorders has very limited clinical utlility due to extensive genetic heterogeneity of short stature.A comprehensive new approach is needed in order to investigate all short stature genes in the genome.For this reason,we implemented a next generation sequencing(NGS)based assay for detecting single nucleotide variants(SNV)and small insertion/deletions,and chromosomal microarray analysis(CMA)for detecting copy number variants(CNV: deletions and duplications)in genome-wide manner.We first performed gene curation.We assembled a total of 1,276 genes by serarching public database and literature as short stature associated gene.We evaluated the evidence for both support and against the gene-disease relationship and classified genes following the ClinGen gene curation protocol.As a result,a list of 705 genes was identified as bona fide short stature disease genes.This gene list is the basis for the subsequent panel design and sequencing data analysis.Next,we performed next generation sequencing analysis for a total of 1135 short stature patients refered from 25 hospitals in China.We found 326 pathogenic variants or likely pathogenic variants in 279 patients' genomes.These variants are located in 128 genes.Of all these variants,53.4% are not previously reported.The overall diagnostic yield is 24.6%.We also identified a number of novel short stature candidate genes such as DHX8,MAP4K4,FRS2,COL27 A,etc.In addition,we tested 221 patients for copy number variation by CMA and detected pathogenic or likely pathogenic variants in 38 of them,which resulted in a diagnostic rate of 17.2%.Novel candidate short stature loci(genes)are also detected such as 4q21(HNRNPD,HNRNPDL)and 2q36(EPHA4).In this study,two genome-wide molecular diagnostic techniques,NGS and CMA,effectively detected the Mendelian genetic causes for more than 20% of short stature patients.This is by far the largest genome-wide study which revealed a comprehensive genotype and phenotype spectra in Chinese patients with short stature.The findings not only benefit the individuals for better clinical management and genetic counseling,it will also greatly facilitate the discoveries of new etiologies for short stature.