Journal Article

Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

Alqahtani, Maha, Abdulwahab, Firdous, AlSheddi, Tarfa, AlObeid, Eman, Helaby, Rana, Monies, Dorota, Maddirevula, Sateesh, Alsaleem, Badr, Umarov, Ramzan, Patel, Nisha, Shamseldin, Hanan E., Ewida, Nour, Alsagheir, Afaf, Al Ali, Hatoon, Gao, Xin, AlAli, Maha, Alhashem, Amal, Kuwahara, Hiroyuki, Alzahrani, Fatema, Alhebbi, Hamoud, Alkuraya, Fowzan S., Hashem, Mais, Alenazi, Mona, Hanna, Nadine, Derar, Nada, Alsaif, Hessa S., Wali, Sami, Ibrahim, Niema

2020

Overview

Background At least 50% of patients with suspected Mendelian disorders remain undiagnosed after whole-exome sequencing (WES), and the extent to which non-coding variants that are not captured by WES contribute to this fraction is unclear. Whole transcriptome sequencing is a promising supplement to WES, although empirical data on the contribution of RNA analysis to the diagnosis of Mendelian diseases on a large scale are scarce. Results Here, we describe our experience with transcript-deleterious variants (TDVs) based on a cohort of 5647 families with suspected Mendelian diseases. We first interrogate all families for which the respective Mendelian phenotype could be mapped to a single locus to obtain an unbiased estimate of the contribution of TDVs at 18.9%. We examine the entire cohort and find that TDVs account for 15% of all “solved” cases. We compare the results of RT-PCR to in silico prediction. Definitive results from RT-PCR are obtained from blood-derived RNA for the overwhelming majority of variants (84.1%), and only a small minority (2.6%) fail analysis on all available RNA sources (blood-, skin fibroblast-, and urine renal epithelial cells-derived), which has important implications for the clinical application of RNA-seq. We also show that RNA analysis can establish the diagnosis in 13.5% of 155 patients who had received “negative” clinical WES reports. Finally, our data suggest a role for TDVs in modulating penetrance even in otherwise highly penetrant Mendelian disorders. Conclusions Our results provide much needed empirical data for the impending implementation of diagnostic RNA-seq in conjunction with genome sequencing.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Bioinformatics / Biomedical and Life Sciences / Blood / Clear cell-type renal cell carcinoma / computer simulation / Diagnosis / Disease / Epithelial cells / epithelium / Evolutionary Biology / Family medical history / Fibroblasts / Gene expression / genome / Genomes / Human Genetics / Life Sciences / loci / Mapping / Mendelian / Microbial Genetics and Genomics / Mutation / Negative WES / penetrance / phenotype / Phenotypes / Plant Genetics and Genomics / Polymerase chain reaction / prediction / Proteins / Ribonucleic acid / RNA / RNA-based diagnostics / sequence analysis / Skin / Transcription / transcriptome / Transcriptomics / urine / Whole genome sequencing