Whole-Transcriptome Analysis by Rna Sequencing for Genetic Diagnosis of Mendelian Skin Disorders in the Context of Consanguinity Publisher Pubmed



Youssefian L^{1, 2, 3} ; Saeidian AH^{1, 2, 3} ; Palizban F⁴ ; Bagherieh A⁵ ; Abdollahimajd F⁶ ; Sotoudeh S⁷ ; Mozafari N⁶ ; Farahani RA⁸ ; Mahmoudi H⁹ ; Babashah S⁵ ; Zabihi M¹⁰ ; Zeinali S¹⁰ ; Fortina P^{11, 12} ; Salasalanis JC¹³ Show All Authors Show Affiliations
Source: Clinical Chemistry Published:2021

Abstract

Background: Among the approximately 8000 Mendelian disorders, >1000 have cutaneous manifestations. In many of these conditions, the underlying mutated genes have been identified by DNA-based techniques which, however, can overlook certain types of mutations, such as exonic-synonymous and deep-intronic sequence variants. Whole-transcriptome sequencing by RNA sequencing (RNA-seq) can identify such mutations and provide information about their consequences. Methods: We analyzed the whole transcriptome of 40 families with different types of Mendelian skin disorders with extensive genetic heterogeneity. The RNA-seq data were examined for variant detection and prioritization, pathogenicity confirmation, RNA expression profiling, and genome-wide homozygosity mapping in the case of consanguineous families. Among the families examined, RNA-seq was able to provide information complementary to DNA-based analyses for exonic and intronic sequence variants with aberrant splicing. In addition, we tested the possibility of using RNA-seq as the first-tier strategy for unbiased genome-wide mutation screening without information from DNA analysis. Results: We found pathogenic mutations in 35 families (88%) with RNA-seq in combination with other next-generation sequencing methods, and we successfully prioritized variants and found the culprit genes. In addition, as a novel concept, we propose a pipeline that increases the yield of variant calling from RNA-seq by concurrent use of genome and transcriptome references in parallel. Conclusions: Our results suggest that clinical RNA-seqcould serve as a primary approach for mutation detection in inherited diseases, particularly in consanguineous families, provided that tissues and cells expressing the relevant genes are available for analysis. © 2021 American Association for Clinical Chemistry. All rights reserved.