Whole-Transcriptome Analysis by RNA Sequencing for Genetic Diagnosis of Mendelian Skin Disorders in the Context of Consanguinity. (10th May 2021)

• Record Type: Journal Article
• Authors: Youssefian, Leila; Saeidian, Amir Hossein; Palizban, Fahimeh; Bagherieh, Atefeh; Abdollahimajd, Fahimeh; Sotoudeh, Soheila; Mozafari, Nikoo; Farahani, Rahele A; Mahmoudi, Hamidreza; Babashah, Sadegh; Zabihi, Masoud; Zeinali, Sirous; Fortina, Paolo; Salas-Alanis, Julio C; South, Andrew P; Vahidnezhad, Hassan; Uitto, Jouni
• Is Part Of: Clinical chemistry. Volume 67:Number 6(2021)
• Page Start: 876
• Page End: 888
• Publication Date: 2021-05-10
• Subjects: whole-transcriptome sequencing -- RNA-seq -- mutation detection -- heritable skin diseases -- epidermolysis bullosa -- familial consanguinity; Clinical chemistry -- Periodicals; Pharmaceutical chemistry -- Periodicals; Biochemistry -- Periodicals; Biochimie -- Périodiques; Diagnostics biologiques -- Périodiques; Biochemistry; Clinical chemistry; Pharmaceutical chemistry; Biochemistry; Laboratory Techniques and Procedures; Klinische chemie; Periodicals; 616.075605
• DOI: 10.1093/clinchem/hvab042
• Languages: English
• ISSNs: 0009-9147

Abstract

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-seq" could 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.