Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

Abstract

One Sentence Summary: Transcriptome sequencing improves the diagnostic rate for Mendelian disease in patients for whom genetic analysis has not returned a diagnosis. AbstractExome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25-50%. Here, we explore the utility of transcriptome sequencing (RNA-seq) as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to over 180 control skeletal muscle samples. We demonstrate the power of RNA-seq to validate candidate splice-disrupting mutations and to identify splice-altering variants in both exonic and deep intronic regions, yielding an overall diagnosis rate of 35%. We also report the discovery of a highly recurrent de novo intronic mutation in COL6A1 that results in a dominantly acting splice-gain event, disrupting the critical glycine repeat motif of the triple helical domain. We identify this pathogenic variant in a total of 27 genetically unsolved patients in an external collagen VI-like dystrophy cohort, thus explaining approximately 25% of patients clinically suggestive of collagen VI dystrophy in whom prior genetic analysis is negative. Overall, this study represents a large systematic application of transcriptome sequencing to rare disease diagnosis and highlights its utility for the detection and interpretation of variants missed by current standard diagnostic approaches. IntroductionThe advent of exome (WES) and whole genome (WGS) sequencing has greatly accelerated our capacity to identify variants that explain many Mendelian diseases in both known and new disease genes. While these technologies are mainstays in Mendelian disease diagnosis, their success rate for detecting causal variants is far from complete, ranging from 25-50% (1-4). The primary challenge of these genome-based diagnostics is that the capacity of WES and WGS to discover genetic variants substantially exceeds our ability to interpret their functional and clinical impact (5-7).

Genomic testing in myeloid malignancy

“…In Mendelian disorders, RNA-seq has proved a useful method to identify novel disease-associated genes, through the use of outlier expression, monoallelic expression, and splicing analyses. 28,29 Translation of RNA-seq into the clinic is challenging due to both inter-and intralaboratory technical variation in establishing appropriate thresholds. 30…”

Genetic and clinical findings in a Chinese cohort of patients with collagen VI‐related myopathies

“…Recently, a highly recurrent de novo intronic mutation in COL6A1 was discovered through RNA sequencing and explained approximately 25% of patients clinically suggestive of collagen VI-related myopathy in which prior genetic analysis is negative. Therefore, RNA sequencing is valuable to check the elusive variants missed by current standard diagnostic approaches and further study need to do to improve diagnose rate in undetermined patients 19. In our cohort, genotype-phenotype correlations have started to emerge.…”

Clinical sequencing: From raw data to diagnosis with lifetime value

“…102 In the next years, the detection of CNVs and STR expansions by appropriate HTS methods as well as the combination of DNA and transcriptome sequencing will increase the diagnostic yield. 103 Fueled by technological advances, HTS has led to the current situation in which our ability to sequence is greater than our ability to interpret the detected sequence variants. Indeed, the effects of VUS and non-exonic sequence variants pose a challenge for variant interpretation.…”