Molecular diagnostics of Mendelian disorders via combined DNA and RNA sequencing

Holger Prokisch

doi:10.1007/s11825-019-0241-7

Abstract

Abstract The diagnostic yield in rare disorders is currently less than 50% although sequencing technologies in use are able to detect the majority of possible variants in our genome. The diagnostic gap is in part due to limitations in prioritizing and interpreting identified variants. The integration of functional data, such as transcriptomics, is emerging as a powerful complementary tool in diagnostics. It is able to quantify aberrant splicing, validate nonsense-mediated mRNA decay for potential loss-of-function variants, identify mono-allelically expressed variants, and help prioritize variants not predicted to change the encoded protein. Moreover, RNA-sequencing has been validated as a tool for the discovery of pathogenic variants in novel Mendelian disease genes. As RNA sequencing provides complementary information to DNA sequencing and can easily be established in addition to DNA sequencing, it has great potential for implementation as a routine tool for improving molecular diagnosis.

Highlights

The diagnostic yield in rare disorders is currently less than 50% sequencing technologies in use are able to detect the majority of possible variants in our genome
In a patient with a mitochondrial disorder, we found homozygous, protein-truncating variants in LYRM7 and MTO1, two genes encoding essential mitochondrial proteins
Aberrant expression, identified as gene expression outliers, occurs when expression is outside their physical range and usually implies impaired gene expression of both alleles with decreased expression levels of less than 50% of the controls

Summary

Limitations in DNA variant interpretation

A definitive diagnosis is based on the discovery of known pathogenic variant(s) in a patient with a specific clinical presentation similar to the clinical picture reported multiple times, usually listed in the disease-variant database ClinVar [9]. This is not the common situation, neither on a variant nor on a phenotype level. Identification of possible protein-truncating variants in genes for which nontruncating/in-frame pathogenic loss-offunction variants are known can already be challenging. A recent systematic study shows that exons present only in tissue specific isoforms may not be essential for protein function [5]. Data describing the functional consequences on the molecular level are required to advance diagnostics

Practical conclusion

Findings

Compliance with ethical guidelines