A guide for the diagnosis of rare and undiagnosed disease: beyond the exome

Abstract

Rare diseases affect 30 million people in the USA and more than 300–400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25–35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.

RNA-sequencing improves diagnosis for neurodevelopmental disorders by identifying pathogenic non-coding variants and reinterpretation of coding variants

“…multidisciplinary team re-evaluation of an individual phenotype after multi-omics tests—becomes increasingly relevant in the modern genome-first diagnostic approach to NDD and was instrumental for the identification of the deep-intronic pathogenic DCC variant in our cohort (68). Altogether, accurate clinical/reverse phenotyping, DNA- and RNA-based diagnostics and functional testing complement each other and are all essential in providing a definitive diagnosis in an individual with a rare genetic disorder (69).…”

A Formative Study of the Implementation of Whole Genome Sequencing in Northern Ireland

“…Further multiomic functional analyses of rare diseases, conducted collaboratively between clinicians and researchers, following recommendations for application of PS3/BS3 ACMG criteria, is vital to fully explore phenotypically plausible variants which may not always be feasible to explore in a clinical environment [ 44 ]. Several recent studies have highlighted the power of multiomics for improving our understanding of the biological mechanisms of disease where genetics alone is insufficient, for example in common complex diseases such as hypertension and diabetes mellitus [ 45 , 46 ] as well as rare diseases [ 47 , 48 , 49 ]. A multidisciplinary, collaborative approach exploring additional variants based on prior genotype-phenotype relationships helps maximise diagnostic yield from WGS [ 50 ].…”

Clinically available testing options resulting in diagnosis in post-exome clinic at one medical center

“…Furthermore approaches could include long-read sequencing, optical genome mapping, and integration of the RNA sequencing data with DNA sequencing. Long-read sequencing will allow for repeat expansions to be evaluated that may cause human disease as well as assess haplotype phasing (Liu et al, 2020) (Marwaha et al, 2022). Optical genome mapping will allow for structural variations to be detected including aspects that are not obtained on standard microarrays balanced translocation and orientation of microduplications and deletions (Mantere et al, 2021).…”

“…RNA sequencing elucidates the effect of a DNA variant allowing for pathogenicity to be further assessed (Lee et al, 2020). Using these tools clinically increases the chance of a diagnosis (Marwaha et al, 2022). Other approaches can include research analysis pipelines, functional assays to assess the effect of candidate variants, and RNA sequencing.…”