Functional genomics provide key insights to improve the diagnostic yield of hereditary ataxia

Abstract

Improvements in functional genomic annotation have led to a critical mass of neurogenetic discoveries. This is exemplified in hereditary ataxia, a heterogeneous group of disorders characterised by incoordination from cerebellar dysfunction. Associated pathogenic variants in more than 300 genes have been described, leading to a detailed genetic classification partitioned by age-of-onset. Despite these advances, up to 75% of patients with ataxia remain molecularly undiagnosed even following whole genome sequencing, as exemplified in the 100,000 Genomes Project. This study aimed to understand whether we can improve our knowledge of the genetic architecture of hereditary ataxia by leveraging functional genomic annotations, and as a result, generate insights and strategies that raise the diagnostic yield. To achieve these aims, we used publicly-available multi-omics data to generate 294 genic features, capturing information relating to a gene’s structure, genetic variation, tissue-specific, cell-type-specific and temporal expression, as well as protein products of a gene. We studied these features across genes typically causing childhood-onset, adult-onset or both types of disease first individually, then collectively. This led to the generation of testable hypotheses which we investigated using whole genome sequencing data from up to 2,182 individuals presenting with ataxia and 6,658 non-neurological probands recruited in the 100,000 Genomes Project. Using this approach, we demonstrated a high short tandem repeat (STR) density within childhood-onset genes suggesting that we may be missing pathogenic repeat expansions within this cohort. This was verified in both childhood- and adult-onset ataxia patients from the 100,000 Genomes Project who were unexpectedly found to have a trend for higher repeat sizes even at naturally-occurring STRs within known ataxia genes, implying a role for STRs in pathogenesis. Using unsupervised analysis, we found significant similarities in genomic annotation across the gene panels, which suggested adult- and childhood-onset patients should be screened using a common diagnostic gene set. We tested this within the 100,000 Genomes Project by assessing the burden of pathogenic variants among childhood-onset genes in adult-onset patients and vice versa. This demonstrated a significantly higher burden of rare, potentially pathogenic variants in conventional childhood-onset genes among individuals with adult-onset ataxia. Our analysis has implications for the current clinical practice in genetic testing for hereditary ataxia. We suggest that the diagnostic rate for hereditary ataxia could be increased by removing the age-of-onset partition, and through a modified screening for repeat expansions in naturally-occurring STRs within known ataxia-associated genes, in effect treating these regions as candidate pathogenic loci.

Adaptive Long‐Read Sequencing Reveals GGC Repeat Expansion in ZFHX3 Associated with Spinocerebellar Ataxia Type 4

“…The HPA data for ZFHX3 are based on a rabbit anti‐ZFHX3 polyclonal antibody (Atlas Antibodies #HPA059353, 2,683,987). Protein expression was quantified as “not detected,” “low,” “medium,” or “high.” As several 16q‐associated ataxias have emerged, 6,9,10 we studied the genetic architecture of this region through functional genomic annotation to gain further biological insights into the region more broadly 19 . Similarly, we used functional genomic annotations to characterize the causative gene as previously described.…”

“…As several 16q-associated ataxias have emerged, 6,9,10 we studied the genetic architecture of this region through functional genomic annotation to gain further biological insights into the region more broadly. 19 Similarly, we used functional genomic annotations to characterize the causative gene as previously described. Specific to the pathogenic mechanisms of these ataxias, we used resources generated through application of Tandem Repeats Finder 20 to the human reference genome (GRCh38) in HipSTR (https://github.com/HipSTR-Tool/ HipSTR-references) 21 to create a metric of short tandem repeat (STR) density, size, number of nucleotides within each STR, and location of STRs as annotated by Ensembl v.72 22 across the entire genome.…”

“…genomic annotation of pathogenic genes has previously been shown to provide insights into the genetic architecture of ataxia and strategies to improve its diagnostic yield. 19 Through this approach, we were able to prioritize potentially pathogenic STRs in an unsolved cohort exemplified by the repeat expansion in FGF14 associated with SCA27B. 5,27 We predicted that genes harboring a high density of naturally occurring STRs are candidate loci for pathogenic repeat expansions.…”

New Horizons on the Diagnosis of Hereditary Ataxia

“…2 Day after day, we now understand the important and practical role of non-coding variants altering gene expression and causing hereditary diseases. 3 The paper by Chen Z et al 4 is an important contribution in this direction, in the field of hereditary ataxias. Although hundreds of genes have been implicated in this group of disorders by comprehensive sequencing of coding and noncoding elements, the amount of "missing heritability" is still high.…”

“…The paper by Chen Z et al 4 is an important contribution in this direction, in the field of hereditary ataxias. Although hundreds of genes have been implicated in this group of disorders by comprehensive sequencing of coding and noncoding elements, the amount of “missing heritability” is still high.…”