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Published on: August 3, 2011
Targeted RNAseq Improves Clinical Diagnosis of Very Early-Onset Pediatric Immune Dysregulation
Kiera Berger1, Dalia Arafat1, Shanmuganathan Chandrakasan2
1School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
Abstract:
Despite increased use of whole exome sequencing (WES) for the clinical analysis of rare disease, overall diagnostic yield for most disorders hovers around 30%. Previous studies of mRNA have succeeded in increasing diagnoses for clearly defined disorders of monogenic inheritance. We asked if targeted RNA sequencing could provide similar benefits for primary immunodeficiencies (PIDs) and very early-onset inflammatory bowel disease (VEOIBD), both of which are difficult to diagnose due to high heterogeneity and variable severity. We performed targeted RNA sequencing of a panel of 260 immune-related genes for a cohort of 13 patients (seven suspected PID cases and six VEOIBD) and analyzed variants, splicing, and exon usage. Exonic variants were identified in seven cases, some of which had been previously prioritized by exome sequencing. For four cases, allele specific expression or lack thereof provided additional insights into possible disease mechanisms. In addition, we identified five instances of aberrant splicing associated with four variants. Three of these variants had been previously classified as benign in ClinVar based on population frequency. Digenic or oligogenic inheritance is suggested for at least two patients. In addition to validating the use of targeted RNA sequencing, our results show that rare disease research will benefit from incorporating contributing genetic factors into the diagnostic approach.
Insights
Targeted RNA sequencing improves rare disease diagnosis by analyzing gene expression and splicing. This method offers new insights for primary immunodeficiencies and inflammatory bowel disease cases, enhancing diagnostic yield.
Area of Science:
- Genetics
- Immunology
- Gastroenterology
Background:
- Whole exome sequencing (WES) has a diagnostic yield of approximately 30% for rare diseases.
- mRNA studies have improved diagnoses for monogenic disorders.
- Primary immunodeficiencies (PIDs) and very early-onset inflammatory bowel disease (VEOIBD) are challenging to diagnose due to genetic heterogeneity.
Purpose of the Study:
- To evaluate the utility of targeted RNA sequencing for diagnosing PIDs and VEOIBD.
- To assess the impact of analyzing variants, splicing, and exon usage on diagnostic yield.
Main Methods:
- Targeted RNA sequencing of 260 immune-related genes was performed on 13 patients (7 suspected PID, 6 VEOIBD).
- Analysis included exonic variants, allele-specific expression, and exon usage.
- Variants were cross-referenced with existing databases like ClinVar.
Main Results:
- Exonic variants were found in 7 cases, with some previously identified by WES.
- Allele-specific expression provided insights into disease mechanisms in 4 cases.
- Five instances of aberrant splicing were linked to 4 variants, including 3 previously classified as benign.
- Digenic or oligogenic inheritance was suggested in at least 2 patients.
Conclusions:
- Targeted RNA sequencing is a valuable tool for rare disease diagnosis, particularly for PIDs and VEOIBD.
- Incorporating RNA sequencing enhances diagnostic yield by revealing splicing abnormalities and complex inheritance patterns.
- This approach aids in understanding disease mechanisms and identifying previously overlooked genetic factors.
