Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report

UniVar: A variant interpretation platform enhancing rare disease diagnosis through robust filtering and unified analysis of SNV, INDEL, CNV and SV

BACKGROUND

Interpreting the pathogenicity of genetic variants associated with rare diseases is a laborious and time-consuming endeavour. To streamline the diagnostic process and lighten the burden of variant interpretation, it is crucial to automate variant annotation and prioritization. Unfortunately, currently available variant interpretation tools lack a unified and comprehensive workflow that can collectively assess the clinical significance of these types of variants together: small nucleotide variants (SNVs), small insertions/deletions (INDELs), copy number variants (CNVs) and structural variants (SVs).

RESULTS

The Unified Variant Interpretation Platform (UniVar) is a free web server tool that offers an automated and comprehensive workflow on annotation, filtering and prioritization for SNV, INDEL, CNV and SV collectively to identify disease-causing variants for rare diseases in one interface, ensuring accessibility for users even without programming expertise. To filter common CNVs/SVs, a diverse SV catalogue has been generated, that enables robust filtering of common SVs based on population allele frequency. Through benchmarking our SV catalogue, we showed that it is more complete and accurate than the state-of-the-art SV catalogues. Furthermore, to cope with those patients without detailed clinical information, we have developed a novel computational method that enables variant prioritization from gene panels. Our analysis shows that our approach could prioritize pathogenic variants as effective as using HPO terms assigned by clinicians, which adds value for cases without specific clinically assigned HPO terms. Lastly, through a practical case study of disease-causing compound heterozygous variants across SNV and SV, we demonstrated the uniqueness and effectiveness in variant interpretation of UniVar, edging over any existing interpretation tools.

CONCLUSIONS

UniVar is a unified and versatile platform that empowers researchers and clinicians to identify and interpret disease-causing variants in rare diseases efficiently through a single holistic interface and without a prerequisite for HPO terms. It is freely available without login and installation at https://univar.live/.

The natural history of ataxia-telangiectasia (A-T): A systematic review

BACKGROUND

Ataxia-telangiectasia is an autosomal recessive, multi-system, and life-shortening disease caused by mutations in the ataxia-telangiectasia mutated gene. Although widely reported, there are no studies that give a comprehensive picture of this intriguing condition.

OBJECTIVES

Understand the natural history of ataxia-telangiectasia (A-T), as reported in scientific literature.

SEARCH METHODS

107 search terms were identified and divided into 17 searches. Each search was performed in PubMed, Ovid SP (MEDLINE) 1946-present, OVID EMBASE 1980 -present, Web of Science core collection, Elsevier Scopus, and Cochrane Library.

SELECTION CRITERIA

All human studies that report any aspect of A-T.

DATA COLLECTION AND ANALYSIS

Search results were de-duplicated, data extracted (including author, publication year, country of origin, study design, population, participant characteristics, and clinical features). Quality of case-control and cohort studies was assessed by the Newcastle-Ottawa tool. Findings are reported descriptively and where possible data collated to report median (interquartile range, range) of outcomes of interest.

MAIN RESULTS

1314 cases reported 2134 presenting symptoms. The most common presenting symptom was abnormal gait (1160 cases; 188 studies) followed by recurrent infections in classical ataxia-telangiectasia and movement disorders in variant ataxia-telangiectasia. 687 cases reported 752 causes of death among which malignancy was the most frequently reported cause. Median (IQR, range) age of death (n = 294) was 14 years 0 months (10 years 0 months to 23 years 3 months, 1 year 3 months to 76 years 0 months).

CONCLUSIONS

This review demonstrates the multi-system involvement in A-T, confirms that neurological symptoms are the most frequent presenting features in classical A-T but variants have diverse manifestations. We found that most individuals with A-T have life limited to teenage or early adulthood. Predominance of case reports, and case series demonstrate the lack of robust evidence to determine the natural history of A-T. We recommend population-based studies to fill this evidence gap.

Unusual clinical manifestations and predominant stopgain ATM gene variants in a single centre cohort of ataxia telangiectasia from North India

Germline ATM gene variations result in phenotypic heterogeneity characterized by a variable degree of disease severity. We retrospectively collected clinical, genetic, and immunological data of 26 cases with A-T. Clinical manifestations included oculocutaneous telangiectasia (100%), ataxia (100%), fever, loose stools or infection (67%), cerebellar atrophy (50%), nystagmus (8%), dysarthria (15.38%), and visual impairment (8%). Genetic analysis confirmed ATM gene variations in 16 unrelated cases. The most common type of variation was stopgain variants (56%). Immunoglobulin profile indicated reduced IgA, IgG, and IgM in 94%, 50%, and 20% cases, respectively. T cell lymphopenia was observed in 80% of cases among those investigated. Unusual presentations included an EBV-associated smooth muscle tumour located in the liver in one case and Hyper IgM syndrome-like presentation in two cases. Increased immunosenescence was observed in T-cell subsets (CD4+CD57+ and CD8+CD57+). T-cell receptor excision circles (TRECs) were reduced in 3/8 (37.50%) cases.