Potential of RNA sequencing for ADA-SCID diagnosis highlighted
Published Date: 17/7/19Access Full Text Article
medwireNews: RNA sequencing could serve as a complementary modality to standard DNA testing to aid the molecular diagnosis of adenosine deaminase-deficient severe combined immunodeficiency (ADA-SCID), suggest UK researchers.
They describe the case of a 7-year-old girl who was diagnosed with late-onset ADA deficiency caused by two previously unreported mutations, one of which was only identified after RNA-based analysis.
The child had recurrent chest infections over a 12-month period that led to a referral to the paediatric immunology clinic. She had generally been in good health during childhood, with no complications during immunisations or special educational needs, and no family history indicative of a primary immunodeficiency.
Immunological investigations revealed lymphopenia across all subsets, and records indicated that the child had been lymphopenic on at least two occasions in the past 18 months, with lymphocyte levels of 0.2 and 0.3×109/L versus reference values in the range of 1.5–4.5×109/L.
Sinisa Savic (St James’s University Hospital, Leeds) and co-authors therefore suspected a combined immunodeficiency, and used clinical exome sequencing to determine the presence of mutations in a panel of 37 genes associated with primary immunodeficiency disorders.
The analysis identified a heterozygous missense variant in exon 10 of ADA that was not present in the population controls, and subsequent biochemical analysis showed “an almost complete loss of ADA activity”, with the corresponding presence of deoxyadenosine triphosphate (245 μmol/L), deoxyadenosine diphosphate (19 μmol/L) and deoxyadenosine monophosphate (3 μmol/L).
The detected variant – c.961G>A (Glu321Lys) – was found to be of paternal origin, but “complete molecular genetic characterisation of the disorder could not be confirmed in the absence of a second pathogenic mutation”, say the study authors.
This prompted them to use whole-transcriptome RNA sequencing to provide additional information, and the results were consistent with “monoallelic ADA expression”, Savic and colleagues write in the Journal of Clinical Immunology.
Subsequent whole-genome sequencing showed the presence of a 3.2 kb deletion that included exon 1 of ADA in the maternal DNA, and the authors were able to confirm that “the deletion-containing allele was inherited by the proband from her mother.”
They note that “[t]he complete molecular characterisation of both pathogenic alleles provides the possibility to determine carrier status amongst the extended family and prenatal diagnosis in future pregnancies.”
Savic et al highlight “the utility of RNA as a complementary specimen type to aid molecular diagnosis”, and they add: “To enable its routine adoption and to upskill the molecular diagnostic workforce, we support the view that cases with an unresolved second pathogenic mutation should be prioritised for RNA-based analysis.”
In terms of the patient’s clinical state, the authors report that she responded to treatment with pegylated-ADA and went onto receive a successful haematopoietic stem cell transplantation.
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