Pitfalls in the diagnosis of apparent homozygous mutations: two cases of IL10RA deficiency inflammatory bowel disease and a literature review.

Background: In East Asia, IL10RA is the predominant pathogenic gene in patients with very early-onset inflammatory bowel disease (VEO-IBD), frequently characterised by refractory diarrhoea and severe perianal disease, resulting in elevated death rates. IL10RA-deficient IBD, an autosomal recessive genetic disorder, has been documented to be inherited through the conventional compound heterozygous or homozygous mutation patterns from both parents. We present two cases with apparent homozygosity resulting from distinct causes, both of which seem homozygous on the genetic map. Further investigation reveals that detecting hidden genetic patterns is essential for accurate diagnosis, genetic counselling, and disease mechanism analysis.

Methods: Peripheral blood samples were collected from two patients and their parents. Whole-exome sequencing (WES), Sanger sequencing, Comparative genomic hybridisation (CGH) and SNP array, Capture-based CNV (CapCNV) analysis, and real-time quantitative PCR (qPCR) were employed to investigate the genetic mechanisms and variants within the families. Both patients were followed up, and descriptive analyses were performed to characterise their clinical phenotypes, biochemical parameters, endoscopic findings, and intestinal histopathology. Multiple databases were systematically searched to review all cases of IBD with large IL10RA deletions.

Results: Two families underwent WES, and a homozygous mutation was identified in the IL10RA gene on chromosome 11 in both families. In patient 1, pedigree analysis, CGH and SNP 4 × 180 K microarray testing identified paternal uniparental diploidy (c.301C > T/11q12.3-11q25del) [upd (11) pat] on chromosome 11. Patient 2 had compound heterozygosity (c. 299 T > G/exon2_3del), comprising a point mutation and an overlapping exon deletion mutation in IL10RA, as determined using familial analysis, Sanger sequencing, CapCNV analysis, and qPCR validation. In addition, the study systematically reviewed 15 cases of IBD patients with large deletions in the IL10RA gene from the literature.

Conclusions: This is the first description of two cases of apparent homozygosity in IL10RA. This report emphasizes the importance of optimizing the genetic analysis workflow, especially when there is doubt about the initial whole exome sequencing results.