Brief Report: whole-exome sequencing revealing somatic NLRP3 mosaicism in a patient with chronic infantile neurologic, cutaneous, articular syndrome

Abstract

Objective: To identify the genetic cause of chronic infantile neurologic, cutaneous, articular syndrome (CINCA syndrome) using whole-exome sequencing in a child who had typical clinical features but who was NLRP3 mutation negative based on conventional Sanger sequencing.

Methods: We performed whole-exome sequencing on DNA from peripheral blood, using Illumina TruSeq Exome capture and the HiSeq sequencing platform. Exome data were analyzed in the Galaxy Web-based suite. Whole-exome sequencing findings were confirmed by massively parallel sequencing.

Results: Analysis of variants in known autoinflammatory genes led to the identification of the pathogenic p.F556L NLRP3 missense mutation in 17.7% of Illumina reads (25 of 141). No new candidate genes were identified. Massively parallel sequencing of DNA from peripheral blood (performed in duplicate) unequivocally confirmed the presence of this mutation in 14.5% of alleles. Reexamination of the original Sanger chromatograms revealed a small peak at nucleotide position c.1698 corresponding to the mutated allele. This had initially been regarded as background noise, but in retrospect is completely consistent with somatic mosaicism for the p.F556L NLRP3 mutation in this child with CINCA syndrome.

Conclusion: This is the first description of somatic NLRP3 mosaicism detected using whole-exome sequencing in a "mutation-negative" patient with CINCA syndrome. Our findings suggest that whole-exome sequencing could be an important diagnostic tool for detecting somatic mosaicism, as well as for the discovery of novel causative gene mutations, in patients with clinical features of cryopyrin-associated periodic syndromes who are NLRP3 mutation negative by conventional sequencing. This approach could also be applicable to patients with other autosomal-dominant autoinflammatory diseases characterized by gain-of-function mutations who are mutation negative by conventional Sanger sequencing.

Figure 1

Clinical features of chronic infantile neurologic, cutaneous, articular syndrome in the patient. A, Persistent urticaria-like skin rash despite canakinumab treatment (4 mg/kg every 8 weeks). At the time this photograph was taken (when the patient was 7 years old), the cryopyrin-associated periodic syndromes Disease Activity Score (DAS) was 11 of 20, and the serum amyloid A (SAA) level was elevated at 154 mg/liter (normal <10). B, Improvement of the skin rash 8 weeks after the dosage of canakinumab was increased to 8 mg/kg every 8 weeks. At the time this photograph was taken, the DAS had declined to 1 of 20, but the SAA level was still elevated at 118 mg/liter. C, Patellar and tibial bony overgrowth, seen on a radiograph obtained when the patient was 7 years old.

Figure 2

A, Illumina data from the mapped reads as visualized in Integrative Genomics Viewer, providing evidence of the presence of c.1698C>A transversion. B, Sanger chromatograms showing the subtle peak for the mutated A allele at the c.1698 position in the patient sample (arrow), but absent in a healthy control sample.