Neurofibromatosis 1 (NF1) gene testing reveals rising variant allele fraction as an early warning sign of juvenile myelomonocytic leukemia.

Abstract

Molecular analysis of the NF1 gene is part of the diagnostic criteria for neurofibromatosis type 1 (NF1) and is particularly useful in young children who do not yet exhibit sufficient clinical signs for diagnosis. Juvenile myelomonocytic leukemia (JMML) is a rare pediatric myelodysplastic/myeloproliferative neoplasm that can be associated with NF1. Here, we describe a child in whom NF1 testing performed for diagnostic purposes revealed an unexpectedly high variant allele fraction in DNA isolated from peripheral blood. Multiplex ligation-dependent probe amplification (MLPA) targeting exon 25 (legacy numbering exon 19b) of the NF1 gene showed an average dosage score of 0.236 across two runs, consistent with reduced probe binding and suggesting loss of one allele in the majority of circulating leukocytes. Sanger sequencing of exon 25 identified the pathogenic variant c.3295_3298dup, predicted to cause a frameshift leading to a truncated protein, p.(Ser1100Ter). Analysis of DNA from buccal mucosa detected the same variant at an allele fraction of 59%, consistent with a constitutionally heterozygosity. During follow-up, the variant allele fraction in blood increased to 94%, indicating loss of heterozygosity consistent with acquired uniparental disomy, the most common mechanism underlying JMML in patients with NF1. The diagnosis of JMML was confirmed in peripheral blood and bone marrow samples while the child remained clinically asymptomatic. This case highlights the importance of genetic testing in establishing an NF1 diagnosis in young children. An increasing variant allele fraction may signal an emerging JMML, and early testing can provide a critical time window for timely and effective treatment.