Specific HLA Class I and II alleles are associated with a higher risk for tumor formation in Neurofibromatosis type 1

Neurofibromatosis type 1 (NF1) is a common autosomal dominant genetic tumor predisposition syndrome.1 NF1 patients display remarkable phenotypic variability, even within families carrying the same NF1 mutation.2 With few exceptions, the identification of specific genotype-phenotype correlations has remained elusive.3-6 We utilized RNA-seq data and direct DNA sequencing to determine HLA genotypes for individuals with NF1-associated high-grade glioma (HGG, n=25), low-grade glioma (LGG, n=79), and malignant peripheral nerve sheath tumors (MPNST, n=105). Odds ratios (OR), binomial p-values and false discovery values were calculated by comparing observed carrier frequencies against expected frequencies derived from ethnicity-matched population data. We find that specific HLA class I and II alleles are associated with different NF1 tumor types. For example, HLA-B*40:02 is significantly associated with NF1-MPNST (OR=3.71, p=0.001, Q=0.02), increasing the lifetime risks for MPNST from 10% to about 29%. The relative cancer risk for an individual in the general population carrying a risk allele can be high, however, that individuals absolute risk for cancer typically remains very low. In contrast, individuals that carry a risk allele and are also burdened with a tumor predisposition syndrome will have a substantially higher absolute risk to develop a tumor, simply because they start at a higher baseline susceptibility for tumors. The identification of HLA-risk alleles for NF1 tumor development is therefore important, as it will allow for a risk-adapted screening or more aggressive treatment of individuals with a specific HLA haplotype. If confirmed, this study will thus improve clinical care and potential outcomes of individuals with NF1.