High-Resolution HLA Typing by Next-Generation Sequencing and Risk of Follicular Lymphoma
Authors: Skibola Christine F. , Conde Lucia , Akers Nicholas K , Smith Martyn T. , Bracci Paige M 
Published: October 2019

Abstract
Abstract 5092
The molecular basis of follicular lymphoma (FL) has been fairly well characterized, although its root causes remain less clear. Recently, in two genome-wide association studies in European-Americans, we identified novel genetic susceptibility loci for FL, narrowed down to two independent regions on chromosome 6p21.3 in the major histocompatibility complex (MHC) (Skibola et al., Nat Gen 41(8):873-5., 2009; Conde et al., Nat Gen 42(8):661-4, 2010). The first susceptibility locus, rs6457327 (combined allelic p-value=4.7 × 10-11 in 645 patients and 3,377 controls), is part of a 26-kb region of high linkage disequilibrium (LD) in the MHC Class 1 region at 6p21.33 in close proximity to the psoriasis susceptibility region 1 (PSORS1). In a second locus in the MHC Class II region at 6p21.32, upstream of HLA-DQB1, two SNPs in high LD, rs10484561 and rs7755224, were associated with 2-fold increased risks for FL in 1,465 patients and 6,958 controls (combined p-values=1.12×10-29, 2.00×10-19). Using tag SNPs as surrogates for HLA allelotypes, the latter loci were found to be part of an extended haplotype that includes HLA-DRB1*0101-HLA-DQA1*0101-HLA-DQB1*0501 and that was associated with increased FL risk [odds ratio (OR) = 2.07, 95% confidence interval (CI) = 1.40–3.06]. To confirm these findings, we determined HLA-DQB1 allelotypes in a subset of 265 FL cases and 757 controls. We corroborated the positive association between FL and the HLA-DQB1*05 allele group (OR=1.56, 95% CI 1.22–1.99; adjusted p-value=7.7×10-3), and identified an allele group inversely associated with FL risk, HLA-DQB1*06 (OR=0.53, 95% CI 0.40–0.69; adjusted p-value=1.98×10-5).
To gain further insight into the role of HLA alleles in FL susceptibility, high-resolution HLA typing by next-generation sequencing of the HLA class I (A, B, C) and Class II (DRB1/3/4/5, DQA1, DQB1, DPB1) genes is underway in 222 FL patients and 220 sex- and age-matched controls. HLA typing is being conducted by sequencing the exons that code for the region of the peptide-binding groove of the HLA molecule (exon 2 for the Class II genes, HLA-DQA1, -DQB1, -DRB1, -DRB1/3/4/5 and -DPB1, and exons 2–4 for the Class I genes HLA-A, HLA-B and HLA-C) as described previously (Bentley, G et al. Tissue Antigens. 74:393-403, 2009). Allele and haplotype frequencies for cases and controls will be estimated using the iterative Expectation-Maximization (EM) algorithm implemented in the Pypop software (Lancaster et al. Tissue Antigens. 69 Suppl 1:192-197, 2007). Statistical significance of estimated ORs and 95% CIs, and differences in the distribution of the alleles or haplotypes between cases and controls will be assessed using a two-tailed Fisher's exact test.
To our knowledge, this study will present the highest resolution (up to 8-digit) HLA typing reported in a sample of European-Americans, and is an important next step to determine the role of MHC genetic variation in the pathogenesis of FL.

Disclosures:
No relevant conflicts of interest to declare.