Meta-GWAS identifies the heritability of acute radiation-induced toxicities in head and neck cancer.
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Naderi Elnaz, Schack Line M H, Welsh Ceilidh, Sim Adelene Y L, Aguado-Barrera Miguel E, Dudding Tom, Summersgil Holly, Martínez-Calvo Laura, Ong Enya H W, Odding Yasmin, Varela-Pazos Ana, Steenbakkers Roel J H M, Crijns Anne P G, Jena Rajesh, Pring Miranda, Dennis Joe, Lobato-Busto Ramón, Alsner Jan, Ness Andy, Nutting Christopher, Thomson David J, Gómez-Caamaño Antonio, Eriksen Jesper G, Thomas Steve J, Bates Amy M, Overgaard Jens, Cascallar-Caneda Luis M, Duprez Fréderic, Barnett Gillian C, Dorling Leila, Chua Melvin L K, Vega Ana, West Catharine M L, Langendijk Johannes A, Nicolaj Andreassen Christian, Alizadeh Behrooz Z, On the behalf of the Radiogenomics Consortium
Аннотация
MATERIALS AND METHODS: We performed the largest meta-GWAS of seven European cohorts (n = 4,042). Patients were scored weekly during radiotherapy for acute RITs including dysphagia, mucositis, and xerostomia. We analyzed the effect of variants on the average burden (measured as area under curve, AUC) per each RIT, and standardized total average acute toxicity (STATacute) score using a multivariate linear regression. We tested suggestive variants (p < 1.0x10-5) in discovery set (three cohorts; n = 2,640) in a replication set (four cohorts; n = 1,402). We meta-analysed all cohorts to calculate RITs specific SNP-based heritability, and effect of polygenic risk scores (PRSs), and genetic correlations among RITS.
RESULTS: From 393 suggestive SNPs identified in discovery set; 37 were nominally significant (preplication < 0.05) in replication set, but none reached genome-wide significance (pcombined < 5 × 10-8). In-silico functional analyses identified "3'-5'-exoribonuclease activity" (FDR = 1.6e-10) for dysphagia, "inositol phosphate-mediated signalling" for mucositis (FDR = 2.20e-09), and "drug catabolic process" for STATacute (FDR = 3.57e-12) as the most enriched pathways by the RIT specific suggestive genes. The SNP-based heritability (±standard error) was 29 ± 0.08 % for dysphagia, 9 ± 0.12 % (mucositis) and 27 ± 0.09 % (STATacute). Positive genetic correlation was rg = 0.65 (p = 0.048) between dysphagia and STATacute. PRSs explained limited variation of dysphagia (3 %), mucositis (2.5 %), and STATacute (0.4 %).
CONCLUSION: In HNC patients, acute RITs are modestly heritable, sharing 10 % genetic susceptibility, when PRS explains < 3 % of their variance. We identified numerus suggestive SNPs, which remain to be replicated in larger studies.