1. Multi-ancestry genome-wide association study of 4069 children with glioma identifies 9p21.3 risk locus
- Author
-
Foss-Skiftesvik, Jon, Li, Shaobo, Rosenbaum, Adam, Hagen, Christian Munch, Stoltze, Ulrik Kristoffer, Ljungqvist, Sally, Hjalmars, Ulf, Schmiegelow, Kjeld, Morimoto, Libby, de Smith, Adam J, Mathiasen, René, Metayer, Catherine, Hougaard, David, Melin, Beatrice, Walsh, Kyle M, Bybjerg-Grauholm, Jonas, Dahlin, Anna M, and Wiemels, Joseph L
- Subjects
Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Human Genome ,Cancer Genomics ,Cancer ,Pediatric ,Prevention ,Neurosciences ,Genetics ,Brain Cancer ,Rare Diseases ,Pediatric Cancer ,Brain Disorders ,Aetiology ,2.1 Biological and endogenous factors ,Humans ,Child ,Genome-Wide Association Study ,Glioma ,Genotype ,Genetic Predisposition to Disease ,RNA ,Long Noncoding ,Astrocytoma ,Polymorphism ,Single Nucleotide ,Childhood brain tumors ,genetic susceptibility ,glioma ,GWAS ,pediatric neuro-oncology ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
BackgroundAlthough recent sequencing studies have revealed that 10% of childhood gliomas are caused by rare germline mutations, the role of common variants is undetermined and no genome-wide significant risk loci for pediatric central nervous system tumors have been identified to date.MethodsMeta-analysis of 3 population-based genome-wide association studies comprising 4069 children with glioma and 8778 controls of multiple genetic ancestries. Replication was performed in a separate case-control cohort. Quantitative trait loci analyses and a transcriptome-wide association study were conducted to assess possible links with brain tissue expression across 18 628 genes.ResultsCommon variants in CDKN2B-AS1 at 9p21.3 were significantly associated with astrocytoma, the most common subtype of glioma in children (rs573687, P-value of 6.974e-10, OR 1.273, 95% CI 1.179-1.374). The association was driven by low-grade astrocytoma (P-value of 3.815e-9) and exhibited unidirectional effects across all 6 genetic ancestries. For glioma overall, the association approached genome-wide significance (rs3731239, P-value of 5.411e-8), while no significant association was observed for high-grade tumors. Predicted decreased brain tissue expression of CDKN2B was significantly associated with astrocytoma (P-value of 8.090e-8).ConclusionsIn this population-based genome-wide association study meta-analysis, we identify and replicate 9p21.3 (CDKN2B-AS1) as a risk locus for childhood astrocytoma, thereby establishing the first genome-wide significant evidence of common variant predisposition in pediatric neuro-oncology. We furthermore provide a functional basis for the association by showing a possible link to decreased brain tissue CDKN2B expression and substantiate that genetic susceptibility differs between low- and high-grade astrocytoma.
- Published
- 2023