Table 2. List of most significantly associated candidate CNVRs identified from GWAS cohort.
| Cytoband | Risk allele | Intersecting genes | Potential function in cancer | CNV from Database of Genomic Variants | Previous studies (Association to cancer/ NPC) | Previous studies (Differential expression in NPC tissue)a |
|---|---|---|---|---|---|---|
| Chromosome 11q14.3 | Amp | GRM5 | Glutamatergic signalling has been shown to stimulate proliferation and migration of tumour cell lines.[42] | Yes | - Implicated in melanoma,[42] oral squamous cell carcinoma[43] | Upregulated |
| Chromosome 6p21.3 | Del | MICA, HCP5, HCG26 | Cytolytic responses of T cells and NK cells against MICA-expressing tumour cells were activated when NKG2D binds with MICA.[51] | Yes | - CNV association with several NPC study cohort[14, 47] | No differential expression for all genes. |
| Chromosome 19q13.42 | Del | LILRB3, LILRA6 | B cell receptor signalling. | Yes | - CNV associated to NPC in NPC Taiwan genome-wide study cohort[14] | No differential expression |
| Chromosome 12q14.2 | Amp | DPY19L2 | Unknown. | Yes | - Loss of heterozygosity associated with lung adenocarcinoma[52] | No differential expression |
| Chromosome 5p13.3 | Amp | GOLPH3 | Vesicular trafficking. | Yes | - Associated with various cancers e.g. lung cancer,[53] prostate cancer,[54] gastric cancer [55] | No differential expression |
| Chromosome 14q11.2 | Del | RNase3, RNase2 | Ribonuclease family | Yes | - Associated with pancreatic cancer[56] | Downregulated |
Amp (Amplification); Del (Deletion); GRM5 (Metabotropic glutamate receptor 5); MICA (MHC class I polypeptide-related sequence A); HCP5 (HLA complex 5); HCG26 (HLA complex group 26); LILRB3 (Leukocyte immunoglobulin-like receptor subfamily B member 3); LILRA6 (Leukocyte immunoglobulin-like receptor subfamily A member 6; DPY19L2 (Dpy-19-like protein 2); GOLPH3 (Golgi phosphoprotein 3); RNase3 (Ribonuclease, RNase A family, 3); RNase2 (Ribonuclease, RNase A family, 2).