Table 2. Candidates for tumor PAI: recurrent SCNA loci from TCGA that overlap cancer-associated SNPs (NHGRI GWAS Catalog) identified in matching tumor types.
| SCNA type | TCGA Peak Name | Cytoband | Chromosome* | Start | End | Size (bp) | Heritable SNP association cancer type** | SCNA tumor types ‡ |
|---|---|---|---|---|---|---|---|---|
| Amplifications | TERC | 3q26.2 | 3 | 169389459 | 169490555 | 101096 | Bladder; glioma; melanoma; multiple myeloma | BLCA, LUAD, LUSC, UCEC |
| FGFR3 | 4p16.3 | 4 | 1778797 | 1817427 | 38630 | Bladder | BLCA, GBM, OV, UCEC | |
| TERT | 5p15.33 | 5 | 1287704 | 1300024 | 12320 | Basal cell carcinoma; bladder; breast; lung adenocarcinoma; glioma; melanoma; prostate; testicular germ cell | BLCA, CRC, GBM, HNSC, LUAD, LUSC, OV, UCEC | |
| EGFR | 7p11.2 | 7 | 55075808 | 55093954 | 18146 | Glioma | BLCA, BRCA, GBM, HNSC, LUAD, LUSC | |
| MYC | 8q24.21 | 8 | 128739772 | 128762863 | 23091 | Bladder; breast; CLL; CRC; ovarian; prostate; renal cell carcinoma | BLCA, BRCA, GBM, KIRC, OV, UCEC | |
| CCND1 | 11q13.3 | 11 | 69464719 | 69502928 | 38209 | Breast; multiple myeloma; renal cell carcinoma | BRCA, LUAD | |
| KDM5A | 12p13.33 | 12 | 1 | 980639 | 980638 | CRC | BRCA, CRC, HNSC, LUAD, LUSC, OV | |
| CCNE1 | 19q12 | 19 | 30306758 | 30316875 | 10117 | Bladder | BLCA, BRCA, GBM, LUSC, OV, UCEC | |
| Deletions | IKZF2 | 2q34 | 2 | 211542637 | 214143899 | 2601262 | Breast; non-small cell lung cancer | BLCA, LUSC, UCEC |
| LINC00290 | 4q34.3 | 4 | 178911874 | 183060693 | 4148819 | Multiple myeloma; non-small cell lung cancer | BLCA, GBM, KIRC, LUAD, LUSC, OV, UCEC | |
| 5q15 | 5q15 | 5 | 73236070 | 114508587 | 41272517 | Breast; CRC; GBM; gallbladder; Hodgkin's lymphoma; prostate; Wilms tumor | CRC, LUAD, LUSC | |
| CDKN2A | 9p21.3 | 9 | 21865498 | 22448737 | 583239 | ALL; basal cell carcinoma; breast; CLL; glioma; nasopharyngeal carcinoma; melanoma | BLCA, BRCA, CRC, GBM, HNSC, KIRC, LUAD, LUSC | |
| 9p21.2 | 9p21.2 | 9 | 27572512 | 28982153 | 1409641 | Endometrial | UCEC | |
| RAD51B | 14q24.1 | 14 | 68275375 | 69288431 | 1013056 | Breast; prostate | BRCA, CRC, OV | |
| 15q12 | 15q12 | 15 | 1 | 32929863 | 32929862 | Bladder; CRC; multiple myeloma | BLCA, LUSC | |
| 22q13.32 | 22q13.32 | 22 | 48026910 | 51304566 | 3277656 | Endometrial; Pancreatic | BLCA, GBM, LUAD, OV, UCEC |
SNP associations and tumor types highlighted in bold indicate those whereby cancer type of SNP associations matches tumor type in which recurrent SCNAs were identified.
* Chromosomal locations based on human genome build hg19.
** Cancer type of SNP association loci that overlap SCNA regions (SNPs retrieved from January 2015 version of NHGRI GWAS catalog).
‡ Tumor type in which recurrent SCNAs were detected in TCGA.
ALL = acute lymphoblastic leukemia; BLCA = bladder; BRCA = breast; CLL = chronic lymphoblastic leukemia; CRC = colorectal; GBM = glioblastoma multiforme; HNSC = head and neck squamous cell carcinoma; KIRC = kidney renal cell carcinoma; LAML = acute myeloid leukemia; LUAD = lung adenocarcinoma; LUSC = lung squamous cell carcinoma; OV = serous ovarian carcinoma; UCEC = endometrial (uterine).