Spreadsheet: 042ccb2b-9af9-4b0d-aac5-3c48c6edec6b
Sheet: Table S2

Table S2 Validation results, genes-of-interest approach
 |  |  | UMU |  |  |  |  |  | TCGA
Locus | Gene | Event  c | Variant | n (major) b | n (major) event b | n(rare+hz) b | n(rare+hz) event b | P | Variant | n (major) | n (major) event | n(rare+hz) | n(rare+hz) event | P | Validation region a | Sign.
chr1:51206954-51212894 | CDKN2C | CN>2 | rs4947979 | 44 (31/13) | 5 (4/1) | 37 (24/13) | 0 (0/0) | 0.042386431 | rs4947979 | 184 | 18 | 101 | 5 | 0.111931544 | chr1p33
chr1:51206954-51212894 | CDKN2C | LOH | [NAME] | 33 (20/13) | 2 (1/1) | 48 (35/13) | 11 (6/5) | 0.038420116 | rs12150298 | 122 | 5 | 163 | 5 | 0.787037893 | chr1p33
chr1:51206954-51212894 | CDKN2C | LOSS | [NAME] | 33 (20/13) | 3 (2/1) | 48 (35/13) | 13 (8/5) | 0.040055087 | rs12150298 | 122 | 5 | 163 | 6 | 0.691328672 | chr1p33
chr1:202752129-202793871 | MDM4 | LOH | [NAME] | 33 (20/13) | 0 (0/0) | 48 (35/13) | 6 (4/2) | 0.037811992 | rs12150298 | 122 | 5 | 163 | 8 | 0.490394948 | MDM4
chr1:202752129-202793871 | MDM4 | LOH | rs9635726 | 44 (27/17) | 0 (0/0) | 37 (28/9) | 6 (4/2) | 0.007163316 | rs9635726 | 186 | 9 | 99 | 4 | 0.720414943 | MDM4
chr1:241729643-242073207 | AKT3 | LOH | rs9635726 | 44 (27/17) | 0 (0/0) | 37 (28/9) | 5 (3/2) | 0.017012875 | rs9635726 | 186 | 3 | 99 | 3 | 0.346664332 | AKT3
chr2:208809197-208828051 | IDH1 | LOSS | [NAME] | 33 (20/13) | 0 (0/0) | 48 (35/13) | 8 (4/4) | 0.011731937 | rs12150298 | 122 | 6 | 163 | 9 | 0.521498456 | chr2q33.3
chr2:208809197-208828051 | IDH1 | LOSS | rs9635726 | 44 (27/17) | 1 (0/1) | 37 (28/9) | 7 (4/3) | 0.015284321 | rs9635726 | 186 | 9 | 99 | 6 | 0.42629676 | chr2q33.3
chr3:180349004-180435191 | PIK3CA | LOH | rs9635726 | 44 (27/17) | 1 (1/0) | 37 (28/9) | 6 (4/2) | 0.032378187 | rs9635726 | 186 | 5 | 99 | 4 | 0.383516136 | PIK3CA
chr4:54790020-54859169 | PDGFRA | LOH | [NAME] | 33 (20/13) | 2 (2/0) | 48 (35/13) | 11 (7/4) | 0.038420116 | rs12150298 | 122 | 8 | 163 | 8 | 0.805216318 | PDGFRA
chr4:54790020-54859169 | PDGFRA | CN>2 | rs9635726 | 44 (27/17) | 3 (2/1) | 37 (28/9) | 9 (6/3) | 0.028513445 | rs9635726 | 186 | 34 | 99 | 15 | 0.795991786 | PDGFRA
chr4:54790020-54859169 | PDGFRA | LOH | rs9635726 | 44 (27/17) | 3 (3/0) | 37 (28/9) | 10 (6/4) | 0.014670829 | rs9635726 | 186 | 11 | 99 | 5 | 0.709582533 | PDGFRA
chr7:55054218-55242525 | EGFR | LOH | rs1015793 | 60 (41/19) | 19 (15/4) | 21 (14/7) | 2 (2/0) | 0.038531329 | rs17172430 | 236 | 57 | 49 | 6 | 0.045541788 | EGFR
chr7:55054218-55242525 | EGFR | CN>2 | rs634537 | 17 (8/9) | 7 (3/4) | 64 (47/17) | 47 (37/10) | 0.014734725 | rs1412829 | 89 | 78 | 196 | 178 | 0.266645572 | EGFR
chr8:128817496-128822862 | MYC | LOH | rs9635726 | 44 (27/17) | 2 (2/0) | 37 (28/9) | 8 (6/2) | 0.02254336 | rs9635726 | 186 | 9 | 99 | 5 | 0.571986587 | chr8q24.21
chr8:128817496-128822862 | MYC | LOSS | rs9635726 | 44 (27/17) | 1 (1/0) | 37 (28/9) | 7 (5/2) | 0.015284321 | rs9635726 | 186 | 10 | 99 | 4 | 0.779786286 | chr8q24.21
chr8:130433119-130761667 | CCDC26 | LOH | rs9635726 | 44 (27/17) | 2 (2/0) | 37 (28/9) | 7 (5/2) | 0.044320476 | rs9635726 | 186 | 9 | 99 | 5 | 0.571986587 | CCDC26
chr8:130433119-130761667 | CCDC26 | LOSS | rs9635726 | 44 (27/17) | 1 (1/0) | 37 (28/9) | 6 (4/2) | 0.032378187 | rs9635726 | 186 | 10 | 99 | 5 | 0.6448315 | CCDC26
chr9:21957750-21965132 | CDKN2A | HD | rs1015793 | 60 (41/19) | 35 (28/7) | 21 (14/7) | 6 (5/1) | 0.017473904 | rs17172430 | 236 | 53 | 49 | 8 | 0.226671652 | chr9p21.3
chr9:21957750-21965132 | CDKN2A | HD | rs10245472 | 57 (39/18) | 33 (26/7) | 24 (16/8) | 8 (7/1) | 0.037406016 | rs11979158 | 209 | 51 | 76 | 10 | 0.026738904 | chr9p21.3
chr9:21992901-21999312 | CDKN2B | HD | rs1015793 | 60 (41/19) | 34 (27/7) | 21 (14/7) | 5 (4/1) | 0.008829383 | rs17172430 | 236 | 134 | 49 | 20 | 0.029960891 | CDKN2B
chr9:21992901-21999312 | CDKN2B | HD | rs10245472 | 57 (39/18) | 32 (25/7) | 24 (16/8) | 7 (6/1) | 0.023317074 | rs11979158 | 209 | 122 | 76 | 32 | 0.01068502 | CDKN2B
chr10:89613174-89718512 | PTEN | LOH | rs4977756 | 18 (10/8) | 8 (6/2) | 63 (45/18) | 51 (40/11) | 0.003736237 | rs4977756 | 92 | 79 | 193 | 175 | 0.15516766 | PTEN
chr10:89613174-89718512 | PTEN | LOSS | rs4977756 | 18 (10/8) | 7 (5/2) | 63 (45/18) | 49 (40/9) | 0.002680488 | rs4977756 | 92 | 79 | 193 | 176 | 0.123539863 | PTEN
chr10:89613174-89718512 | PTEN | LOH | rs634537 | 17 (8/9) | 6 (4/2) | 64 (47/17) | 53 (42/11) | 0.000274503 | rs1412829 | 89 | 77 | 196 | 177 | 0.225021468 | PTEN
chr10:89613174-89718512 | PTEN | LOSS | rs634537 | 17 (8/9) | 6 (4/2) | 64 (47/17) | 50 (41/9) | 0.001297239 | rs1412829 | 89 | 76 | 196 | 179 | 0.097943748 | PTEN
chr10:89613174-89718512 | PTEN | CNNE | [NAME] | 33 (20/13) | 0 (0/0) | 48 (35/13) | 6 (3/3) | 0.037811992 | rs12150298 | 122 | 3 | 163 | 3 | 0.782119826 | PTEN
chr11:117982422-118033958 | PHLDB1 | LOH | [NAME] | 33 (20/13) | 2 (2/0) | 48 (35/13) | 11 (8/3) | 0.038420116 | rs12150298 | 122 | 9 | 163 | 8 | 0.869065279 | PHLDB1
chr13:47775883-47954027 | RB1 | LOH | rs4977756 | 18 (10/8) | 3 (2/1) | 63 (45/18) | 28 (19/9) | 0.027874329 | rs4977756 | 92 | 31 | 193 | 72 | 0.323609732 | RB1
chr13:47775883-47954027 | RB1 | LOH | rs634537 | 17 (8/9) | 2 (1/1) | 64 (47/17) | 29 (20/9) | 0.009413284 | rs1412829 | 89 | 33 | 196 | 70 | 0.640239189 | RB1
chr15:88428215-88446712 | IDH2 | LOSS | [NAME] | 33 (20/13) | 1 (1/0) | 48 (35/13) | 10 (6/4) | 0.019666405 | rs12150298 | 122 | 12 | 163 | 27 | 0.070633019 | IDH2
chr17:7512444-7531593 | TP53 | CNNE | rs6470745 | 43 (30/13) | 4 (3/1) | 38 (25/13) | 12 (6/6) | 0.012215676 | rs4295627 | 198 | 28 | 87 | 9 | 0.858342018 | TP53
chr17:7512444-7531593 | TP53 | LOSS | [NAME] | 33 (20/13) | 3 (2/1) | 48 (35/13) | 13 (9/4) | 0.040055087 | rs12150298 | 122 | 19 | 163 | 24 | 0.644309969 | TP53
chr17:35109779-35138441 | ERBB2 | LOSS | [NAME] | 33 (20/13) | 2 (1/1) | 48 (35/13) | 11 (7/4) | 0.038420116 | rs12150298 | 122 | 16 | 163 | 15 | 0.892408146 | chr17q12
chr20:61759606-61798050 | RTEL1 | CN>2 | rs634537 | 17 (8/9) | 6 (3/3) | 64 (47/17) | 40 (32/8) | 0.0415078 | rs1412829 | 89 | 31 | 196 | 53 | 0.929217999 | RTEL1
n number, major samples homozygous for the major allele, rare+hz samples homozygous for the rare allele plus heterozygous samples, event samples positive for given event
a   In case there was a lack of probe coverage for a gene in the TCGA data, the validation region was expanded to include the whole cytoband harboring the gene of interest.
b   total number of samples (glioblastoma samples / non-glioblastoma samples)
c   HD homozygous deletion, LOH loss of heterozygosity, CN>2 copy number increase, CNNE copy number neutral event