Spreadsheet: 07442bd7-905a-4411-ab34-a1c27007c508
Sheet: Table S1

Table S1 Validation results, global approach
 |  | UMU a |  |  |  |  |  | TCGA
Region | 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 | sign
chr4:55085251-55109929 | LOH&CN>2 | rs9635726 | 44 (27/17) | 0 (0/0) | 37 (28/9) | 5 (4/1) | 0.0170128746078113 | rs9635726 | 186 | 1 | 99 | 1 | NA
chr7:54808835-55029721 | AMP | rs4977756 | 18 (10/8) | 0 (0/0) | 63 (45/18) | 12 (11/1) | 0.050790305542514 | rs4977756 | 92 | 43 | 193 | 84 | 0.738566169683538
chr7:54893660-54990895 | LOH&CN>2 | rs634537 | 17 (8/9) | 1 (1/0) | 64 (47/17) | 19 (16/3) | 0.0357567228876843 | rs1412829 | 89 | 14 | 196 | 43 | 0.145450788419537
chr7:54893660-54990895 | AMP | rs634537 | 17 (8/9) | 0 (0/0) | 64 (47/17) | 12 (11/1) | 0.046436850781727 | rs1412829 | 89 | 40 | 196 | 96 | 0.307327148471413
chr7:55337706-55358484 | AMP | rs4947979 | 44 (31/13) | 7 (6/1) | 37 (24/13) | 0 (0/0) | 0.011020471948742 | rs4947979 | 184 | 50 | 101 | 36 | 0.947182142284405
chr7:55459690-58058034 | CN>2 | rs634537 | 17 (8/9) | 4 (1/3) | 64 (47/17) | 44 (35/9) | 0.00148077772125766 | rs1412829 | 89 | 73 | 196 | 159 | 0.630531913544232
chr9:21750254-21836327 | HD | rs1015793 | 60 (41/19) | 28 (21/7) | 21 (14/7) | 2 (1/1) | 0.00373843779195585 | rs17172430 | 236 | 101 | 49 | 16 | 0.123742593909843
chr9:21842671-21849194 | HD | rs1015793 | 60 (41/19) | 28 (21/7) | 21 (14/7) | 3 (2/1) | 0.00710004042550721 | rs17172430 | 236 | 107 | 49 | 17 | 0.112722010433449
chr9:21961989-21978896 | HD | rs1015793 | 60 (41/19) | 35 (28/7) | 21 (14/7) | 5 (4/1) | 0.00615110624018313 | rs17172430 | 236 | 135 | 49 | 20 | 0.0264292565000728
chr9:22010493-22055620 | HD | rs1015793 | 60 (41/19) | 33 (27/6) | 21 (14/7) | 4 (3/1) | 0.00398461929398043 | rs17172430 | 236 | 132 | 49 | 19 | 0.0210071168078251
chr9:22073831-22129684 | HD | rs1015793 | 60 (41/19) | 30 (24/6) | 21 (14/7) | 3 (2/1) | 0.00495764159995254 | rs17172430 | 236 | 118 | 49 | 18 | 0.0618791193748782
chr9:22237076-22346187 | HD | rs1015793 | 60 (41/19) | 26 (22/4) | 21 (14/7) | 2 (1/1) | 0.00540171152587313 | rs17172430 | 236 | 97 | 49 | 15 | 0.112836100378105
chr10:[PHONE] | LOH | rs4977756 | 18 (10/8) | 6 (4/2) | 63 (45/18) | 48 (37/11) | 0.00179223612211072 | rs4977756 | 92 | 75 | 193 | 160 | 0.447351114437508
chr10:59083-39194226 | LOSS | rs634537 | 17 (8/9) | 4 (2/2) | 64 (47/17) | 49 (39/10) | 0.000258172382746978 | rs1412829 | 89 | 68 | 196 | 166 | 0.0654073910387701
chr10:59083-41982473 | LOH | rs634537 | 17 (8/9) | 4 (2/2) | 64 (47/17) | 51 (41/10) | 5.3457995226451e-05 | rs1412829 | 89 | 70 | 196 | 164 | 0.194429935298653
chr10:152102-773901 | LOSS | rs4977756 | 18 (10/8) | 5 (3/2) | 63 (45/18) | 45 (35/10) | 0.00110431381389016 | rs4977756 | 92 | 74 | 193 | 160 | 0.361868711722907
chr10:1499658-38646511 | LOH | rs4977756 | 18 (10/8) | 6 (4/2) | 63 (45/18) | 49 (39/10) | 0.00113685052043895 | rs4977756 | 92 | 73 | 193 | 161 | 0.24833739561758
chr10:2437411-39194226 | LOSS | rs4977756 | 18 (10/8) | 5 (3/2) | 63 (45/18) | 48 (38/10) | 0.000703050867162462 | rs4977756 | 92 | 72 | 193 | 163 | 0.132080002715438
chr10:41676351-41862435 | LOH | rs4977756 | 18 (10/8) | 6 (5/1) | 63 (45/18) | 47 (38/9) | 0.00179223612211072 | rs4977756 | 92 | 70 | 193 | 156 | 0.220148259012727
chr10:42133106-42178160 | LOH | rs634537 | 17 (8/9) | 5 (3/2) | 64 (47/17) | 47 (38/9) | 0.00120724648283334 | rs1412829 | NA | NA | NA | NA | NA
chr10:42267633-45632595 | LOH | rs634537 | 17 (8/9) | 5 (3/2) | 64 (47/17) | 51 (41/10) | 0.000291239619415753 | rs1412829 | 89 | 69 | 196 | 162 | 0.193992500739111
chr10:47070415-48684758 | LOH | rs634537 | 17 (8/9) | 5 (3/2) | 64 (47/17) | 50 (40/10) | 0.000481464918767195 | rs1412829 | 89 | 72 | 196 | 170 | 0.136822365754279
chr10:48983251-51055913 | LOH | rs634537 | 17 (8/9) | 5 (3/2) | 64 (47/17) | 49 (39/10) | 0.000481464918767195 | rs1412829 | 89 | 72 | 196 | 170 | 0.136822365754279
chr10:50726298-51172184 | LOSS | rs634537 | 17 (8/9) | 4 (3/1) | 64 (47/17) | 45 (37/8) | 0.00148077772125766 | rs1412829 | NA | NA | NA | NA | NA
chr10:51163572-51172184 | LOH | rs634537 | 17 (8/9) | 4 (3/1) | 64 (47/17) | 45 (35/10) | 0.000646029290522213 | rs1412829 | NA | NA | NA | NA | NA
chr10:51188053-51493176 | LOSS | rs634537 | 17 (8/9) | 5 (3/2) | 64 (47/17) | 47 (39/8) | 0.00183996254955759 | rs1412829 | 89 | 70 | 196 | 168 | 0.0954044153679922
chr10:51202373-70306842 | LOH | rs634537 | 17 (8/9) | 6 (3/3) | 64 (47/17) | 53 (41/12) | 0.000481464918767195 | rs1412829 | 89 | 73 | 196 | 174 | 0.0877938752367715
chr10:69018764-69111178 | LOSS | rs634537 | 17 (8/9) | 6 (3/3) | 64 (47/17) | 49 (38/11) | 0.00203497153013729 | rs1412829 | 89 | 75 | 196 | 173 | 0.227379925478796
chr10:69118295-70607572 | LOSS | rs4977756 | 18 (10/8) | 7 (4/3) | 63 (45/18) | 52 (39/13) | 0.0010222489230268 | rs4977756 | 92 | 79 | 193 | 171 | 0.316746805119562
chr10:69761929-70306842 | LOSS | rs634537 | 17 (8/9) | 7 (3/4) | 64 (47/17) | 52 (40/12) | 0.00199195284400618 | rs1412829 | 89 | 76 | 196 | 174 | 0.266826900575439
chr10:70769919-70812426 | CNNE | [NAME] | 33 (20/13) | 0 (0/0) | 48 (35/13) | 13 (9/4) | 0.000513950512314199 | rs12150298 | 122 | 3 | 163 | 4 | 0.655714724475967
chr10:70769919-73415482 | LOH | rs634537 | 17 (8/9) | 6 (3/3) | 64 (47/17) | 52 (40/12) | 0.000801482403137656 | rs1412829 | 89 | 77 | 196 | 174 | 0.357912362989898
chr10:73187526-73545567 | LOSS | rs634537 | 17 (8/9) | 5 (2/3) | 64 (47/17) | 47 (38/9) | 0.00148077772125766 | rs1412829 | 89 | 75 | 196 | 175 | 0.158305538414976
chr10:73399644-73550680 | LOSS | rs4977756 | 18 (10/8) | 6 (3/3) | 63 (45/18) | 48 (37/11) | 0.000614990509168294 | rs4977756 | 92 | 78 | 193 | 172 | 0.196407934308489
chr10:76251152-76787562 | LOSS | rs4977756 | 18 (10/8) | 6 (4/2) | 63 (45/18) | 48 (37/11) | 0.00113685052043895 | rs4977756 | 92 | 78 | 193 | 173 | 0.161665582569345
chr10:76251152-76787611 | LOH | rs4977756 | 18 (10/8) | 7 (5/2) | 63 (45/18) | 50 (39/11) | 0.00168454848269421 | rs4977756 | 92 | 78 | 193 | 173 | 0.161665582569345
chr10:76251152-81040192 | LOH | rs634537 | 17 (8/9) | 6 (3/3) | 64 (47/17) | 51 (41/10) | 0.000291239619415753 | rs1412829 | 89 | 76 | 196 | 173 | 0.309518260785347
chr10:76790462-76793657 | LOSS | rs634537 | 17 (8/9) | 5 (3/2) | 64 (47/17) | 46 (36/10) | 0.00183996254955759 | rs1412829 | NA | NA | NA | NA | NA
chr10:76810870-77156632 | LOSS | rs634537 | 17 (8/9) | 4 (3/1) | 64 (47/17) | 44 (36/8) | 0.00217742661918642 | rs1412829 | 89 | 75 | 196 | 175 | 0.158305538414976
chr10:81487496-81511601 | LOSS | rs4977756 | 18 (10/8) | 4 (3/1) | 63 (45/18) | 42 (34/8) | 0.000946568590394004 | rs4977756 | NA | NA | NA | NA | NA
chr10:81487496-81689218 | LOSS | rs634537 | 17 (8/9) | 4 (3/1) | 64 (47/17) | 45 (37/8) | 0.000988072549945516 | rs1412829 | 89 | 75 | 196 | 175 | 0.158305538414976
chr10:81529851-96842309 | LOH | rs634537 | 17 (8/9) | 7 (4/3) | 64 (47/17) | 54 (42/12) | 0.000150776443947496 | rs1412829 | 89 | 77 | 196 | 175 | 0.311538222896533
chr10:81692190-90364037 | LOSS | rs634537 | 17 (8/9) | 5 (3/2) | 64 (47/17) | 51 (41/10) | 0.000772747408399088 | rs1412829 | 89 | 75 | 196 | 176 | 0.128681421266846
chr10:83624151-83646506 | LOH | rs4977756 | 18 (10/8) | 7 (5/2) | 63 (45/18) | 50 (41/9) | 0.00168454848269421 | rs4977756 | NA | NA | NA | NA | NA
chr10:83971944-88506401 | LOH | rs4977756 | 18 (10/8) | 7 (5/2) | 63 (45/18) | 51 (41/10) | 0.00168454848269421 | rs4977756 | 92 | 78 | 193 | 173 | 0.161665582569345
chr10:87691459-89247305 | LOSS | rs4977756 | 18 (10/8) | 5 (3/2) | 63 (45/18) | 50 (40/10) | 0.00113685052043895 | rs4977756 | 92 | 80 | 193 | 173 | 0.314446973377567
chr10:88730692-89206800 | LOH | rs4977756 | 18 (10/8) | 6 (4/2) | 63 (45/18) | 50 (40/10) | 0.000699926785991117 | rs4977756 | 92 | 79 | 193 | 173 | 0.229843890840762
chr10:93067055-93905633 | LOSS | rs634537 | 17 (8/9) | 6 (4/2) | 64 (47/17) | 51 (41/10) | 0.00129723879867818 | rs1412829 | 89 | 76 | 196 | 178 | 0.12457527684321
[NAME] | LOSS | rs634537 | 17 (8/9) | 6 (4/2) | 64 (47/17) | 51 (41/10) | 0.000801482403137656 | rs1412829 | 89 | 77 | 196 | 178 | 0.18613907129131
chr10:96843354-120427653 | LOH | rs634537 | 17 (8/9) | 6 (4/2) | 64 (47/17) | 54 (42/12) | 0.000150776443947496 | rs1412829 | 89 | 78 | 196 | 176 | 0.361782820066922
chr10:96843431-97120440 | LOSS | rs634537 | 17 (8/9) | 6 (4/2) | 64 (47/17) | 49 (39/10) | 0.00203497153013729 | rs1412829 | 89 | 77 | 196 | 176 | 0.267019048406902
chr10:120443158-120629967 | LOH | rs634537 | 17 (8/9) | 7 (5/2) | 64 (47/17) | 53 (41/12) | 0.0012112940503813 | rs1412829 | 89 | 78 | 196 | 178 | 0.266645571723441
chr10:120755847-120782693 | LOH | rs634537 | 17 (8/9) | 7 (5/2) | 64 (47/17) | 53 (41/12) | 0.0012112940503813 | rs1412829 | 89 | 78 | 196 | 178 | 0.266645571723441
chr10:121074899-131824003 | LOH | rs634537 | 17 (8/9) | 7 (5/2) | 64 (47/17) | 54 (42/12) | 0.0012112940503813 | rs1412829 | 89 | 78 | 196 | 176 | 0.361782820066922
chr10:121831934-123970935 | LOSS | rs634537 | 17 (8/9) | 5 (3/2) | 64 (47/17) | 47 (37/10) | 0.00120724648283334 | rs1412829 | 89 | 77 | 196 | 178 | 0.18613907129131
chr10:135284978-135374311 | LOH | rs4977756 | 18 (10/8) | 5 (4/1) | 63 (45/18) | 44 (35/9) | 0.00169353677250608 | rs4977756 | NA | NA | NA | NA | NA
chr10:135284978-135374311 | LOH | rs634537 | 17 (8/9) | 4 (3/1) | 64 (47/17) | 45 (36/9) | 0.000646029290522213 | rs1412829 | NA | NA | NA | NA | NA
chr14:103624674-103624674 | CN>2 | rs6470745 | 43 (30/13) | 3 (1/2) | 38 (25/13) | 15 (7/8) | 0.000464819708410702 | rs4295627 | NA | NA | NA | NA | NA
chr16:2725159-2806900 | CN>2 | rs6010620 | 52 (35/17) | 15 (10/5) | 29 (20/9) | 0 (0/0) | 0.000550266364703753 | rs6010620 | 201 | 10 | 84 | 4 | 0.602413982597759
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   The event frequency may vary within each region. Data in Supplementary Table 1 represents one point in the region, where the event frequency of the risk group is at a maximum.
b   total number of samples (glioblastoma samples / non-glioblastoma samples)
c   HD homozygous deletion, LOH loss of heterozygosity, AMP amplification, CN>2 copy number increase, LOH&CN>2 simultaneous LOH and copy number increase, CNNE copy number neutral event