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Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas

Background: The disease course of patients with diffuse low-grade glioma is notoriously unpredictable. Temporal and spatially distinct samples may provide insight into the evolution of clinically relevant copy number aberrations (CNAs). The purpose of this study is to identify CNAs that are indicative of aggressive tumor behaviour and can thereby complement the prognostically favorable 1p/19q co-deletion. Results: Genome-wide, 50 base pair single-end, sequencing was performed to detect CNAs in a clinically well-characterized cohort of 98 formalin-fixed paraffin-embedded low-grade gliomas. CNAs are correlated with overall survival as an endpoint. Seventy-five additional samples from spatially distinct regions and paired recurrent tumors of the discovery cohort were analysed to interrogate the intratumoral heterogeneity and spatial evolution. Loss of 10q25.2-qter is a frequent subclonal event and significantly correlates with an unfavorable prognosis. A significant correlation is furthermore observed in a validation set of 126 and confirmation set of 184 patients. Loss of 10q25.2-qter arises in a longitudinal manner in paired recurrent tumor specimens, whereas the prognostically favorable 1p/ 19q co-deletion is the only CNA that is stable across spatial regions and recurrent tumors. Conclusions: CNAs in low-grade gliomas display extensive intratumoral heterogeneity. Distal loss of 10q is a late onset event and a marker for reduced overall survival in low-grade glioma patients. Intratumoral heterogeneity and higher frequencies of distal 10q loss in recurrences suggest this event is involved in outgrowth to the recurrent tumor.

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Data originating from patient samples

The Amsterdam UMC, tumor genome analysis core, allows access to published datasets upon written application and signature of a Data Access Agreement (DAA). In addition, applications to clinical datasets require approval by a Data Access Committee (DAC), who assess whether the proposed work is allowed given patient consent, as well as the scientific purpose. To aid this process we ask you to provide the information below. Requests will be prioritised according to novelty of the research question. Applications with insufficient detail on objectives, justification, and methods/planned analyses are unlikely to be accepted. 1.Reference number for the dataset 2.Full legal name and address of university/institution 3.Name(s) of the Principle Investigator who will use the data: 4.Name(s) and job title(s) of any other investigators who will use the data: 5.Please provide a minimum of one reference to a publication that can be found on PubMed and where the Principle Investigator is an author: 6.How will the data be stored and where will it be stored? 7.What is the proposed study title and what are the objectives and outcomes of the study in which the data will be used 8.Please provide a brief justification or rationale for the proposed study (max 250 words) 9.Please provide a brief description of planned data analyses (max 250 words): 10.Will the results arising from use of the data be used for the creation of products for sale or for any commercial purpose?

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001000643 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00000605176 fastq.gz 477.1 MB
EGAF00000605177 fastq.gz 441.2 MB
EGAF00000605178 fastq.gz 415.3 MB
EGAF00000605179 fastq.gz 333.4 MB
EGAF00000605180 fastq.gz 511.0 MB
EGAF00000605181 fastq.gz 340.4 MB
EGAF00000605182 fastq.gz 1.3 GB
EGAF00000605183 fastq.gz 263.5 MB
EGAF00000605184 fastq.gz 364.5 MB
EGAF00000605185 fastq.gz 343.1 MB
EGAF00000605186 fastq.gz 886.1 MB
EGAF00000605187 fastq.gz 501.0 MB
EGAF00000605188 fastq.gz 348.7 MB
EGAF00000605189 fastq.gz 345.5 MB
EGAF00000605190 fastq.gz 484.9 MB
EGAF00000605191 fastq.gz 358.9 MB
EGAF00000605192 fastq.gz 358.4 MB
EGAF00000605193 fastq.gz 670.2 MB
EGAF00000605194 fastq.gz 396.5 MB
EGAF00000605195 fastq.gz 366.8 MB
EGAF00000605196 fastq.gz 332.4 MB
EGAF00000605197 fastq.gz 321.3 MB
EGAF00000605198 fastq.gz 558.9 MB
EGAF00000605199 fastq.gz 488.8 MB
EGAF00000605200 fastq.gz 229.8 MB
EGAF00000605201 fastq.gz 647.3 MB
EGAF00000605202 fastq.gz 431.9 MB
EGAF00000605203 fastq.gz 280.9 MB
EGAF00000605204 fastq.gz 312.4 MB
EGAF00000605205 fastq.gz 528.5 MB
EGAF00000605206 fastq.gz 573.3 MB
EGAF00000605207 fastq.gz 480.9 MB
EGAF00000605208 fastq.gz 568.4 MB
EGAF00000605209 fastq.gz 527.0 MB
EGAF00000605210 fastq.gz 597.1 MB
EGAF00000605211 fastq.gz 496.4 MB
EGAF00000605212 fastq.gz 373.1 MB
EGAF00000605213 fastq.gz 569.1 MB
EGAF00000605214 fastq.gz 663.8 MB
EGAF00000605215 fastq.gz 751.4 MB
EGAF00000605216 fastq.gz 258.7 MB
EGAF00000605217 fastq.gz 226.3 MB
EGAF00000605218 fastq.gz 637.3 MB
EGAF00000605219 fastq.gz 536.8 MB
EGAF00000605220 fastq.gz 446.3 MB
EGAF00000605221 fastq.gz 264.5 MB
EGAF00000605222 fastq.gz 1.2 GB
EGAF00000605223 fastq.gz 267.2 MB
EGAF00000605224 fastq.gz 334.1 MB
EGAF00000605225 fastq.gz 1.9 GB
EGAF00000605226 fastq.gz 344.6 MB
EGAF00000605227 fastq.gz 599.2 MB
EGAF00000605228 fastq.gz 304.5 MB
EGAF00000605229 fastq.gz 556.8 MB
EGAF00000605230 fastq.gz 232.0 MB
EGAF00000605231 fastq.gz 468.1 MB
EGAF00000605232 fastq.gz 180.4 MB
EGAF00000605233 fastq.gz 273.3 MB
EGAF00000605234 fastq.gz 257.7 MB
EGAF00000605235 fastq.gz 621.5 MB
EGAF00000605236 fastq.gz 308.0 MB
EGAF00000605237 fastq.gz 403.6 MB
EGAF00000605238 fastq.gz 274.4 MB
EGAF00000605239 fastq.gz 305.5 MB
EGAF00000605240 fastq.gz 317.1 MB
EGAF00000605241 fastq.gz 354.1 MB
EGAF00000605242 fastq.gz 372.7 MB
EGAF00000605243 fastq.gz 431.4 MB
EGAF00000605244 fastq.gz 692.9 MB
EGAF00000605245 fastq.gz 385.2 MB
EGAF00000605246 fastq.gz 503.1 MB
EGAF00000605247 fastq.gz 348.1 MB
EGAF00000605248 fastq.gz 579.3 MB
EGAF00000605249 fastq.gz 511.7 MB
EGAF00000605250 fastq.gz 583.1 MB
EGAF00000605251 fastq.gz 478.9 MB
EGAF00000605252 fastq.gz 1.6 GB
EGAF00000605253 fastq.gz 332.3 MB
EGAF00000605254 fastq.gz 282.3 MB
EGAF00000605255 fastq.gz 481.1 MB
EGAF00000605256 fastq.gz 530.7 MB
EGAF00000605257 fastq.gz 429.6 MB
EGAF00000605258 fastq.gz 447.0 MB
EGAF00000605259 fastq.gz 331.8 MB
EGAF00000605260 fastq.gz 337.6 MB
EGAF00000605261 fastq.gz 392.9 MB
EGAF00000605262 fastq.gz 2.9 GB
EGAF00000605263 fastq.gz 1.9 GB
EGAF00000605264 fastq.gz 2.2 GB
EGAF00000605265 fastq.gz 1.2 GB
EGAF00000605266 fastq.gz 1.5 GB
EGAF00000605267 fastq.gz 2.6 GB
EGAF00000605268 fastq.gz 1.4 GB
EGAF00000605269 fastq.gz 1.0 GB
EGAF00000605270 fastq.gz 1.5 GB
EGAF00000605271 fastq.gz 1.5 GB
EGAF00000605272 fastq.gz 1.1 GB
EGAF00000605273 fastq.gz 3.0 GB
EGAF00000605274 fastq.gz 1.4 GB
EGAF00000605275 fastq.gz 1.3 GB
EGAF00000605276 fastq.gz 1.8 GB
EGAF00000605277 fastq.gz 1.6 GB
EGAF00000605278 fastq.gz 2.0 GB
EGAF00000605279 fastq.gz 416.5 MB
EGAF00000605280 fastq.gz 1.3 GB
EGAF00000605281 fastq.gz 3.1 GB
EGAF00000605282 fastq.gz 1.6 GB
EGAF00000605283 fastq.gz 1.3 GB
EGAF00000605284 fastq.gz 715.0 MB
EGAF00000605285 fastq.gz 544.0 MB
EGAF00000605286 fastq.gz 1.5 GB
EGAF00000605287 fastq.gz 1.4 GB
EGAF00000605288 fastq.gz 980.5 MB
EGAF00000605289 fastq.gz 1.7 GB
EGAF00000605290 fastq.gz 308.5 MB
EGAF00000605291 fastq.gz 1.7 GB
EGAF00000605292 fastq.gz 1.2 GB
EGAF00000605293 fastq.gz 1.7 GB
EGAF00000605294 fastq.gz 2.1 GB
EGAF00000605295 fastq.gz 1.9 GB
EGAF00000605296 fastq.gz 2.1 GB
EGAF00000605297 fastq.gz 1.8 GB
EGAF00000605298 fastq.gz 474.5 MB
EGAF00000605299 fastq.gz 271.5 MB
EGAF00000605300 fastq.gz 349.8 MB
EGAF00000605301 fastq.gz 852.9 MB
EGAF00000605302 fastq.gz 566.6 MB
EGAF00000605303 fastq.gz 372.2 MB
EGAF00000605304 fastq.gz 613.8 MB
EGAF00000605305 fastq.gz 239.6 MB
EGAF00000605306 fastq.gz 684.5 MB
EGAF00000605307 fastq.gz 187.0 MB
EGAF00000605308 fastq.gz 193.7 MB
EGAF00000605309 fastq.gz 296.2 MB
EGAF00000605310 fastq.gz 272.6 MB
EGAF00000605311 fastq.gz 311.6 MB
EGAF00000605312 fastq.gz 1.2 GB
EGAF00000605313 fastq.gz 995.1 MB
EGAF00000605314 fastq.gz 1.3 GB
EGAF00000605315 fastq.gz 396.9 MB
EGAF00000605316 fastq.gz 457.6 MB
EGAF00000605317 fastq.gz 256.3 MB
EGAF00000605318 fastq.gz 345.0 MB
EGAF00000605319 fastq.gz 333.0 MB
EGAF00000605320 fastq.gz 309.7 MB
EGAF00000605321 fastq.gz 1.1 GB
EGAF00000605322 fastq.gz 807.4 MB
EGAF00000605323 fastq.gz 1.5 GB
EGAF00000605324 fastq.gz 661.7 MB
EGAF00000605325 fastq.gz 769.0 MB
EGAF00000605326 fastq.gz 309.1 MB
EGAF00000605327 fastq.gz 581.0 MB
EGAF00000605328 fastq.gz 3.0 GB
EGAF00000605329 fastq.gz 1.7 GB
EGAF00000605330 fastq.gz 2.9 GB
EGAF00000605331 fastq.gz 699.4 MB
EGAF00000605332 fastq.gz 681.7 MB
EGAF00000605333 fastq.gz 1.5 GB
EGAF00000605334 fastq.gz 1.6 GB
EGAF00000605335 fastq.gz 315.2 MB
EGAF00000605336 fastq.gz 1.1 GB
EGAF00000605337 fastq.gz 686.5 MB
EGAF00000605338 fastq.gz 1.0 GB
EGAF00000605339 fastq.gz 710.3 MB
EGAF00000605340 fastq.gz 2.0 GB
EGAF00000605341 fastq.gz 1.2 GB
EGAF00000605342 fastq.gz 1.5 GB
EGAF00000605343 fastq.gz 819.9 MB
EGAF00000605344 fastq.gz 695.2 MB
EGAF00000605345 fastq.gz 2.3 GB
EGAF00000605346 fastq.gz 1.3 GB
EGAF00000605347 fastq.gz 1.6 GB
EGAF00000605348 fastq.gz 1.9 GB
EGAF00000605349 fastq.gz 1.8 GB
EGAF00000605350 fastq.gz 2.0 GB
EGAF00000605351 fastq.gz 2.3 GB
EGAF00000605352 fastq.gz 2.6 GB
EGAF00000605353 fastq.gz 962.9 MB
EGAF00000605354 fastq.gz 2.3 GB
EGAF00000605355 fastq.gz 2.2 GB
EGAF00000605356 fastq.gz 2.0 GB
EGAF00000605357 fastq.gz 1.6 GB
EGAF00000605358 fastq.gz 208.5 MB
EGAF00000605359 fastq.gz 576.5 MB
EGAF00000605360 fastq.gz 2.8 GB
EGAF00000605361 fastq.gz 2.8 GB
EGAF00000605362 fastq.gz 3.3 GB
EGAF00000605363 fastq.gz 204.0 MB
EGAF00000605364 fastq.gz 319.5 MB
EGAF00000605365 fastq.gz 188.7 MB
EGAF00000605366 fastq.gz 327.2 MB
EGAF00000605367 fastq.gz 1.8 GB
EGAF00000605368 fastq.gz 3.7 GB
EGAF00000605369 fastq.gz 1.3 GB
EGAF00000605370 fastq.gz 2.4 GB
EGAF00000605371 fastq.gz 1.6 GB
EGAF00000605372 fastq.gz 1.1 GB
EGAF00000605373 fastq.gz 970.8 MB
EGAF00000605374 fastq.gz 2.7 GB
EGAF00000605375 fastq.gz 267.9 MB
EGAF00000605376 fastq.gz 926.4 MB
EGAF00000605377 fastq.gz 1.1 GB
EGAF00000605378 fastq.gz 2.0 GB
EGAF00000605379 fastq.gz 2.8 GB
EGAF00000605380 fastq.gz 662.6 MB
EGAF00000605381 fastq.gz 1.9 GB
EGAF00000605382 fastq.gz 642.3 MB
EGAF00000605383 fastq.gz 1.0 GB
EGAF00000605384 fastq.gz 1.0 GB
EGAF00000605385 fastq.gz 1.6 GB
EGAF00000605386 fastq.gz 388.4 MB
EGAF00000605387 fastq.gz 762.0 MB
EGAF00000605388 fastq.gz 1.2 GB
EGAF00000605389 fastq.gz 454.1 MB
EGAF00000605390 fastq.gz 1.2 GB
EGAF00000605391 fastq.gz 307.5 MB
EGAF00000605392 fastq.gz 431.6 MB
EGAF00000605393 fastq.gz 1.1 GB
EGAF00000605394 fastq.gz 2.3 GB
EGAF00000605395 fastq.gz 904.7 MB
EGAF00000605396 fastq.gz 196.3 MB
EGAF00000605397 fastq.gz 284.1 MB
EGAF00000605398 fastq.gz 1.8 GB
EGAF00000605399 fastq.gz 255.3 MB
EGAF00000605400 fastq.gz 383.4 MB
EGAF00000605401 fastq.gz 384.4 MB
EGAF00000605402 fastq.gz 1.1 GB
EGAF00000605403 fastq.gz 229.9 MB
EGAF00000605404 fastq.gz 369.9 MB
EGAF00000605405 fastq.gz 381.6 MB
EGAF00000605406 fastq.gz 463.1 MB
EGAF00000605407 fastq.gz 272.5 MB
EGAF00000605408 fastq.gz 253.9 MB
EGAF00000605409 fastq.gz 211.9 MB
EGAF00000605410 fastq.gz 452.6 MB
EGAF00000605411 fastq.gz 340.6 MB
EGAF00000605412 fastq.gz 304.1 MB
EGAF00000605413 fastq.gz 562.5 MB
EGAF00000605414 fastq.gz 740.9 MB
EGAF00000605415 fastq.gz 629.2 MB
EGAF00000605416 fastq.gz 443.2 MB
EGAF00000605417 fastq.gz 264.4 MB
EGAF00000605418 fastq.gz 532.5 MB
EGAF00000605419 fastq.gz 520.9 MB
EGAF00000605420 fastq.gz 308.1 MB
EGAF00000605421 fastq.gz 563.9 MB
EGAF00000605422 fastq.gz 758.5 MB
EGAF00000605423 fastq.gz 950.7 MB
EGAF00000605424 fastq.gz 826.8 MB
EGAF00000605425 fastq.gz 385.5 MB
EGAF00000605426 fastq.gz 327.2 MB
EGAF00000605427 fastq.gz 295.2 MB
EGAF00000605428 fastq.gz 476.8 MB
EGAF00000605429 fastq.gz 771.5 MB
EGAF00000605430 fastq.gz 384.2 MB
EGAF00000605431 fastq.gz 646.1 MB
EGAF00000605432 fastq.gz 319.7 MB
EGAF00000605433 fastq.gz 291.5 MB
EGAF00000605434 fastq.gz 372.1 MB
EGAF00000605435 fastq.gz 424.7 MB
EGAF00000605436 fastq.gz 551.2 MB
EGAF00000605437 fastq.gz 210.8 MB
EGAF00000605438 fastq.gz 523.6 MB
EGAF00000605439 fastq.gz 443.2 MB
EGAF00000605440 fastq.gz 333.9 MB
EGAF00000605441 fastq.gz 613.9 MB
EGAF00000605442 fastq.gz 477.3 MB
EGAF00000605443 fastq.gz 342.0 MB
EGAF00000605444 fastq.gz 301.7 MB
EGAF00000605445 fastq.gz 287.7 MB
EGAF00000605446 fastq.gz 775.3 MB
EGAF00000605447 fastq.gz 334.5 MB
EGAF00000605448 fastq.gz 373.1 MB
EGAF00000605449 fastq.gz 235.5 MB
EGAF00000605450 fastq.gz 483.7 MB
EGAF00000605451 fastq.gz 369.6 MB
EGAF00000605452 fastq.gz 397.3 MB
EGAF00000605453 fastq.gz 284.6 MB
EGAF00000605454 fastq.gz 360.4 MB
EGAF00000605455 fastq.gz 275.7 MB
EGAF00000605456 fastq.gz 288.0 MB
EGAF00000605457 fastq.gz 837.1 MB
EGAF00000605458 fastq.gz 726.8 MB
EGAF00000605459 fastq.gz 319.7 MB
EGAF00000605460 fastq.gz 512.7 MB
EGAF00000605461 fastq.gz 351.2 MB
EGAF00000605462 fastq.gz 222.0 MB
EGAF00000605463 fastq.gz 379.9 MB
EGAF00000605464 fastq.gz 525.1 MB
EGAF00000605465 fastq.gz 336.8 MB
EGAF00000605466 fastq.gz 213.4 MB
EGAF00000605467 fastq.gz 430.5 MB
EGAF00000605468 fastq.gz 299.3 MB
EGAF00000605469 fastq.gz 335.0 MB
EGAF00000605470 fastq.gz 114.0 MB
EGAF00000605471 fastq.gz 323.8 MB
296 Files (245.2 GB)