Whole genome analyses of the childhood cancer neuroblastoma
Neuroblastomas are tumors of peripheral sympathetic neurons and are the most common solid tumor in children. To determine the genetic basis for neuroblastoma we performed whole-genome sequencing (6 cases), exome sequencing (16 cases), genome-wide rearrangement analyses (32 cases), and targeted analyses of specific genomic loci (40 cases) using massively parallel sequencing. On average each tumor had 19 somatic alterations in coding genes (range, 3-70). Among genes not previously known to be involved in neuroblastoma, chromosomal deletions and sequence alterations of chromatin remodeling genes, ARID1A and ARID1B, were identified in 8 of 71 tumors (11%) and were associated with early treatment failure and decreased survival. Using tumor-specific structural alterations, we developed an approach to identify rearranged DNA fragments in sera, providing personalized biomarkers for minimal residual disease detection and monitoring. These results highlight dysregulation of chromatin remodeling in pediatric tumorigenesis and provide new approaches for the management of neuroblastoma patients.
- 27/05/2015
- 114 samples
- DAC: EGAC00001000085
- Technologies: Illumina Genome Analyzer IIx, Illumina HiSeq 2000
Neuroblastoma Data Access Committee Policy
European Genome-Phenome Archivec/o European Bioinformatics InstituteWellcome Trust Genome CampusHinxtonCambridgeCB10 1SDUnited KingdomTo whom it may concern:This document refers to the data set, EGAS00001000369, which has been submitted to the European Genome Archive (EGA) for the restricted access by legitimate academic institutions that have agreed to comply with the terms of a Data Access Agreement drafted by the Neuroblastoma Data Access Committee. There are a number of steps that a researcher must take to obtain access to these data and the process is overseen by the Neuroblastoma Data Access Committee headed by Dr. Michael D. Hogarty (HOGARTYM@email.chop.edu).Michael Hogarty is a PI of this project and is authorized to approve researchers to have encrypted access to the data submitted to the EGA. Please be advised that Mark Sausen (msausen1@gmail.com) is authorized to upload data to the EGA for archiving and distribution as part of your submission process, which will enable approved researchers to have encrypted access to the data. We can confirm that this submission is consistent with the informed consent of the participants of the study or has been granted ethical approval and is in accordance with the applicable laws and regulations.Sincerely,Victor VelculescuJohns Hopkins Sidney Kimmel Comprehensive Cancer CenterMichael D. HogartyChildren's Hospital of PhiladelphiaPerelman School of Medicine at the University of Pennsylvania
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 |
|---|---|---|
| EGAS00001000369 | 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 | |
|---|---|---|---|---|
| EGAF00000146275 | fastq.gz | 3.3 GB | ||
| EGAF00000146276 | fastq.gz | 3.3 GB | ||
| EGAF00000146277 | fastq.gz | 3.2 GB | ||
| EGAF00000146278 | fastq.gz | 3.2 GB | ||
| EGAF00000146279 | fastq.gz | 3.3 GB | ||
| EGAF00000146280 | fastq.gz | 3.3 GB | ||
| EGAF00000146281 | fastq.gz | 3.5 GB | ||
| EGAF00000146282 | fastq.gz | 3.5 GB | ||
| EGAF00000146283 | fastq.gz | 3.7 GB | ||
| EGAF00000146284 | fastq.gz | 3.8 GB | ||
| EGAF00000146285 | fastq.gz | 5.0 GB | ||
| EGAF00000146286 | fastq.gz | 5.1 GB | ||
| EGAF00000146287 | fastq.gz | 5.4 GB | ||
| EGAF00000146288 | fastq.gz | 5.7 GB | ||
| EGAF00000146289 | fastq.gz | 3.8 GB | ||
| EGAF00000146290 | fastq.gz | 3.8 GB | ||
| EGAF00000146291 | fastq.gz | 3.1 GB | ||
| EGAF00000146292 | fastq.gz | 3.1 GB | ||
| EGAF00000146293 | fastq.gz | 3.6 GB | ||
| EGAF00000146294 | fastq.gz | 3.6 GB | ||
| EGAF00000146295 | fastq.gz | 3.0 GB | ||
| EGAF00000146296 | fastq.gz | 3.0 GB | ||
| EGAF00000146297 | fastq.gz | 5.4 GB | ||
| EGAF00000146298 | fastq.gz | 5.5 GB | ||
| EGAF00000146299 | fastq.gz | 3.7 GB | ||
| EGAF00000146300 | fastq.gz | 3.8 GB | ||
| EGAF00000146301 | fastq.gz | 3.3 GB | ||
| EGAF00000146302 | fastq.gz | 3.4 GB | ||
| EGAF00000146303 | fastq.gz | 3.0 GB | ||
| EGAF00000146304 | fastq.gz | 3.1 GB | ||
| EGAF00000146305 | fastq.gz | 3.7 GB | ||
| EGAF00000146306 | fastq.gz | 3.8 GB | ||
| EGAF00000146307 | fastq.gz | 3.1 GB | ||
| EGAF00000146308 | fastq.gz | 3.1 GB | ||
| EGAF00000146309 | fastq.gz | 5.5 GB | ||
| EGAF00000146310 | fastq.gz | 5.5 GB | ||
| EGAF00000146311 | fastq.gz | 5.5 GB | ||
| EGAF00000146312 | fastq.gz | 5.6 GB | ||
| EGAF00000146313 | fastq.gz | 3.3 GB | ||
| EGAF00000146314 | fastq.gz | 3.3 GB | ||
| EGAF00000146315 | fastq.gz | 4.0 GB | ||
| EGAF00000146316 | fastq.gz | 4.3 GB | ||
| EGAF00000146317 | fastq.gz | 3.4 GB | ||
| EGAF00000146318 | fastq.gz | 3.7 GB | ||
| EGAF00000146319 | fastq.gz | 3.7 GB | ||
| EGAF00000146320 | fastq.gz | 4.0 GB | ||
| EGAF00000146321 | fastq.gz | 3.5 GB | ||
| EGAF00000146322 | fastq.gz | 3.7 GB | ||
| EGAF00000146323 | fastq.gz | 3.7 GB | ||
| EGAF00000146324 | fastq.gz | 4.0 GB | ||
| EGAF00000146325 | fastq.gz | 3.5 GB | ||
| EGAF00000146326 | fastq.gz | 3.8 GB | ||
| EGAF00000146327 | fastq.gz | 3.5 GB | ||
| EGAF00000146328 | fastq.gz | 3.8 GB | ||
| EGAF00000146329 | fastq.gz | 3.4 GB | ||
| EGAF00000146330 | fastq.gz | 3.6 GB | ||
| EGAF00000146331 | fastq.gz | 4.6 GB | ||
| EGAF00000146332 | fastq.gz | 4.8 GB | ||
| EGAF00000146333 | fastq.gz | 4.1 GB | ||
| EGAF00000146334 | fastq.gz | 4.4 GB | ||
| EGAF00000146335 | fastq.gz | 4.1 GB | ||
| EGAF00000146336 | fastq.gz | 4.4 GB | ||
| EGAF00000146337 | fastq.gz | 4.1 GB | ||
| EGAF00000146338 | fastq.gz | 4.4 GB | ||
| EGAF00000146339 | fastq.gz | 44.8 GB | ||
| EGAF00000146340 | fastq.gz | 45.9 GB | ||
| EGAF00000146341 | fastq.gz | 50.0 GB | ||
| EGAF00000146342 | fastq.gz | 51.2 GB | ||
| EGAF00000146343 | fastq.gz | 41.7 GB | ||
| EGAF00000146344 | fastq.gz | 42.9 GB | ||
| EGAF00000146345 | fastq.gz | 52.0 GB | ||
| EGAF00000146346 | fastq.gz | 52.9 GB | ||
| EGAF00000146347 | fastq.gz | 46.7 GB | ||
| EGAF00000146348 | fastq.gz | 48.2 GB | ||
| EGAF00000146349 | fastq.gz | 48.8 GB | ||
| EGAF00000146350 | fastq.gz | 49.5 GB | ||
| EGAF00000146351 | fastq.gz | 44.8 GB | ||
| EGAF00000146352 | fastq.gz | 45.8 GB | ||
| EGAF00000146353 | fastq.gz | 46.5 GB | ||
| EGAF00000146354 | fastq.gz | 47.8 GB | ||
| EGAF00000146355 | fastq.gz | 40.4 GB | ||
| EGAF00000146356 | fastq.gz | 41.9 GB | ||
| EGAF00000146357 | fastq.gz | 45.7 GB | ||
| EGAF00000146358 | fastq.gz | 45.7 GB | ||
| EGAF00000146359 | fastq.gz | 55.4 GB | ||
| EGAF00000146360 | fastq.gz | 55.7 GB | ||
| EGAF00000146361 | fastq.gz | 45.7 GB | ||
| EGAF00000146362 | fastq.gz | 46.6 GB | ||
| EGAF00000146363 | fastq.gz | 1.3 GB | ||
| EGAF00000146364 | fastq.gz | 1.3 GB | ||
| EGAF00000146365 | fastq.gz | 1.4 GB | ||
| EGAF00000146366 | fastq.gz | 1.4 GB | ||
| EGAF00000146367 | fastq.gz | 1.2 GB | ||
| EGAF00000146368 | fastq.gz | 1.2 GB | ||
| EGAF00000146369 | fastq.gz | 1.5 GB | ||
| EGAF00000146370 | fastq.gz | 1.5 GB | ||
| EGAF00000146371 | fastq.gz | 1.3 GB | ||
| EGAF00000146372 | fastq.gz | 1.4 GB | ||
| EGAF00000146373 | fastq.gz | 1.2 GB | ||
| EGAF00000146374 | fastq.gz | 1.2 GB | ||
| EGAF00000146375 | fastq.gz | 1.6 GB | ||
| EGAF00000146376 | fastq.gz | 1.6 GB | ||
| EGAF00000146377 | fastq.gz | 1.4 GB | ||
| EGAF00000146378 | fastq.gz | 1.4 GB | ||
| EGAF00000146379 | fastq.gz | 1.6 GB | ||
| EGAF00000146380 | fastq.gz | 1.7 GB | ||
| EGAF00000146381 | fastq.gz | 1.3 GB | ||
| EGAF00000146382 | fastq.gz | 1.4 GB | ||
| EGAF00000146383 | fastq.gz | 1.4 GB | ||
| EGAF00000146384 | fastq.gz | 1.4 GB | ||
| EGAF00000146385 | fastq.gz | 1.4 GB | ||
| EGAF00000146386 | fastq.gz | 1.4 GB | ||
| EGAF00000146387 | fastq.gz | 1.1 GB | ||
| EGAF00000146388 | fastq.gz | 1.1 GB | ||
| EGAF00000146389 | fastq.gz | 1.1 GB | ||
| EGAF00000146390 | fastq.gz | 1.1 GB | ||
| EGAF00000146391 | fastq.gz | 1.5 GB | ||
| EGAF00000146392 | fastq.gz | 1.5 GB | ||
| EGAF00000146393 | fastq.gz | 1.1 GB | ||
| EGAF00000146394 | fastq.gz | 1.1 GB | ||
| EGAF00000146395 | fastq.gz | 1.1 GB | ||
| EGAF00000146396 | fastq.gz | 1.1 GB | ||
| EGAF00000146397 | fastq.gz | 1.3 GB | ||
| EGAF00000146398 | fastq.gz | 1.3 GB | ||
| EGAF00000146399 | fastq.gz | 1.1 GB | ||
| EGAF00000146400 | fastq.gz | 1.1 GB | ||
| EGAF00000146401 | fastq.gz | 1.1 GB | ||
| EGAF00000146402 | fastq.gz | 1.2 GB | ||
| EGAF00000146403 | fastq.gz | 1.1 GB | ||
| EGAF00000146404 | fastq.gz | 1.1 GB | ||
| EGAF00000146405 | fastq.gz | 1.2 GB | ||
| EGAF00000146406 | fastq.gz | 1.2 GB | ||
| EGAF00000146407 | fastq.gz | 1.3 GB | ||
| EGAF00000146408 | fastq.gz | 1.4 GB | ||
| EGAF00000146409 | fastq.gz | 1.2 GB | ||
| EGAF00000146410 | fastq.gz | 1.2 GB | ||
| EGAF00000146411 | fastq.gz | 1.1 GB | ||
| EGAF00000146412 | fastq.gz | 1.2 GB | ||
| EGAF00000146413 | fastq.gz | 1.2 GB | ||
| EGAF00000146414 | fastq.gz | 1.2 GB | ||
| EGAF00000146415 | fastq.gz | 997.6 MB | ||
| EGAF00000146416 | fastq.gz | 1.0 GB | ||
| EGAF00000146417 | fastq.gz | 950.2 MB | ||
| EGAF00000146418 | fastq.gz | 959.3 MB | ||
| EGAF00000146419 | fastq.gz | 1.3 GB | ||
| EGAF00000146420 | fastq.gz | 1.3 GB | ||
| EGAF00000146421 | fastq.gz | 1.5 GB | ||
| EGAF00000146422 | fastq.gz | 1.5 GB | ||
| EGAF00000146423 | fastq.gz | 1.3 GB | ||
| EGAF00000146424 | fastq.gz | 1.4 GB | ||
| EGAF00000146425 | fastq.gz | 1.0 GB | ||
| EGAF00000146426 | fastq.gz | 1.0 GB | ||
| EGAF00000146427 | fastq.gz | 1.4 GB | ||
| EGAF00000146428 | fastq.gz | 1.4 GB | ||
| EGAF00000146429 | fastq.gz | 1.1 GB | ||
| EGAF00000146430 | fastq.gz | 1.2 GB | ||
| EGAF00000146431 | fastq.gz | 938.2 MB | ||
| EGAF00000146432 | fastq.gz | 951.6 MB | ||
| EGAF00000146433 | fastq.gz | 974.2 MB | ||
| EGAF00000146434 | fastq.gz | 977.4 MB | ||
| EGAF00000146435 | fastq.gz | 1.1 GB | ||
| EGAF00000146436 | fastq.gz | 1.1 GB | ||
| EGAF00000146437 | fastq.gz | 1.3 GB | ||
| EGAF00000146438 | fastq.gz | 1.3 GB | ||
| EGAF00000146439 | fastq.gz | 1.1 GB | ||
| EGAF00000146440 | fastq.gz | 1.1 GB | ||
| EGAF00000146441 | fastq.gz | 889.2 MB | ||
| EGAF00000146442 | fastq.gz | 902.8 MB | ||
| EGAF00000146443 | fastq.gz | 965.3 MB | ||
| EGAF00000146444 | fastq.gz | 975.9 MB | ||
| EGAF00000146445 | fastq.gz | 1.6 GB | ||
| EGAF00000146446 | fastq.gz | 1.7 GB | ||
| EGAF00000146447 | fastq.gz | 8.4 GB | ||
| EGAF00000146448 | fastq.gz | 8.5 GB | ||
| EGAF00000146449 | fastq.gz | 10.2 GB | ||
| EGAF00000146450 | fastq.gz | 10.4 GB | ||
| EGAF00000146451 | fastq.gz | 14.0 GB | ||
| EGAF00000146452 | fastq.gz | 14.2 GB | ||
| EGAF00000146453 | fastq.gz | 13.3 GB | ||
| EGAF00000146454 | fastq.gz | 13.5 GB | ||
| EGAF00000146455 | fastq.gz | 13.5 GB | ||
| EGAF00000146456 | fastq.gz | 13.8 GB | ||
| EGAF00000146457 | fastq.gz | 4.0 GB | ||
| EGAF00000146458 | fastq.gz | 4.1 GB | ||
| EGAF00000146459 | fastq.gz | 4.2 GB | ||
| EGAF00000146460 | fastq.gz | 4.3 GB | ||
| EGAF00000146461 | fastq.gz | 9.1 GB | ||
| EGAF00000146462 | fastq.gz | 9.2 GB | ||
| EGAF00000146463 | fastq.gz | 9.2 GB | ||
| EGAF00000146464 | fastq.gz | 9.3 GB | ||
| EGAF00000146465 | fastq.gz | 8.7 GB | ||
| EGAF00000146466 | fastq.gz | 8.8 GB | ||
| EGAF00000146467 | fastq.gz | 8.6 GB | ||
| EGAF00000146468 | fastq.gz | 8.7 GB | ||
| EGAF00000146469 | fastq.gz | 9.0 GB | ||
| EGAF00000146470 | fastq.gz | 9.1 GB | ||
| EGAF00000146471 | fastq.gz | 9.1 GB | ||
| EGAF00000146472 | fastq.gz | 9.2 GB | ||
| EGAF00000146473 | fastq.gz | 9.2 GB | ||
| EGAF00000146474 | fastq.gz | 9.3 GB | ||
| EGAF00000146475 | fastq.gz | 8.8 GB | ||
| EGAF00000146476 | fastq.gz | 8.9 GB | ||
| EGAF00000146477 | fastq.gz | 8.6 GB | ||
| EGAF00000146478 | fastq.gz | 8.8 GB | ||
| EGAF00000146479 | fastq.gz | 8.8 GB | ||
| EGAF00000146480 | fastq.gz | 8.9 GB | ||
| EGAF00000146481 | fastq.gz | 8.6 GB | ||
| EGAF00000146482 | fastq.gz | 8.8 GB | ||
| EGAF00000146483 | fastq.gz | 9.4 GB | ||
| EGAF00000146484 | fastq.gz | 9.6 GB | ||
| EGAF00000146485 | fastq.gz | 8.8 GB | ||
| EGAF00000146486 | fastq.gz | 8.9 GB | ||
| EGAF00000146487 | fastq.gz | 9.6 GB | ||
| EGAF00000146488 | fastq.gz | 9.8 GB | ||
| EGAF00000146489 | fastq.gz | 9.7 GB | ||
| EGAF00000146490 | fastq.gz | 9.9 GB | ||
| EGAF00000146491 | fastq.gz | 7.7 GB | ||
| EGAF00000146492 | fastq.gz | 7.8 GB | ||
| EGAF00000146493 | fastq.gz | 8.5 GB | ||
| EGAF00000146494 | fastq.gz | 8.7 GB | ||
| EGAF00000146495 | fastq.gz | 8.7 GB | ||
| EGAF00000146496 | fastq.gz | 8.9 GB | ||
| EGAF00000146497 | fastq.gz | 8.9 GB | ||
| EGAF00000146498 | fastq.gz | 9.1 GB | ||
| EGAF00000146499 | fastq.gz | 7.3 GB | ||
| EGAF00000146500 | fastq.gz | 7.5 GB | ||
| EGAF00000146501 | fastq.gz | 7.8 GB | ||
| EGAF00000146502 | fastq.gz | 7.9 GB | ||
| 228 Files (2.0 TB) | ||||