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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.

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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)