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Inter and intra - tumor heterogeneity in Colorectal Cancer

The dataset consists of two main sample groups. 1) The inter-tumour sample group contains a total of 97 samples from 27 patients. Each patient has a single normal and primary sample as well as one or more metastases. All samples were sequenced using IonTorrent PGM and a custom colorectal cancer (CRC) panel. 2) The intra-tumour sample group contains a total of 68 samples from a single tumour as well as a normal tissue sample. All 68 samples were sequenced using IonTorrent PGM and a custom CRC panel. Shallow whole genome sequencing was additionally applied to 10 of the samples using Illumina HiSeq 4000.

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DKTK Berlin partner site data access policy

DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom DKTK partner site Berlin grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: DKTK partner site Berlin and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. DKTK partner site Berlin: Campus Charité Mitte, Charité Comprehensive Cancer Center (CCCC) CC10, Charitéplatz 1 10117 Berlin 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. The User Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. The User Institution agrees not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (http://www.oecd.org/science/biotech/36198812.pdf ). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify DKTK partner site Berlin within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify DKTK partner site Berlin prior to any significant changes to the protocol for the Project. 14. The User Institution will notify DKTK partner site Berlin as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. DKTK partner site Berlin may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than DKTK partner site Berlin. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of Germany and shall be subject to the exclusive jurisdiction of the German courts. Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for DKTK partner site Berlin Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) Name of project that created the dataset Names of other data producers/collaborators Specific limitations on areas of research Minimum protection measures required File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (500 words max) All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* All Individuals that should have an account created at the EGA Name of Registered User Email Job Title APPENDIX III – PUBLICATION POLICY DKTK partner site Berlin intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. DKTK partner site Berlin anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until 6 months after these data were first made available on the relevant hosting database, unless DKTK partner site Berlin has provided written consent to earlier submission. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with DKTK partner site Berlin.

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
EGAS00001002150 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
EGAF00001432354 bam 147.9 MB
EGAF00001432355 bam 196.7 MB
EGAF00001432356 bam 88.0 MB
EGAF00001432357 bam 164.9 MB
EGAF00001432358 bam 132.9 MB
EGAF00001432359 bam 137.7 MB
EGAF00001432360 bam 119.2 MB
EGAF00001432361 bam 159.6 MB
EGAF00001432362 bam 118.3 MB
EGAF00001432363 bam 159.4 MB
EGAF00001432364 bam 147.2 MB
EGAF00001432365 bam 104.6 MB
EGAF00001432366 bam 138.3 MB
EGAF00001432367 bam 138.5 MB
EGAF00001432368 bam 136.5 MB
EGAF00001432369 bam 149.8 MB
EGAF00001432370 bam 158.7 MB
EGAF00001432371 bam 149.4 MB
EGAF00001432372 bam 174.1 MB
EGAF00001432373 bam 126.1 MB
EGAF00001432374 bam 140.5 MB
EGAF00001432375 bam 82.0 MB
EGAF00001432376 bam 160.4 MB
EGAF00001432377 bam 116.1 MB
EGAF00001432378 bam 131.0 MB
EGAF00001432379 bam 106.9 MB
EGAF00001432380 bam 121.8 MB
EGAF00001432381 bam 132.2 MB
EGAF00001432382 bam 152.4 MB
EGAF00001432383 bam 88.6 MB
EGAF00001432384 bam 144.0 MB
EGAF00001432385 bam 150.2 MB
EGAF00001432386 bam 143.2 MB
EGAF00001432387 bam 155.5 MB
EGAF00001432388 bam 151.8 MB
EGAF00001432389 bam 133.9 MB
EGAF00001432390 bam 133.2 MB
EGAF00001432391 bam 113.6 MB
EGAF00001432392 bam 131.1 MB
EGAF00001432393 bam 128.0 MB
EGAF00001432394 bam 133.8 MB
EGAF00001432395 bam 165.2 MB
EGAF00001432396 bam 72.1 MB
EGAF00001432397 bam 124.7 MB
EGAF00001432398 bam 121.5 MB
EGAF00001432399 bam 163.1 MB
EGAF00001432400 bam 103.0 MB
EGAF00001432401 bam 131.7 MB
EGAF00001432402 bam 137.4 MB
EGAF00001432403 bam 112.6 MB
EGAF00001432404 bam 150.3 MB
EGAF00001432405 bam 133.5 MB
EGAF00001432406 bam 137.3 MB
EGAF00001432407 bam 150.3 MB
EGAF00001432408 bam 120.7 MB
EGAF00001432409 bam 109.3 MB
EGAF00001432410 bam 137.5 MB
EGAF00001432411 bam 129.6 MB
EGAF00001432412 bam 123.3 MB
EGAF00001432413 bam 163.1 MB
EGAF00001432414 bam 148.6 MB
EGAF00001432415 bam 103.8 MB
EGAF00001432416 bam 127.5 MB
EGAF00001432417 bam 138.4 MB
EGAF00001432418 bam 130.4 MB
EGAF00001432419 bam 151.0 MB
EGAF00001432420 bam 141.6 MB
EGAF00001432421 bam 134.8 MB
EGAF00001432422 bam 144.8 MB
EGAF00001432423 bam 272.8 MB
EGAF00001432424 bam 885.3 MB
EGAF00001432425 bam 502.2 MB
EGAF00001432426 bam 308.8 MB
EGAF00001432427 bam 18.9 MB
EGAF00001432428 bam 607.6 MB
EGAF00001432429 bam 483.5 MB
EGAF00001432430 bam 306.8 MB
EGAF00001432431 bam 687.7 MB
EGAF00001432432 bam 598.3 MB
EGAF00001432433 bam 528.7 MB
EGAF00001432434 bam 564.3 MB
EGAF00001432435 bam 929.4 MB
EGAF00001432436 bam 1.1 GB
EGAF00001432437 bam 417.3 MB
EGAF00001432438 bam 524.9 MB
EGAF00001432439 bam 834.4 MB
EGAF00001432440 bam 21.4 MB
EGAF00001432441 bam 768.3 MB
EGAF00001432442 bam 912.2 MB
EGAF00001432443 bam 574.4 MB
EGAF00001432444 bam 17.8 MB
EGAF00001432445 bam 424.1 MB
EGAF00001432446 bam 733.6 MB
EGAF00001432447 bam 838.1 MB
EGAF00001432448 bam 18.6 MB
EGAF00001432449 bam 759.8 MB
EGAF00001432450 bam 564.8 MB
EGAF00001432451 bam 485.8 MB
EGAF00001432452 bam 536.2 MB
EGAF00001432453 bam 696.1 MB
EGAF00001432454 bam 670.8 MB
EGAF00001432455 bam 468.5 MB
EGAF00001432456 bam 455.0 MB
EGAF00001432457 bam 694.7 MB
EGAF00001432458 bam 105.9 MB
EGAF00001432459 bam 729.6 MB
EGAF00001432460 bam 886.2 MB
EGAF00001432461 bam 175.3 MB
EGAF00001432462 bam 744.7 MB
EGAF00001432463 bam 694.0 MB
EGAF00001432464 bam 642.3 MB
EGAF00001432465 bam 587.3 MB
EGAF00001432466 bam 721.6 MB
EGAF00001432467 bam 662.7 MB
EGAF00001432468 bam 611.3 MB
EGAF00001432469 bam 695.9 MB
EGAF00001432470 bam 31.4 MB
EGAF00001432472 bam 604.9 MB
EGAF00001432473 bam 779.0 MB
EGAF00001432474 bam 726.6 MB
EGAF00001432475 bam 457.2 MB
EGAF00001432476 bam 18.8 MB
EGAF00001432477 bam 702.6 MB
EGAF00001432478 bam 559.9 MB
EGAF00001432479 bam 31.1 MB
EGAF00001432480 bam 372.3 MB
EGAF00001432481 bam 1.1 GB
EGAF00001432482 bam 668.4 MB
EGAF00001432483 bam 703.1 MB
EGAF00001432484 bam 17.4 MB
EGAF00001432485 bam 721.7 MB
EGAF00001432486 bam 773.1 MB
EGAF00001432487 bam 460.4 MB
EGAF00001432488 bam 348.9 MB
EGAF00001432489 bam 552.7 MB
EGAF00001432490 bam 600.3 MB
EGAF00001432491 bam 516.5 MB
EGAF00001432492 bam 696.1 MB
EGAF00001432493 bam 313.9 MB
EGAF00001432494 bam 516.1 MB
EGAF00001432495 bam 716.5 MB
EGAF00001432496 bam 701.4 MB
EGAF00001432497 bam 303.5 MB
EGAF00001432498 bam 490.0 MB
EGAF00001432499 bam 626.2 MB
EGAF00001432500 bam 699.4 MB
EGAF00001432501 bam 816.6 MB
EGAF00001432502 bam 530.3 MB
EGAF00001432503 bam 680.8 MB
EGAF00001432504 bam 504.9 MB
EGAF00001432505 bam 518.2 MB
EGAF00001432506 bam 298.4 MB
EGAF00001432507 bam 772.3 MB
EGAF00001432508 bam 523.7 MB
EGAF00001432509 bam 969.2 MB
EGAF00001432510 bam 651.7 MB
EGAF00001432511 bam 275.5 MB
EGAF00001432512 bam 580.3 MB
EGAF00001432513 bam 777.5 MB
EGAF00001432514 bam 1.0 GB
EGAF00001432515 bam 207.2 MB
EGAF00001432516 bam 436.7 MB
EGAF00001432517 bam 637.5 MB
EGAF00001432518 bam 104.8 MB
EGAF00001432519 bam 170.5 MB
EGAF00001432520 bam 526.7 MB
EGAF00001432521 bam 485.5 MB
EGAF00001432522 bam 363.1 MB
EGAF00001432523 bam 574.2 MB
EGAF00001432524 bam 599.4 MB
EGAF00001432525 bam 550.8 MB
EGAF00001432526 bam 362.6 MB
EGAF00001432527 bam 551.3 MB
EGAF00001432528 bam 621.4 MB
EGAF00001432529 bam 554.1 MB
EGAF00001432530 bam 213.6 MB
EGAF00001432531 bam 657.2 MB
EGAF00001432532 bam 667.6 MB
EGAF00001432533 bam 621.3 MB
EGAF00001432534 bam 602.6 MB
EGAF00001432535 bam 348.3 MB
EGAF00001432536 bam 562.8 MB
EGAF00001432537 bam 609.7 MB
EGAF00001432538 bam 569.0 MB
EGAF00001432539 bam 401.5 MB
EGAF00001432540 bam 736.1 MB
EGAF00001432543 fastq.gz 1.8 GB
EGAF00001432544 fastq.gz 1.9 GB
EGAF00001432545 fastq.gz 1.4 GB
EGAF00001432546 fastq.gz 1.5 GB
EGAF00001432547 fastq.gz 1.3 GB
EGAF00001432548 fastq.gz 1.3 GB
EGAF00001432549 fastq.gz 1.4 GB
EGAF00001432550 fastq.gz 1.5 GB
EGAF00001432551 fastq.gz 1.2 GB
EGAF00001432552 fastq.gz 1.3 GB
EGAF00001432553 fastq.gz 1.6 GB
EGAF00001432554 fastq.gz 1.7 GB
EGAF00001432555 fastq.gz 1.5 GB
EGAF00001432556 fastq.gz 1.6 GB
EGAF00001432557 fastq.gz 2.0 GB
EGAF00001432558 fastq.gz 2.1 GB
EGAF00001432559 fastq.gz 1.0 GB
EGAF00001432560 fastq.gz 1.1 GB
EGAF00001432561 fastq.gz 1.4 GB
EGAF00001432562 fastq.gz 1.4 GB
EGAF00001432563 fastq.gz 1.4 GB
EGAF00001432564 fastq.gz 1.5 GB
EGAF00001432565 fastq.gz 1.7 GB
EGAF00001432566 fastq.gz 1.8 GB
EGAF00001432567 fastq.gz 1.5 GB
EGAF00001432568 fastq.gz 1.6 GB
EGAF00001432569 fastq.gz 1.6 GB
EGAF00001432570 fastq.gz 1.8 GB
EGAF00001432571 fastq.gz 2.4 GB
EGAF00001432572 fastq.gz 2.6 GB
EGAF00001432573 fastq.gz 1.8 GB
EGAF00001432574 fastq.gz 2.0 GB
EGAF00001432575 fastq.gz 2.5 GB
EGAF00001432576 fastq.gz 2.6 GB
EGAF00001432577 fastq.gz 2.1 GB
EGAF00001432578 fastq.gz 2.2 GB
EGAF00001432579 fastq.gz 1.6 GB
EGAF00001432580 fastq.gz 1.8 GB
EGAF00001432581 fastq.gz 1.8 GB
EGAF00001432582 fastq.gz 2.0 GB
EGAF00001432583 fastq.gz 1.2 GB
EGAF00001432584 fastq.gz 1.3 GB
EGAF00001432585 fastq.gz 1.4 GB
EGAF00001432586 fastq.gz 1.5 GB
EGAF00001589886 bam 578.8 MB
EGAF00001589887 bam 449.2 MB
EGAF00001589889 bam 536.1 MB
EGAF00001590150 bam 478.2 MB
EGAF00001590151 bam 509.9 MB
EGAF00001590152 bam 668.6 MB
EGAF00001591528 bam 760.7 MB
237 Files (150.9 GB)