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Wilm's tumor sequencing data

No. of samples: 80 (28 ULP-WGS, 26 WES, 26 RNA-SEQ) File types: FASTQ (28 ULP-WGS, 19 WES, 18 RNA) and BAM (7 WES, 8 RNA) Technology used: Sequencing - Illumina Novoseq 6000; Map/Align - Illumina DRAGEN v3.7.5; Genome assembly - GrCh38p13 Filename nomenclature: - SampleName_Passage_SampleType_TissueType_SequencingType - Passage of: PX = unknown; PZ = from patient; P0 = first passage from patient on plastic; P1 = first passage from plastic/PDX/organoid - SampleType: STN = normal; STT = tumor - SampleType STN: 00 = tissue unknown; 01 = adjacent normal; 02 = fibroblast; 03 = germline blood; 21 = cell line from patient tissue; 22 = cell line from PDX; 23 = cell line from patient fibroblast - SampleType STT: 00 = tissue unknown; 01 = primary tumor; 21 = cell line from patient; 22 = cell line from PDX - TissueType: WT = Wilm's tumor; 00 = kidney unknown; 01 = kidney left; 02 = kidney right - SequencingType: 00 = unknown; 02 = ultra-low pass whole-genome sequencing; 20 = whole-exome; 61 = bulk RNA-sequencing

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Andrew L. Hong Lab 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 Pediatric Solid Tumor Data Access Committee 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: Pediatric Solid Tumor Data Access Committee 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. Pediatric Solid Tumor Data Access Committee: Andrew Hong, Emory University, 1760 Haygood Drive NE, Atlanta, GA 30322; andrew.hong2@emory.edu 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 Pediatric Solid Tumor Data Access Committee within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Pediatric Solid Tumor Data Access Committee prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Pediatric Solid Tumor Data Access Committee as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Pediatric Solid Tumor Data Access Committee 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 Pediatric Solid Tumor Data Access Committee. 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. 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 Pediatric Solid Tumor Data Access Committee 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) EGA Study ID: Pending Dataset details: WGS, WES and/or RNA-seq from up to 10 Wilms Tumor tumors, matched cell lines along with adjacent normal tissue and matched cell lines. Name of project that created the dataset Targeting TRIP13 in Wilms Tumor with Nuclear Export Inhibitors Names of other data producers/collaborators Karuna Mittal1,2*, Benjamin P. Lee1,2*, Garrett W. Cooper1,2*, Yongdong Su1,2, Katie T. Skinner1,2, Jenny Shim1,2, Hunter C. Jonus1,2, Won Jun Kim3,4, Mihir Doshi3,4, Diego Almanza3,4, Bryan D. Kynnap3,4, Amanda L. Christie3, Xiaoping Yang4, Glenn S. Cowley4, Brittaney A. Leeper5, Christopher L. Morton6, Bhakti Dwivedi7, Taylor Lawrence1,2, Manali Rupji8, Paula Keskula4, Stephanie Meyer9, Catherine M. Clinton9, Manoj Bhasin1,2,8, Brian D. Crompton4,9, Yuen-Yi Tseng4, Jesse S. Boehm4, Keith L. Ligon4,10,11, David E. Root4, Andrew J. Murphy6, David M. Weinstock4,9, Prafulla C. Gokhale5, Jennifer M. Spangle7,8, Miguel N. Rivera4,12, Elizabeth A. Mullen4, Kimberly Stegmaier4,9, Kelly C. Goldsmith1,2,8, William C. Hahn3,4**, Andrew L. Hong1,2,8** 1Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 2Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA 3Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA 4Broad Institute of MIT and Harvard, Cambridge, MA, USA 5Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts. 6Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 7Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 8Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 9Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA 10Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA 11Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA 12Department of Pathology, Massachusetts General Hospital, Boston, MA, USA Specific limitations on areas of research DUO:0000042 General Research Use 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 Pediatric Solid Tumor Data Access Committee 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. Pediatric Solid Tumor Data Access Committee anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. 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 3 months after these data were first made available on the relevant hosting database, unless Pediatric Solid Tumor Data Access Committee 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 Pediatric Solid Tumor Data Access Committee.

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
EGAS00001007389 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
EGAF00008118280 fq.gz 890.3 MB
EGAF00008118281 fq.gz 930.0 MB
EGAF00008118282 fq.gz 1.0 GB
EGAF00008118283 fq.gz 1.1 GB
EGAF00008118284 fq.gz 4.5 GB
EGAF00008118285 fq.gz 4.8 GB
EGAF00008118286 fq.gz 1.0 GB
EGAF00008118287 fq.gz 1.1 GB
EGAF00008118288 fq.gz 3.2 GB
EGAF00008118289 fq.gz 3.3 GB
EGAF00008118290 fq.gz 1.4 GB
EGAF00008118291 fq.gz 1.5 GB
EGAF00008118292 fq.gz 3.3 GB
EGAF00008118293 fq.gz 3.5 GB
EGAF00008118294 fq.gz 1.7 GB
EGAF00008118295 fq.gz 1.8 GB
EGAF00008118296 fq.gz 1.1 GB
EGAF00008118297 fq.gz 1.1 GB
EGAF00008118298 fq.gz 1.1 GB
EGAF00008118299 fq.gz 1.1 GB
EGAF00008118300 fq.gz 3.5 GB
EGAF00008118301 fq.gz 3.7 GB
EGAF00008118302 fq.gz 1.0 GB
EGAF00008118303 fq.gz 1.1 GB
EGAF00008118304 fq.gz 3.3 GB
EGAF00008118305 fq.gz 3.4 GB
EGAF00008118306 fq.gz 1.8 GB
EGAF00008118307 fq.gz 1.9 GB
EGAF00008118308 fq.gz 4.9 GB
EGAF00008118309 fq.gz 5.2 GB
EGAF00008118310 fq.gz 1.6 GB
EGAF00008118311 fq.gz 1.7 GB
EGAF00008118312 fq.gz 1.0 GB
EGAF00008118313 fq.gz 1.1 GB
EGAF00008118314 fq.gz 1.1 GB
EGAF00008118315 fq.gz 1.1 GB
EGAF00008118316 fq.gz 4.2 GB
EGAF00008118317 fq.gz 4.3 GB
EGAF00008118318 fq.gz 2.0 GB
EGAF00008118319 fq.gz 2.0 GB
EGAF00008118320 fq.gz 5.5 GB
EGAF00008118321 fq.gz 5.8 GB
EGAF00008118322 fq.gz 2.0 GB
EGAF00008118323 fq.gz 2.1 GB
EGAF00008118324 fq.gz 991.4 MB
EGAF00008118325 fq.gz 1.1 GB
EGAF00008118326 fq.gz 2.1 GB
EGAF00008118327 fq.gz 2.2 GB
EGAF00008118328 fq.gz 1.1 GB
EGAF00008118329 fq.gz 1.1 GB
EGAF00008118330 fq.gz 1.7 GB
EGAF00008118331 fq.gz 1.8 GB
EGAF00008118332 fq.gz 1.1 GB
EGAF00008118333 fq.gz 1.1 GB
EGAF00008118334 fq.gz 1.6 GB
EGAF00008118335 fq.gz 1.6 GB
EGAF00008118336 fq.gz 2.0 GB
EGAF00008118337 fq.gz 2.0 GB
EGAF00008118338 fq.gz 1.5 GB
EGAF00008118339 fq.gz 1.6 GB
EGAF00008118340 fq.gz 990.0 MB
EGAF00008118341 fq.gz 1.0 GB
EGAF00008118342 fq.gz 1.5 GB
EGAF00008118343 fq.gz 1.6 GB
EGAF00008118344 fq.gz 1.8 GB
EGAF00008118345 fq.gz 1.8 GB
EGAF00008118346 fq.gz 1.9 GB
EGAF00008118347 fq.gz 2.1 GB
EGAF00008118348 fq.gz 622.0 MB
EGAF00008118349 fq.gz 641.5 MB
EGAF00008118350 fq.gz 2.1 GB
EGAF00008118351 fq.gz 2.2 GB
EGAF00008118352 fq.gz 1.9 GB
EGAF00008118353 fq.gz 1.9 GB
EGAF00008118354 fq.gz 435.7 MB
EGAF00008118355 fq.gz 445.8 MB
EGAF00008118356 fq.gz 2.2 GB
EGAF00008118357 fq.gz 2.3 GB
EGAF00008118358 fq.gz 385.0 MB
EGAF00008118359 fq.gz 394.7 MB
EGAF00008118360 fq.gz 1.5 GB
EGAF00008118361 fq.gz 1.6 GB
EGAF00008118362 fq.gz 2.9 GB
EGAF00008118363 fq.gz 3.0 GB
EGAF00008118364 bam 4.4 GB
EGAF00008118365 fq.gz 1.1 GB
EGAF00008118366 fq.gz 1.2 GB
EGAF00008118367 bam 5.6 GB
EGAF00008118368 fq.gz 961.7 MB
EGAF00008118369 fq.gz 1.0 GB
EGAF00008118370 bam 2.8 GB
EGAF00008118371 bam 41.6 GB
EGAF00008118372 bam 3.6 GB
EGAF00008118373 fq.gz 847.3 MB
EGAF00008118374 fq.gz 874.5 MB
EGAF00008118375 fq.gz 1.7 GB
EGAF00008118376 fq.gz 1.8 GB
EGAF00008118377 fq.gz 1.7 GB
EGAF00008118378 fq.gz 1.7 GB
EGAF00008118379 fq.gz 1.2 GB
EGAF00008118380 fq.gz 1.2 GB
EGAF00008118381 fq.gz 997.1 MB
EGAF00008118382 fq.gz 1.1 GB
EGAF00008118383 fq.gz 824.4 MB
EGAF00008118384 fq.gz 876.2 MB
EGAF00008118385 fq.gz 818.0 MB
EGAF00008118386 fq.gz 882.0 MB
EGAF00008118387 fq.gz 1.8 GB
EGAF00008118388 fq.gz 1.9 GB
EGAF00008118389 bam 45.6 GB
EGAF00008118390 bam 3.6 GB
EGAF00008118391 bam 39.3 GB
EGAF00008118392 bam 3.6 GB
EGAF00008118393 fq.gz 821.6 MB
EGAF00008118394 fq.gz 861.7 MB
EGAF00008118395 fq.gz 1.5 GB
EGAF00008118396 fq.gz 1.5 GB
EGAF00008118397 fq.gz 1.8 GB
EGAF00008118398 fq.gz 1.9 GB
EGAF00008118399 fq.gz 1.7 GB
EGAF00008118400 fq.gz 1.7 GB
EGAF00008118401 fq.gz 1.6 GB
EGAF00008118402 fq.gz 1.7 GB
EGAF00008118403 fq.gz 1.1 GB
EGAF00008118404 fq.gz 1.2 GB
EGAF00008118405 fq.gz 1.1 GB
EGAF00008118406 fq.gz 1.2 GB
EGAF00008118407 bam 47.5 GB
EGAF00008118408 bam 4.6 GB
EGAF00008118409 bam 43.7 GB
EGAF00008118410 bam 3.7 GB
EGAF00008118411 fq.gz 813.6 MB
EGAF00008118412 fq.gz 868.7 MB
EGAF00008118413 fq.gz 1.2 GB
EGAF00008118414 fq.gz 1.2 GB
EGAF00008118415 fq.gz 1.7 GB
EGAF00008118416 fq.gz 1.8 GB
EGAF00008118417 fq.gz 1.6 GB
EGAF00008118418 fq.gz 1.7 GB
EGAF00008118419 bam 38.8 GB
EGAF00008118420 bam 4.1 GB
EGAF00008118421 fq.gz 992.3 MB
EGAF00008118422 fq.gz 1.0 GB
143 Files (516.2 GB)