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Exome sequencing data from tumor progression cohort

This dataset, named Stockholm tumor progression cohort, contains exome-sequencing samples of matched primary and metastasis samples from 20 metastatic breast cancer patients. All patients have one or more sequenced normal samples as well. The total number of samples is 125. The dataset has been used, apart from other studies, to explore tumor evolution patterns in metastatic breast cancer at Karolinska Institute Stockholm.

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Data Access Agreement for exome sequencing data from 20 metastatic breast cancer patients sequenced by Karolinska Institute

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 Prof. Jonas Bergh, M.D, Ph.D. F.R.C.P. Professor of Oncology at Karolinska Institute and/or Dr. Johan Hartman, MD, PhD. Associate Professor of Pathology at Karolinska Institute 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: Prof. Jonas Bergh, M.D, Ph.D. F.R.C.P. Professor of Oncology at Karolinska Institute and/or Dr. Johan Hartman, MD, PhD. Associate Professor of Pathology at Karolinska Institute 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. Data producer Institution: Karolinska Institute, Stockholm, Sweden 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 Authorised Personnel within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Authorised Personnel prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Authorised Personnel as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Authorised Personnel 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 Authorised Personnel. 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 Sweden and shall be subject to the exclusive jurisdiction of the Swedish 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 Authorized Personnel 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: EGAS00001002737 This dataset consists of matched primary and metastasis whole-exome sequenced samples from 20 metastatic breast cancer patients (125 paired-end files in FASTQ format). Name of project that created the dataset Evolutionary history of 20 metastatic breast cancer using exome-sequencing data Names of other data producers/collaborators Specific limitations on areas of research Minimum protection measures required The data should be held in encrypted form and can be in unencrypted form only during actual analysis after which it will be again encrypted. 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 Authorised Personnel 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. Authorised Personnel 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 XX months after these data were first made available on the relevant hosting database, unless Authorised Personnel 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 Authorised Personnel.

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
EGAS00001002737 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
EGAF00001794983 fastq.gz 2.7 GB
EGAF00001794984 fastq.gz 2.7 GB
EGAF00001794985 fastq.gz 4.4 GB
EGAF00001794986 fastq.gz 4.4 GB
EGAF00001794987 fastq.gz 2.4 GB
EGAF00001794988 fastq.gz 2.4 GB
EGAF00001794989 fastq.gz 2.3 GB
EGAF00001794990 fastq.gz 2.3 GB
EGAF00001794991 fastq.gz 3.9 GB
EGAF00001794992 fastq.gz 3.9 GB
EGAF00001794993 fastq.gz 3.8 GB
EGAF00001794994 fastq.gz 3.8 GB
EGAF00001794995 fastq.gz 2.4 GB
EGAF00001794996 fastq.gz 2.4 GB
EGAF00001794997 fastq.gz 3.6 GB
EGAF00001794998 fastq.gz 3.6 GB
EGAF00001794999 fastq.gz 7.0 GB
EGAF00001795000 fastq.gz 6.9 GB
EGAF00001795001 fastq.gz 4.4 GB
EGAF00001795002 fastq.gz 4.4 GB
EGAF00001795003 fastq.gz 6.3 GB
EGAF00001795004 fastq.gz 6.3 GB
EGAF00001795005 fastq.gz 4.3 GB
EGAF00001795006 fastq.gz 4.3 GB
EGAF00001795007 fastq.gz 1.7 GB
EGAF00001795008 fastq.gz 1.7 GB
EGAF00001795009 fastq.gz 2.6 GB
EGAF00001795010 fastq.gz 2.6 GB
EGAF00001795011 fastq.gz 1.5 GB
EGAF00001795012 fastq.gz 1.5 GB
EGAF00001795013 fastq.gz 5.5 GB
EGAF00001795014 fastq.gz 5.5 GB
EGAF00001795015 fastq.gz 2.5 GB
EGAF00001795016 fastq.gz 2.5 GB
EGAF00001795017 fastq.gz 5.2 GB
EGAF00001795018 fastq.gz 5.3 GB
EGAF00001795019 fastq.gz 5.1 GB
EGAF00001795020 fastq.gz 5.2 GB
EGAF00001795021 fastq.gz 5.7 GB
EGAF00001795022 fastq.gz 5.8 GB
EGAF00001795023 fastq.gz 6.3 GB
EGAF00001795024 fastq.gz 6.3 GB
EGAF00001795025 fastq.gz 4.7 GB
EGAF00001795026 fastq.gz 4.6 GB
EGAF00001795027 fastq.gz 5.6 GB
EGAF00001795028 fastq.gz 5.6 GB
EGAF00001795029 fastq.gz 2.6 GB
EGAF00001795030 fastq.gz 2.6 GB
EGAF00001795031 fastq.gz 2.3 GB
EGAF00001795032 fastq.gz 2.2 GB
EGAF00001795033 fastq.gz 3.0 GB
EGAF00001795034 fastq.gz 2.9 GB
EGAF00001795035 fastq.gz 8.0 GB
EGAF00001795036 fastq.gz 7.9 GB
EGAF00001795037 fastq.gz 3.2 GB
EGAF00001795038 fastq.gz 3.2 GB
EGAF00001795039 fastq.gz 4.0 GB
EGAF00001795040 fastq.gz 3.9 GB
EGAF00001795041 fastq.gz 3.9 GB
EGAF00001795042 fastq.gz 3.9 GB
EGAF00001795043 fastq.gz 1.9 GB
EGAF00001795044 fastq.gz 1.9 GB
EGAF00001795045 fastq.gz 1.7 GB
EGAF00001795046 fastq.gz 1.7 GB
EGAF00001795047 fastq.gz 2.8 GB
EGAF00001795048 fastq.gz 2.8 GB
EGAF00001795049 fastq.gz 4.5 GB
EGAF00001795050 fastq.gz 4.6 GB
EGAF00001795051 fastq.gz 4.5 GB
EGAF00001795052 fastq.gz 4.6 GB
EGAF00001795053 fastq.gz 3.5 GB
EGAF00001795054 fastq.gz 3.4 GB
EGAF00001795055 fastq.gz 4.5 GB
EGAF00001795056 fastq.gz 4.5 GB
EGAF00001795057 fastq.gz 8.7 GB
EGAF00001795058 fastq.gz 8.8 GB
EGAF00001795059 fastq.gz 2.4 GB
EGAF00001795060 fastq.gz 2.4 GB
EGAF00001795061 fastq.gz 4.3 GB
EGAF00001795062 fastq.gz 4.3 GB
EGAF00001795063 fastq.gz 7.0 GB
EGAF00001795064 fastq.gz 7.0 GB
EGAF00001795065 fastq.gz 4.5 GB
EGAF00001795066 fastq.gz 4.4 GB
EGAF00001795067 fastq.gz 3.5 GB
EGAF00001795068 fastq.gz 3.6 GB
EGAF00001795069 fastq.gz 5.4 GB
EGAF00001795070 fastq.gz 5.3 GB
EGAF00001795071 fastq.gz 8.2 GB
EGAF00001795072 fastq.gz 8.2 GB
EGAF00001795073 fastq.gz 5.6 GB
EGAF00001795074 fastq.gz 5.6 GB
EGAF00001795075 fastq.gz 7.0 GB
EGAF00001795076 fastq.gz 7.0 GB
EGAF00001795077 fastq.gz 5.9 GB
EGAF00001795078 fastq.gz 6.0 GB
EGAF00001795079 fastq.gz 5.0 GB
EGAF00001795080 fastq.gz 5.1 GB
EGAF00001795081 fastq.gz 5.3 GB
EGAF00001795082 fastq.gz 5.4 GB
EGAF00001795083 fastq.gz 1.1 GB
EGAF00001795084 fastq.gz 1.1 GB
EGAF00001795085 fastq.gz 1.7 GB
EGAF00001795086 fastq.gz 1.6 GB
EGAF00001795087 fastq.gz 2.7 GB
EGAF00001795088 fastq.gz 2.7 GB
EGAF00001795089 fastq.gz 2.8 GB
EGAF00001795090 fastq.gz 2.8 GB
EGAF00001795091 fastq.gz 9.6 GB
EGAF00001795092 fastq.gz 9.4 GB
EGAF00001795093 fastq.gz 7.2 GB
EGAF00001795094 fastq.gz 7.1 GB
EGAF00001795095 fastq.gz 5.9 GB
EGAF00001795096 fastq.gz 6.0 GB
EGAF00001795097 fastq.gz 1.0 GB
EGAF00001795098 fastq.gz 988.5 MB
EGAF00001795099 fastq.gz 2.4 GB
EGAF00001795100 fastq.gz 2.3 GB
EGAF00001795101 fastq.gz 9.9 GB
EGAF00001795102 fastq.gz 10.1 GB
EGAF00001795103 fastq.gz 5.8 GB
EGAF00001795104 fastq.gz 5.7 GB
EGAF00001795105 fastq.gz 1.5 GB
EGAF00001795106 fastq.gz 1.4 GB
EGAF00001795107 fastq.gz 4.5 GB
EGAF00001795108 fastq.gz 4.4 GB
EGAF00001795109 fastq.gz 2.4 GB
EGAF00001795110 fastq.gz 2.3 GB
EGAF00001795111 fastq.gz 4.8 GB
EGAF00001795112 fastq.gz 4.7 GB
EGAF00001795113 fastq.gz 9.2 GB
EGAF00001795114 fastq.gz 9.3 GB
EGAF00001795115 fastq.gz 3.5 GB
EGAF00001795116 fastq.gz 3.4 GB
EGAF00001795117 fastq.gz 4.9 GB
EGAF00001795118 fastq.gz 4.8 GB
EGAF00001795119 fastq.gz 4.5 GB
EGAF00001795120 fastq.gz 4.4 GB
EGAF00001795121 fastq.gz 3.6 GB
EGAF00001795122 fastq.gz 3.5 GB
EGAF00001795123 fastq.gz 5.4 GB
EGAF00001795124 fastq.gz 5.5 GB
EGAF00001795125 fastq.gz 3.1 GB
EGAF00001795126 fastq.gz 3.0 GB
EGAF00001795127 fastq.gz 3.9 GB
EGAF00001795128 fastq.gz 3.8 GB
EGAF00001795129 fastq.gz 3.9 GB
EGAF00001795130 fastq.gz 3.8 GB
EGAF00001795131 fastq.gz 12.1 GB
EGAF00001795132 fastq.gz 12.3 GB
EGAF00001795133 fastq.gz 3.9 GB
EGAF00001795134 fastq.gz 3.8 GB
EGAF00001795135 fastq.gz 3.9 GB
EGAF00001795136 fastq.gz 3.9 GB
EGAF00001795137 fastq.gz 4.3 GB
EGAF00001795138 fastq.gz 4.2 GB
EGAF00001795139 fastq.gz 3.4 GB
EGAF00001795140 fastq.gz 3.4 GB
EGAF00001795141 fastq.gz 5.4 GB
EGAF00001795142 fastq.gz 5.3 GB
EGAF00001795143 fastq.gz 4.1 GB
EGAF00001795144 fastq.gz 4.0 GB
EGAF00001795145 fastq.gz 1.4 GB
EGAF00001795146 fastq.gz 1.4 GB
EGAF00001795147 fastq.gz 2.9 GB
EGAF00001795148 fastq.gz 2.8 GB
EGAF00001795149 fastq.gz 396.8 MB
EGAF00001795150 fastq.gz 384.6 MB
EGAF00001795151 fastq.gz 6.7 GB
EGAF00001795152 fastq.gz 6.5 GB
EGAF00001795153 fastq.gz 1.4 GB
EGAF00001795154 fastq.gz 1.4 GB
EGAF00001795155 fastq.gz 2.1 GB
EGAF00001795156 fastq.gz 2.1 GB
EGAF00001795157 fastq.gz 2.2 GB
EGAF00001795158 fastq.gz 2.1 GB
EGAF00001795159 fastq.gz 9.0 GB
EGAF00001795160 fastq.gz 8.9 GB
EGAF00001795161 fastq.gz 8.6 GB
EGAF00001795162 fastq.gz 8.4 GB
EGAF00001795163 fastq.gz 6.3 GB
EGAF00001795164 fastq.gz 6.2 GB
EGAF00001795165 fastq.gz 3.4 GB
EGAF00001795166 fastq.gz 3.4 GB
EGAF00001795167 fastq.gz 5.5 GB
EGAF00001795168 fastq.gz 5.4 GB
EGAF00001795169 fastq.gz 2.4 GB
EGAF00001795170 fastq.gz 2.3 GB
EGAF00001795171 fastq.gz 2.4 GB
EGAF00001795172 fastq.gz 2.3 GB
EGAF00001795173 fastq.gz 3.8 GB
EGAF00001795174 fastq.gz 3.7 GB
EGAF00001795175 fastq.gz 4.2 GB
EGAF00001795176 fastq.gz 4.1 GB
EGAF00001795177 fastq.gz 3.9 GB
EGAF00001795178 fastq.gz 3.8 GB
EGAF00001795179 fastq.gz 3.3 GB
EGAF00001795180 fastq.gz 3.4 GB
EGAF00001795181 fastq.gz 1.8 GB
EGAF00001795182 fastq.gz 1.8 GB
EGAF00001795183 fastq.gz 2.2 GB
EGAF00001795184 fastq.gz 2.2 GB
EGAF00001795185 fastq.gz 1.2 GB
EGAF00001795186 fastq.gz 1.2 GB
EGAF00001795187 fastq.gz 7.1 GB
EGAF00001795188 fastq.gz 7.2 GB
EGAF00001795189 fastq.gz 7.8 GB
EGAF00001795190 fastq.gz 7.9 GB
EGAF00001795191 fastq.gz 6.9 GB
EGAF00001795192 fastq.gz 7.0 GB
EGAF00001795193 fastq.gz 8.3 GB
EGAF00001795194 fastq.gz 8.4 GB
EGAF00001795195 fastq.gz 6.1 GB
EGAF00001795196 fastq.gz 6.2 GB
EGAF00001795197 fastq.gz 7.4 GB
EGAF00001795198 fastq.gz 7.5 GB
EGAF00001795199 fastq.gz 6.0 GB
EGAF00001795200 fastq.gz 6.1 GB
EGAF00001795201 fastq.gz 9.8 GB
EGAF00001795202 fastq.gz 10.0 GB
EGAF00001795203 fastq.gz 3.2 GB
EGAF00001795204 fastq.gz 3.5 GB
EGAF00001795205 fastq.gz 4.3 GB
EGAF00001795206 fastq.gz 4.7 GB
EGAF00001795207 fastq.gz 4.9 GB
EGAF00001795208 fastq.gz 5.2 GB
EGAF00001795209 fastq.gz 5.8 GB
EGAF00001795210 fastq.gz 6.2 GB
EGAF00001795211 fastq.gz 4.0 GB
EGAF00001795212 fastq.gz 4.3 GB
EGAF00001795213 fastq.gz 4.0 GB
EGAF00001795214 fastq.gz 4.3 GB
EGAF00001795215 fastq.gz 3.3 GB
EGAF00001795216 fastq.gz 3.5 GB
EGAF00001795217 fastq.gz 4.0 GB
EGAF00001795218 fastq.gz 4.3 GB
EGAF00001795219 fastq.gz 3.9 GB
EGAF00001795220 fastq.gz 4.2 GB
EGAF00001795221 fastq.gz 6.8 GB
EGAF00001795222 fastq.gz 7.2 GB
EGAF00001795223 fastq.gz 10.3 GB
EGAF00001795224 fastq.gz 10.7 GB
EGAF00001795225 fastq.gz 8.0 GB
EGAF00001795226 fastq.gz 8.4 GB
EGAF00001795227 fastq.gz 5.1 GB
EGAF00001795228 fastq.gz 5.2 GB
EGAF00001795229 fastq.gz 3.5 GB
EGAF00001795230 fastq.gz 3.8 GB
EGAF00001795231 fastq.gz 2.8 GB
EGAF00001795232 fastq.gz 2.8 GB
250 Files (1.1 TB)