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WGS short read and 10X linked read sequencing of HR Deficient breast cancers

A set of tumor/normal paired sequencing experiments, performed in short read WGS and 10X linked read whole genomes. BAM files aligned to hg19 are provided. Sample Alias number and Subject ID reflects patient of origin. T/N distinction discriminates between tumor and normal (peripheral blood) tissue.

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MSKCC, WCM, NYGC PIs for HRD project.

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 Pier Selenica 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: Simon Powell, Jeremy Setton, Nadeem Riaz, Jorge-Reis Filho, Marcin Imielinski 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. Marcin Imielinski: New York Genome Center Simon Powell, Jeremy Setton, Nadeem Riaz, Jorge-Reis Filho: Memorial Sloan Kettering Cancer Center 2 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/w eb_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 3 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 Simon Powell, Jeremy Setton, Nadeem Riaz, or Jorge-Reis Filho, Marcin Imielinski within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Simon Powell, Jeremy Setton, Nadeem Riaz, or Jorge-Reis Filho, Marcin Imielinski prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Simon Powell, Jeremy Setton, Nadeem Riaz, or Jorge-Reis Filho, Marcin Imielinski as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Simon Powell, Jeremy Setton, Nadeem Riaz, or Jorge-Reis Filho, Marcin Imielinski 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 Simon Powell, Jeremy Setton, Nadeem Riaz, or Jorge- Reis Filho, Marcin Imielinski. 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 England and Wales and shall be subject to the exclusive jurisdiction of the English courts.

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
EGAS00001007186 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
EGAF00008041958 bam 31.1 GB
EGAF00008041959 bam 116.5 GB
EGAF00008041960 bam 34.8 GB
EGAF00008041961 bam 78.9 GB
EGAF00008041962 bam 30.1 GB
EGAF00008041963 bam 107.1 GB
EGAF00008041964 bam 35.9 GB
EGAF00008041965 bam 56.9 GB
EGAF00008041966 bam 42.7 GB
EGAF00008041967 bam 93.1 GB
EGAF00008041968 bam 74.8 GB
EGAF00008041969 bam 52.0 GB
EGAF00008041970 bam 34.5 GB
EGAF00008041971 bam 44.5 GB
EGAF00008041972 bam 70.1 GB
EGAF00008041973 bam 111.0 GB
EGAF00008041974 bam 42.1 GB
EGAF00008041975 bam 111.7 GB
EGAF00008041976 bam 20.8 GB
EGAF00008041977 bam 121.0 GB
EGAF00008041978 bam 53.5 GB
EGAF00008041979 bam 112.3 GB
EGAF00008041980 bam 97.7 GB
EGAF00008041981 bam 68.4 GB
EGAF00008041982 bam 55.0 GB
EGAF00008041983 bam 49.7 GB
EGAF00008041984 bam 35.6 GB
EGAF00008041985 bam 128.2 GB
EGAF00008041986 bam 78 Bytes
EGAF00008041987 bam 117.3 GB
EGAF00008041988 bam 38.4 GB
EGAF00008041989 bam 57.8 GB
EGAF00008041990 bam 37.4 GB
EGAF00008041991 bam 41.8 GB
EGAF00008041992 bam 33.1 GB
EGAF00008041993 bam 84.9 GB
EGAF00008041994 bam 37.1 GB
EGAF00008041995 bam 70.5 GB
EGAF00008041996 bam 43.0 GB
EGAF00008041997 bam 53.1 GB
EGAF00008041998 bam 37.1 GB
EGAF00008041999 bam 81.3 GB
EGAF00008042000 bam 30.7 GB
EGAF00008042001 bam 40.5 GB
EGAF00008042002 bam 38.2 GB
EGAF00008042003 bam 51.0 GB
EGAF00008042004 bam 46.2 GB
EGAF00008042005 bam 90.1 GB
EGAF00008042006 bam 30.8 GB
EGAF00008042007 bam 55.8 GB
EGAF00008042008 bam 41.4 GB
EGAF00008042009 bam 79.4 GB
EGAF00008042010 bam 30.3 GB
EGAF00008042011 bam 49.6 GB
EGAF00008042012 bam 43.1 GB
EGAF00008042013 bam 50.7 GB
EGAF00008042014 bam 50.8 GB
EGAF00008042015 bam 79.4 GB
EGAF00008042016 bam 38.6 GB
EGAF00008042017 bam 77.0 GB
EGAF00008042018 bam 38.2 GB
EGAF00008042019 bam 90.3 GB
EGAF00008042020 bam 43.4 GB
EGAF00008042021 bam 60.2 GB
EGAF00008042022 bam 47.3 GB
EGAF00008042023 bam 68.9 GB
EGAF00008042024 bam 26.8 GB
EGAF00008042025 bam 41.0 GB
EGAF00008042026 bam 45.4 GB
EGAF00008042027 bam 69.8 GB
EGAF00008042028 bam 28.5 GB
EGAF00008042029 bam 94.3 GB
EGAF00008042030 bam 25.5 GB
EGAF00008042031 bam 68.4 GB
EGAF00008042032 bam 40.8 GB
EGAF00008042033 bam 56.4 GB
EGAF00008042034 bam 51.5 GB
EGAF00008042035 bam 88.5 GB
EGAF00008042036 bam 34.2 GB
EGAF00008042037 bam 81.0 GB
EGAF00008042038 bam 45.7 GB
EGAF00008042039 bam 89.0 GB
EGAF00008042040 bam 44.9 GB
EGAF00008042041 bam 93.5 GB
EGAF00008042042 bam 22.7 GB
EGAF00008042043 bam 89.6 GB
EGAF00008042044 bam 39.8 GB
EGAF00008042045 bam 61.7 GB
EGAF00008042046 bam 48.1 GB
EGAF00008042047 bam 28.7 GB
EGAF00008042048 bam 44.0 GB
EGAF00008042049 bam 90.3 GB
EGAF00008042050 bam 30.1 GB
EGAF00008042051 bam 64.2 GB
EGAF00008042052 bam 44.0 GB
EGAF00008042053 bam 64.5 GB
EGAF00008042054 bam 56.9 GB
EGAF00008042055 bam 115.3 GB
EGAF00008042057 bam 155.3 GB
EGAF00008042058 bam 76.0 GB
EGAF00008042059 bam 106.6 GB
EGAF00008042060 bam 179.5 GB
EGAF00008042061 bam 484.7 GB
EGAF00008042062 bam 86.4 GB
EGAF00008042063 bam 308.5 GB
EGAF00008042065 bam 310.3 GB
EGAF00008042066 bam 85.7 GB
EGAF00008042067 bam 530.0 GB
EGAF00008042068 bam 90.1 GB
EGAF00008042069 bam 133.2 GB
EGAF00008042070 bam 209.5 GB
EGAF00008042072 bam 60.0 GB
EGAF00008042073 bam 151.9 GB
EGAF00008042074 bam 52.6 GB
EGAF00008042075 bam 95.7 GB
EGAF00008042076 bam 220.5 GB
EGAF00008042077 bam 422.2 GB
EGAF00008042078 bam 61.0 GB
EGAF00008042079 bam 110.1 GB
EGAF00008042080 bam 224.2 GB
EGAF00008042081 bam 402.1 GB
EGAF00008042082 bam 67.4 GB
EGAF00008042083 bam 114.8 GB
EGAF00008042086 bam 172.3 GB
EGAF00008042087 bam 282.9 GB
EGAF00008042088 bam 70.2 GB
EGAF00008042089 bam 121.5 GB
EGAF00008042090 bam 129.7 GB
EGAF00008042091 bam 198.4 GB
EGAF00008042092 bam 119.6 GB
EGAF00008042093 bam 162.2 GB
EGAF00008042094 bam 141.7 GB
EGAF00008042095 bam 260.3 GB
EGAF00008042096 bam 125.5 GB
EGAF00008042097 bam 255.8 GB
EGAF00008042098 bam 113.1 GB
EGAF00008042099 bam 109.0 GB
EGAF00008042100 bam 136.7 GB
EGAF00008042101 bam 218.7 GB
EGAF00008042102 bam 82.1 GB
EGAF00008042103 bam 205.1 GB
EGAF00008042104 bam 96.5 GB
EGAF00008042105 bam 120.0 GB
EGAF00008042107 bam 202.5 GB
EGAF00008042108 bam 132.6 GB
EGAF00008042109 bam 114.9 GB
EGAF00008042110 bam 154.7 GB
EGAF00008042111 bam 255.7 GB
EGAF00008042112 bam 132.7 GB
EGAF00008042113 bam 237.9 GB
EGAF00008042114 bam 146.1 GB
EGAF00008042115 bam 94.4 GB
EGAF00008042116 bam 109.1 GB
EGAF00008042117 bam 232.9 GB
EGAF00008042118 bam 98.9 GB
EGAF00008042119 bam 121.2 GB
EGAF00008042120 bam 202.4 GB
EGAF00008042121 bam 301.2 GB
EGAF00008042122 bam 123.3 GB
EGAF00008042123 bam 207.4 GB
EGAF00008042124 bam 113.5 GB
EGAF00008042125 bam 166.2 GB
EGAF00008042126 bam 63.8 GB
EGAF00008042127 bam 93.5 GB
EGAF00008042128 bam 83.6 GB
EGAF00008042129 bam 160.0 GB
EGAF00008042130 bam 209.4 GB
EGAF00008042131 bam 271.2 GB
EGAF00008042132 bam 166.9 GB
EGAF00008042133 bam 124.3 GB
EGAF00008042134 bam 173.6 GB
EGAF00008042135 bam 244.9 GB
EGAF00008042136 bam 92.3 GB
EGAF00008042137 bam 118.2 GB
EGAF00008042138 bam 120.7 GB
EGAF00008042139 bam 246.8 GB
EGAF00008042140 bam 54.9 GB
EGAF00008042141 bam 128.5 GB
EGAF00008042142 bam 91.5 GB
EGAF00008042143 bam 161.7 GB
EGAF00008042144 bam 77.8 GB
EGAF00008042145 bam 113.7 GB
EGAF00008042146 bam 65.3 GB
EGAF00008042147 bam 126.0 GB
EGAF00008042148 bam 38.3 GB
EGAF00008042149 bam 157.2 GB
EGAF00008042150 bam 70.5 GB
EGAF00008042151 bam 205.5 GB
EGAF00008042152 bam 132.3 GB
EGAF00008042153 bam 171.3 GB
190 Files (20.5 TB)