Whole exome sequencing study of cholesteatoma patients from affected families
This study used whole exome sequencing on 21 patients with cholesteatoma from 10 families in order to identify variants that may attribute to cholesteatoma aetiology. Exomes were enriched for using hybridisation selection and subject to DNA-sequencing. This datasets is formed of two batches as they were sequencing at different times. Batch-1 exomes were selected for using Nimblegen capture (4-plex) and sequenced on Illumina Hiseq 4000 and batch-2 was exome selected using Agilent SureSelect Human All Exon v6 and sequenced on the Illumina NovaSeq 6000. All samples within the same family were processed within the same batch. This dataset is comprised on BAM files mapped using cgpMAP v3.2.0 (bwa-mem) using the GRCh38.
- 46 samples
- DAC: EGAC00001002612
- Technologies: Illumina HiSeq 4000, Illumina NovaSeq 6000
This policy provides a summarised version of the data access agreement (DAA) which can be made available to a user upon request.
Below is a summarised version for policies within our data access agreement (DAA), for the release of the data a signed DAA is required. 1. The User Institution is responsible for determining the purposes for which and manner in which it will process the Data after receipt from the Data Producers. 2. The User Institution agrees to only use these Data for the purpose of the Project and only for Research Purposes. 3. 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. 4. 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. 5. 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. 6. The User Institution warrants that in carrying out its obligations under this agreement it will not breach the Data Protection Legislation or do or omit to do anything that might cause the Data Producers to be in breach of the Data Protection Legislation. 7. 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. 8. 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. 9. The User Institution shall indemnify The Data Producers against any costs, claims, expenses (including reasonable legal costs), damages, liabilities, actions and proceedings brought against the Data Producers by any third party (including but not limited to the Data Subjects) arising out of a breach of this agreement by the User Institution. 10. 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). 11. 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. 12. 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 ). 14. 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, and to confirm to the Data Producers when the Data has been destroyed. 15. The User Institution will notify University of East Anglia within 30 days of any changes or departures of Authorised Personnel. 16. The User Institution will notify University of East Anglia prior to any significant changes to the protocol for the Project. 17. The User Institution will notify University of East Anglia as soon as it becomes aware of a breach of the terms or conditions of this agreement, and in any case within 24 hours of becoming aware of any potential or actual security breach or loss of the Data. 18. Any notice given to a party under or in connection with this agreement shall be in writing and addressed to:
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 |
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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 | |
---|---|---|---|---|
EGAF00006132228 | 1648029960795 | 759.9 MB | ||
EGAF00006132229 | 1648029840315 | 286.5 MB | ||
EGAF00006132230 | 1648030200210 | 806.3 MB | ||
EGAF00006132231 | 1648030260160 | 4.8 GB | ||
EGAF00006132232 | 1648029840315 | 165.3 MB | ||
EGAF00006132233 | 1648029840314 | 289.9 MB | ||
EGAF00006132234 | 1648029840314 | 231.1 MB | ||
EGAF00006132235 | 1648029960795 | 2.1 GB | ||
EGAF00006132236 | 1648030260160 | 2.2 GB | ||
EGAF00006132237 | 1648030200210 | 4.1 GB | ||
EGAF00006132238 | 1648030560402 | 3.5 GB | ||
EGAF00006132239 | 1648030020152 | 1.8 GB | ||
EGAF00006132240 | 1648029900330 | 832.2 MB | ||
EGAF00006132241 | 1648030080212 | 2.8 GB | ||
EGAF00006132242 | 1648030140337 | 2.4 GB | ||
EGAF00006132243 | 1648030020152 | 350.5 MB | ||
EGAF00006132244 | 1648030380147 | 3.3 GB | ||
EGAF00006132245 | 1648030140337 | 3.4 GB | ||
EGAF00006132246 | 1648030140337 | 3.3 GB | ||
EGAF00006132247 | 1648029960795 | 1.6 GB | ||
EGAF00006132248 | 1648029840314 | 473.9 MB | ||
EGAF00006132249 | 1648029900330 | 344.1 MB | ||
EGAF00006132250 | 1648029780196 | 174.5 MB | ||
EGAF00006132251 | 1648029960795 | 2.4 GB | ||
EGAF00006132252 | 1648030200210 | 2.4 GB | ||
EGAF00006132253 | 1648029840314 | 322.6 MB | ||
EGAF00006132254 | 1648030140337 | 2.2 GB | ||
EGAF00006132255 | 1648029900330 | 205.2 MB | ||
EGAF00006132256 | 1648029960795 | 1.8 GB | ||
EGAF00006132257 | 1648030080212 | 1.7 GB | ||
EGAF00006132258 | 1648030200210 | 707.6 MB | ||
EGAF00006132259 | 1648029960795 | 272.0 MB | ||
EGAF00006132260 | 1648030260160 | 2.0 GB | ||
EGAF00006132261 | 1648029960795 | 1.9 GB | ||
EGAF00006132262 | 1648030080212 | 600.3 MB | ||
EGAF00006132263 | 1648030320075 | 2.5 GB | ||
EGAF00006132264 | 1648030020152 | 2.6 GB | ||
EGAF00006132265 | 1648030200210 | 2.4 GB | ||
EGAF00006132266 | 1648030080212 | 2.7 GB | ||
EGAF00006132267 | 1648029900330 | 273.2 MB | ||
EGAF00006132268 | 1648030020152 | 690.8 MB | ||
EGAF00006132269 | 1648029780196 | 261.4 MB | ||
EGAF00006132270 | 1648030320075 | 1.4 GB | ||
EGAF00006132271 | 1648029900330 | 923.9 MB | ||
EGAF00006132272 | 1648029840314 | 198.2 MB | ||
EGAF00006132273 | 1648029840314 | 275.9 MB | ||
46 Files (70.9 GB) |