TRACERx esophageal adenocarcinoma multi-region NGS
This dataset contains whole exome data from 8 esophageal adenocarcinoma tumors, that has been subjected to multiregion sequencing, ranging from 3-8 regions per tumor. In total, 40 tumor samples and 8 normal blood samples have been sequenced on Illumina HiSeq 2500 at a median dept of 90x.
- 27/05/2015
- 47 samples
- DAC: EGAC00001000340
- Technology: Illumina HiSeq 2500
TRACERx esophageal adenocarcinoma m-seq access
Academic Research Access AgreementSequencing DataBETWEEN:(1)FRANCIS CRICK INSTITUTE a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London, NW1 2BE(the ‘Crick’); and(2)[INSERT INSTITUTION DETAILS] (the “Recipient”).BACKGROUNDThe Recipient has requested access to the Data to conduct Research. Crick wishes to make the Data available to the Recipient for that purpose on the following terms and conditions.AGREED AS FOLLOWS1.DEFINITIONS1.1.The following definitions apply in this agreement. “Authorised User” means: (a)a Researcher employed by the Recipient; or(b)another researcher employed by the Recipient who has authored a relevant peer-reviewed article that Crick can locate on PubMed and who is working in the Research field; or(c)a student studying at the Recipient and is conducting Research under the direct supervision of a Researcher; or(d)a new researcher employed by the Recipient and is conducting Research under the direct supervision of a Researcher: in each case that is bound by confidentiality and non-use obligations in respect of Data set out in this Agreement, and “Authorised Users” shall mean each Authorised User based at the Recipient;“Data” means all and any human genetic sequencing data obtained from the Source Project that Crick elects to make available to the Recipient. Data does not include samples or biological materials, among other things;“Data Subject” means the person (irrespective of state of health) to whom Data refers and who has been informed of the purpose for which the Data is held and has given his/her informed consent thereto;“Intellectual Property” means (i) patents, designs, trade marks and trade names (whether registered or unregistered), copyright and related rights, database rights, know-how and confidential information; (ii) all other intellectual property rights and similar or equivalent rights anywhere in the world which currently exist or are recognised in the future; and (iii) applications, extensions and renewals in relation to any such rights;“PI” means Professor Charles Swanton of the Francis Crick Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London WC2A 3LY;“Research” means the research project described in the Schedule, the principal purpose of which is to advance the understanding and treatment of cancer;“Researcher” means an individual who has: (a)authored a relevant peer-reviewed article that Crick can locate on PubMed and who is working in the Research field; and(b)has signed the form set out in the Schedule and has received acknowledgement from Crick of its acceptance; and“Source Project” means the TRAcking small-cell lung Cancer Evolution through theRrapy (TRACERx) pilot study, comprising the sequencing of multi-region oesophageal cancer samples undertaken at Francis Crick Institute, London Research Institute of 44 Lincoln’s Inn Fields, London WC2A 3LY to identify genetic sequence variants and mutations relevant to the development of human cancers.1.1.The words “including”, “include”, “for example”, “in particular” and words of a similar effect shall not limit the general effect of the words which precede them. 1.2.References to persons shall be construed to include natural persons, bodies corporate, unincorporated associations and partnerships (whether or not any of them have separate legal personality).1.3.Headings are all for reference only and shall be ignored when construing this Agreement.2.PURPOSE2.1.The Recipient may use Data for Research only, and shall not use the Data for any other purpose.3.ACCESS3.1.The Recipient shall only give access to any Data, or any identifiable material derived from the Data, to Authorised Users that are properly and directly supervised by one or more Researcher.3.2.The Recipient shall not (and shall procure that no Authorised User shall): (a)copy, duplicate or sell the Data, or any part of it, on any medium; or(b)make the data (or any part of it) available to third parties other than as expressly permitted in Clause 4.2(a) and 9,in each case, without the prior written permission of Crick. The Recipient shall obtain Crick’s consent on a case-by-case basis.3.3.On written notice, Crick may inspect and review the data security and management processes, and related documentation, relied upon by the Recipient. The Recipient shall provide (and shall ensure that its data storage providers provide) Crick with any access rights needed for Crick to carry out that inspection. Unless Crick identifies any deficiencies in the Recipient’s data security and management processes, Crick may not carry out more than one (1) inspection in each calendar year.4.CONFIDENTIALITY4.1.The Recipient acknowledges that the Data is the confidentiality information of Crick. The Recipient shall keep the Data confidential, and shall use all reasonable precautions to do so. Such precautions shall be no less onerous than those that the Recipient applies in respect of its own confidential information.4.2.The Recipient shall not (and shall procure that no Authorised User shall) communicate or disclose any part of the Data to any person other than:(a)to those expressly permitted under Clause 3.1, which shall in each case be on a need to know basis only and subject to them agreeing to be bound by confidentiality and non-use terms no less onerous than those in this Agreement; or(b)if ordered to do so by a court of competent jurisdiction if there is a statutory obligation to do so, in which case the Recipient shall inform Crick in writing as soon as the Recipient is able to do so once such disclosure is sought.5.DATA PROTECTION5.1.The Recipient shall (and shall procure that each Authorised User shall) comply with all duties and obligations (including, among others, those relating to the storage, processing and use of Data, and to any Data Subject) arising under the Data Protection Act 1998, as amended from time to time, or equivalent provisions under EU or local national legislation no less onerous then those contained in the Data Protection Act.5.2.The Recipient shall not, and shall procure that the Authorised Users shall not, analyse or make any use of any Data in any manner that has the potential to identify, or compromise the anonymity of, any Data Subject.6.MAINTENANCE6.1.If the Recipient becomes aware of, or suspects, any errors in the Data, it shall immediately notify Crick and provide details of the errors.7.DATA REISSUE7.1.The Recipient acknowledges that Data may be reissued from time to time and without notice. Upon becoming aware that the Data has been reissued for any reason (which may include at the request of sample donors and/or as the result of other ethical scrutiny), the Recipient shall immediately destroy all earlier versions of the Data.8.INTELLECTUAL PROPERTY8.1.Nothing in this Agreement shall transfer to the Recipient or any Authorised User any intellectual property rights in or relating to the Data. No rights under such intellectual property rights are granted or implied by this agreement other than the use right expressly granted in Clause 2.1.9.PUBLICATIONS9.1.The Recipient and any Authorised User may only publish Data if:(a)the publication comprises only parts of the Data, and not all of the Data;(b)it is not possible to identify the identity of any Data Subject from, or using, the Data contained in the publication;(c)Crick is provided with a copy of the publication at least thirty (30) days in advance of its proposed dissemination and, at Crick’s request and direction during that thirty (30) day review period, the Recipient:(i) delays the proposed dissemination for up to a further six (6) months;(ii) removes from the publication any Data specified by Crick; and(iii)removes any other information or data specified by Crick that Crick has provided to the Recipient in connection with the Research or under this agreement; and(d)the publication complies with Clause 9.2.9.2.The Recipient shall ensure that each work based in whole or part on the Data that is authored by an Authorised User acknowledges the published paper from which the Data derives, the version of the Data, and the role of the Source Project and its funders in its distribution in accordance with customary scientific and academic practice.9.3. Further, within any permitted publication including these data the TRACERx Consortium and The Francis Crick Institute shall be acknowledged in a manner consistent with the usual conventions in the field of research involved.10.TERMINATION10.1.This agreement will expire upon the earlier of:(a)completion of the Research; and(b)the first (1st) anniversary of Crick acknowledging receipt of the completed registration form in respect of the Research.10.2.This agreement will terminate immediately upon any breach of any of its provisions by the Recipient or by any of the Authorised Users.10.3.Either party may terminate this Agreement with immediate effect on written notice to the other.10.4.Upon expiry or termination of this Agreement for any reason, the Recipient shall destroy all Data in its possession and in the possession of any Authorised User.10.5.Expiry and termination of this agreement for any reason shall not affect any rights and duties of either party accrued prior to termination and the following Clauses shall continue to be enforceable: Clauses 4 (confidentiality), 5 (data protection), 8 (intellectual property), 9 (publication), 10.4 (destruction of Data), 10.5 (survival), 11 (costs), 12 (legal statement).11.COSTS11.1.Within thirty (30) days of a request by Crick, the Recipient shall pay any costs reasonably incurred (including administrative costs and costs associated with obtaining appropriate data storage devices) by Crick in providing the Data.12.LEGAL STATEMENT12.1.Neither Crick nor any party or individual involved in the creation, collation, protection or original analysis of the Data:(a)makes any warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of the Data; (b)shall have any liability for any action, claim, proceeding, demand, 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 the Data, or from the unavailability of, or break in access to the Data for whatever reason.12.2.The Recipient hereby indemnifies Crick, and its officers, agents and employees, against all claims, procedures, loss, damages, costs and expenses (including legal costs and expenses) whether successful or otherwise, arising out of any use or application by the Recipient of any of the Data or any breach of this agreement by the Recipient or any Researcher. This indemnity shall survive the termination of this agreement for any reason. The persons identified in this paragraph may enforce the rights granted to them under it.13.GENERAL13.1.Time shall not be of the essence in respect of any of Crick’s obligations under this agreement, and Crick shall have no liability of any kind caused directly or indirectly by any delay in delivery of, or failure to deliver, the Data.13.2.This agreement (and any dispute of any nature related to it or its formation) shall be construed, interpreted and governed by English law. The parties submit to the exclusive jurisdiction of the English courts.AGREED by the parties through their authorised signatoriesFor and on behalf ofFrancis rick Institute:Signed:___________________________________________Name (print):___________________________________________Position:___________________________________________Date:___________________________________________For and on behalf ofthe Recipient:Name of the Recipient:___________________________________________Signed: (Recipient’s signatory)___________________________________________Signatory’s name:(print)___________________________________________Signatory’s position:___________________________________________Date:___________________________________________Address:_________________________________________________________________________________________________________________________________Telephone number:___________________________________________Email address:___________________________________________ScheduleAuthorised User - Registration FormI have read and understood the contents of the agreement between Crick and [insert the Recipient’s name] dated [insert date] and will comply with the Recipient’s obligations under the agreement when using the Data.Name:(print)___________________________________________Signed: ___________________________________________Position:___________________________________________Date:___________________________________________Address:____________________________________________________________________________________________________________________________________________________________________________Telephone number:___________________________________________Email address:___________________________________________Research (describe):_____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________Completed forms to be sent to:Professor Charlie SwantonFrancis Crick InstituteLincoln's Inn Fields Laboratories44 Lincoln's Inn FieldsLondonWC2A 3LYUnited Kingdom
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 | |
---|---|---|---|---|
EGAF00000814039 | bam | 12.4 GB | ||
EGAF00000814040 | bam | 18.1 GB | ||
EGAF00000814067 | bam | 9.6 GB | ||
EGAF00000814068 | bam | 8.6 GB | ||
EGAF00000814069 | bam | 6.5 GB | ||
EGAF00000814070 | bam | 9.1 GB | ||
EGAF00000814071 | bam | 10.2 GB | ||
EGAF00000814072 | bam | 8.1 GB | ||
EGAF00000814073 | bam | 8.5 GB | ||
EGAF00000814074 | bam | 6.9 GB | ||
EGAF00000814075 | bam | 11.2 GB | ||
EGAF00000814076 | bam | 14.0 GB | ||
EGAF00000814077 | bam | 7.4 GB | ||
EGAF00000814078 | bam | 9.1 GB | ||
EGAF00000814079 | bam | 10.7 GB | ||
EGAF00000814080 | bam | 9.8 GB | ||
EGAF00000814081 | bam | 11.0 GB | ||
EGAF00000814082 | bam | 4.6 GB | ||
EGAF00000814083 | bam | 6.7 GB | ||
EGAF00000814084 | bam | 8.2 GB | ||
EGAF00000814085 | bam | 9.3 GB | ||
EGAF00000814086 | bam | 10.5 GB | ||
EGAF00000814087 | bam | 7.1 GB | ||
EGAF00000814088 | bam | 9.7 GB | ||
EGAF00000814089 | bam | 9.3 GB | ||
EGAF00000814120 | bam | 9.3 GB | ||
EGAF00000814122 | bam | 8.4 GB | ||
EGAF00000814123 | bam | 9.9 GB | ||
EGAF00000814124 | bam | 10.9 GB | ||
EGAF00000814125 | bam | 9.6 GB | ||
EGAF00000814126 | bam | 8.7 GB | ||
EGAF00000814127 | bam | 9.6 GB | ||
EGAF00000814128 | bam | 11.9 GB | ||
EGAF00000814129 | bam | 5.7 GB | ||
EGAF00000814130 | bam | 7.1 GB | ||
EGAF00000814131 | bam | 7.9 GB | ||
EGAF00000814132 | bam | 7.7 GB | ||
EGAF00000814133 | bam | 5.5 GB | ||
EGAF00000814134 | bam | 7.7 GB | ||
EGAF00000814135 | bam | 11.8 GB | ||
EGAF00000814136 | bam | 10.7 GB | ||
EGAF00000814137 | bam | 9.4 GB | ||
EGAF00000814138 | bam | 10.4 GB | ||
EGAF00000814139 | bam | 9.9 GB | ||
EGAF00000814140 | bam | 5.6 GB | ||
EGAF00000814141 | bam | 9.5 GB | ||
EGAF00000814142 | bam | 9.0 GB | ||
47 Files (432.8 GB) |