Tagged-amplicon deep sequencing

This dataset contains a collection of tumour samples from high grade serous ovarian carcinoma patients with recurrent disease collected near the point of diagnosis as well as tumour samples collected after patient relapse upon or some time after study entry. Whole blood samples were also collected from patients at study entry for the purpose of germline variant detection. The majority of diagnosis samples were preserved in neutral buffered formalin whereas the majority of post-relapse samples were preserved in universal molecular fixative (UMFIX, Sakura Finetek USA, Inc). DNA was extracted and the tagged-amplicon deep sequencing assay was applied (TAm-Seq, Forshew et al. 2002, Sci Transl Med) with the aid of fluidigm access array technology. Targeted loci were sequenced at very high depths (typically >100X) for the detection of both somatic and germline variants. Sequenced reads were aligned to the GRCh37 reference genome (release hs37d5).

12/06/2023
933 samples
DAC: EGAC00001000388
Technologies: Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq

Access Policy1 Study Files

Metadata

Request Access

The UK Translational Research in Ovarian Cancer (BriTROC) Consortium Data Access and Use Agreement for non personal data.

Between Ovarian Cancer Action, a company limited by guarantee (registered in England and Wales under number 5403443) and a charity (registered in England under number 1109743 and registered in Scotland under number SC043478) of 8 – 12 Camden High St, London NW1 0JH, and Cancer Research UK, a company limited by guarantee (registered in England and Wales under number 4325234) and a charity (registered in England under number 1089464 and registered in Scotland under number SC041666) of Angel Building, 407 St John Street, London, EC1V 4AD, United Kingdom (collectively referred to as the “Funders”), and the undersigned parties. This agreement governs the terms on which access will be granted to the genotype and expression data generated as a result of the activities of the BriTROC Consortium and deposited by members of the Consortium including the Funders. In signing this agreement, you are agreeing with the Funders to be bound by the terms and conditions set out in this agreement. NOW THEREFORE in consideration of the access to the Data provided by the Funders to User Institution, and for other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, and intending to be legally bound hereby, the parties hereto agree as follows: Definitions: “Application” means an application made by an entity (including You) to request access to the Data for a specific project and/or purpose. “Consortium” means the UK Translational Research in Ovarian Cancer consortium, known as BriTROC. “Data Access Committee” means the committee established by BriTROC to consider Applications. “Data” means non personal data including all and any human genetic and raw expression data obtained from the Consortium (which is currently available through the European Genome-phenome Archive). “Data Subject” means a person, who has been informed of the purpose for which the Data was collected, is currently held, and the purposes for which it can and will be distributed and disclosed, and has given his/her informed consent thereto. All references to individual Data Subjects have been removed and the Data is no longer personal data. User means a researcher whose User Institution has signed this Data Access Agreement and has received acknowledgement of the acceptance of its Application. Publications means, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. User Institution means the organisation at which the User is employed, affiliated or enrolled. User Institution is referred to within this Agreement as “You” (and “Your” shall be construed accordingly). Terms and Conditions: 1. You agree to preserve, at all times, the confidentiality and privacy of information and Data pertaining to Data Subjects. In particular, you undertake not to use, or attempt to use the Data to compromise or otherwise breach or infringe the confidentiality and privacy of information on Data Subjects.  2. You agree not to attempt to link the Data to any other data source on the same samples, link the Data to any person or otherwise identify any Data Subject from the Data. We have taken organisational and technical measures to ensure this cannot happen.  3. You agree not to transfer or disclose the Data, in whole or part, to others, except to persons within the User Institution for the fulfilment of the Purpose as reasonably necessary for Data/safety monitoring or programme management. If you wish to disclose the Data to a collaborator outside the User Institution, the third party must make a separate Application for access to the Data and enter into a separate Agreement.  4. You agree to use the Data for the advancement of medical research, and solely for the approved purpose and project described in Your Application and for no other purpose, which is attached hereto as Schedule “B” (the “Purpose”); provided that any use of the Data beyond the scope of the Purpose will require a new Application, approval and Agreement. You agree to destroy the raw data once the project is completed, and upon request of the Consortium, provide written certification of such destruction.  5. You agree that Data may be reissued from time to time, with suitable versioning. If the reissue is at the request of sample donors and/or other ethical scrutiny, you will destroy earlier versions of the Data, and upon request of the Consortium, provide written certification of such destruction.  6. You agree to acknowledge in any work or Publications based in whole or part on the Data, the published paper from which the Data derives, the version of the Data, and the role of the Consortium and the Funders, in accordance with the Publications Policy attached as Schedule “A”.  7. You agree and acknowledge that the Consortium, its members, the original Data creators, depositors or copyright holders, or the Funders:  a) bear no legal responsibility or liability for the accuracy or comprehensiveness of the Data, or from any use of the Data including further analysis or interpretation of such Data; and b) shall have no liability for any direct or indirect, consequential, or incidental damages or losses whatsoever arising out of Your use of the Data, or from the unavailability of, or lack of access to, the Data for whatever reason; and  c) disclaim any and all representations, conditions or warranties (either express, implied or statutory) regarding the Data, including accuracy of the Data or that the Data corresponds with a particular description or is fit for a particular purpose.  8. You shall indemnify, hold harmless and defend each of the Funders, any members of the Consortium and their respective directors, officers, employees and agents against any and all claims (including all associated legal fees and disbursements actually incurred) arising out of this Agreement, including without limitation against any damages or losses, consequential or otherwise, arising in any manner at all from or out of Your use of the Data. Section 8 shall not apply to any public body or institution that is prevented by applicable laws from providing indemnification. 9. You understand and acknowledge that the Data is owned by the Funders and protected by copyright, database rights and other intellectual property rights owned by the Funders. You agree that you shall not reproduce or copy the Data, except as reasonably required to carry out the Purpose and for no other purpose, or sell all or any part of the Data in any circumstances.  10. You recognise that nothing in this Agreement shall operate to transfer to You any ownership or intellectual property rights relating to the Data.  11. You accept that this Agreement will terminate immediately upon any breach of this Agreement by You and You will be required to destroy or return any Data, and upon request, provide written certification of such destruction. For the avoidance of doubt clause 3, 7, 8, 14, 15 will continue to operate in full force and effect.  12. You accept that it may be necessary for the Funders to alter the terms of this Agreement from time to time in order to address new concerns. In this event, one of the Funders or a representative of the Consortium will contact You to inform You of any changes and You agree that Your continued use of the Data shall be dependent on the parties entering into a new version of the Agreement.  13. You agree that you will submit a report to the Consortium Data Access Committee, if requested, on completion of the Purpose. The Consortium Data Access Committee agrees to treat the report and all information, data, results, and conclusions contained within such report as confidential information belonging to the User Institution.  14. You agree that the Data is protected by and subject to applicable international laws, which may include without limitation the UK Data Protection Act 1998 and that you are responsible for ensuring compliance with any such laws. The Funders (via the BriTROC Data Access Committee) reserve the right to request and inspect Your data security and management documentation to ensure the adequacy of data protection measures in countries that have no privacy legislation comparable with that contained herein.  15. Part or all of any section of this Agreement that is indefinite, invalid, illegal or otherwise voidable or unenforceable may be severed and the balance of this agreement will continue in full force and effect.  Schedule “A” Publications Policy Any use of Data must acknowledge BriTROC using the following wording: "This study makes use of data generated by the BriTROC consortium. Funding for the project was provided by Ovraian Cancer Action and Cancer Research UK." and cite the relevant primary BRITROC publications (Piskorz, Ennis, Macintyre et al, Ann. Oncol 2015) which is the source of the Data. Schedule “B” Application form (approved by the Consortium 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
EGAS00001007292	The genomic landscape of recurrent ovarian high grade serous carcinoma: the BriTROC-1 study	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	Quality Report
EGAF00008097069	fq.gz	21.4 MB	Report
EGAF00008097070	fq.gz	25.7 MB	Report
EGAF00008097071	fq.gz	2.3 MB	Report
EGAF00008097072	fq.gz	2.8 MB	Report
EGAF00008097073	fq.gz	21.5 MB	Report
EGAF00008097074	fq.gz	26.6 MB	Report
EGAF00008097075	fq.gz	20.9 MB	Report
EGAF00008097076	fq.gz	25.3 MB	Report
EGAF00008097077	fq.gz	24.3 MB	Report
EGAF00008097078	fq.gz	30.1 MB	Report
EGAF00008097079	fq.gz	25.6 MB	Report
EGAF00008097080	fq.gz	31.3 MB	Report
EGAF00008097081	fq.gz	26.4 MB	Report
EGAF00008097082	fq.gz	32.1 MB	Report
EGAF00008097083	fq.gz	20.6 MB	Report
EGAF00008097084	fq.gz	25.1 MB	Report
EGAF00008097085	fq.gz	30.2 MB	Report
EGAF00008097086	fq.gz	36.6 MB	Report
EGAF00008097087	fq.gz	24.3 MB	Report
EGAF00008097088	fq.gz	29.4 MB	Report
EGAF00008097089	fq.gz	23.2 MB	Report
EGAF00008097090	fq.gz	27.9 MB	Report
EGAF00008097091	fq.gz	30.9 MB	Report
EGAF00008097092	fq.gz	38.1 MB	Report
EGAF00008097093	fq.gz	29.9 MB	Report
EGAF00008097094	fq.gz	36.5 MB	Report
EGAF00008097095	fq.gz	23.1 MB	Report
EGAF00008097096	fq.gz	27.4 MB	Report
EGAF00008097097	fq.gz	25.5 MB	Report
EGAF00008097098	fq.gz	30.7 MB	Report
EGAF00008097099	fq.gz	24.3 MB	Report
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EGAF00008097101	fq.gz	23.2 MB	Report
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EGAF00008097121	fq.gz	25.8 MB	Report
EGAF00008097122	fq.gz	31.2 MB	Report
EGAF00008097123	fq.gz	48.5 MB	Report
EGAF00008097124	fq.gz	58.8 MB	Report
EGAF00008097125	fq.gz	31.1 MB	Report
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EGAF00008097127	fq.gz	32.2 MB	Report
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EGAF00008097131	fq.gz	31.3 MB	Report
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EGAF00008097137	fq.gz	38.5 MB	Report
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EGAF00008097141	fq.gz	31.5 MB	Report
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EGAF00008097144	fq.gz	27.8 MB	Report
EGAF00008097145	fq.gz	31.9 MB	Report
EGAF00008097146	fq.gz	38.0 MB	Report
EGAF00008097147	fq.gz	36.0 MB	Report
EGAF00008097148	fq.gz	43.6 MB	Report
EGAF00008097149	fq.gz	31.6 MB	Report
EGAF00008097150	fq.gz	38.5 MB	Report
EGAF00008097151	fq.gz	28.9 MB	Report
EGAF00008097152	fq.gz	34.8 MB	Report
EGAF00008097153	fq.gz	26.7 MB	Report
EGAF00008097154	fq.gz	32.0 MB	Report
EGAF00008097155	fq.gz	30.8 MB	Report
EGAF00008097156	fq.gz	37.3 MB	Report
EGAF00008097157	fq.gz	41.1 MB	Report
EGAF00008097158	fq.gz	49.8 MB	Report
EGAF00008097159	fq.gz	41.0 MB	Report
EGAF00008097160	fq.gz	49.8 MB	Report
EGAF00008097161	fq.gz	25.9 MB	Report
EGAF00008097162	fq.gz	30.9 MB	Report
EGAF00008097163	fq.gz	4.3 MB	Report
EGAF00008097164	fq.gz	5.0 MB	Report
EGAF00008097165	fq.gz	26.6 MB	Report
EGAF00008097166	fq.gz	31.6 MB	Report
EGAF00008097167	fq.gz	42.2 MB	Report
EGAF00008097168	fq.gz	51.1 MB	Report
EGAF00008097169	fq.gz	33.2 MB	Report
EGAF00008097170	fq.gz	39.2 MB	Report
EGAF00008097171	fq.gz	37.0 MB	Report
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EGAF00008097174	fq.gz	38.6 MB	Report
EGAF00008097175	fq.gz	23.7 MB	Report
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EGAF00008097177	fq.gz	13.5 MB	Report
EGAF00008097178	fq.gz	16.1 MB	Report
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EGAF00008097181	fq.gz	32.8 MB	Report
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EGAF00008097193	fq.gz	26.9 MB	Report
EGAF00008097194	fq.gz	32.2 MB	Report
EGAF00008097195	fq.gz	37.1 MB	Report
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EGAF00008097197	fq.gz	29.2 MB	Report
EGAF00008097198	fq.gz	34.9 MB	Report
EGAF00008097199	fq.gz	34.1 MB	Report
EGAF00008097200	fq.gz	41.6 MB	Report
EGAF00008097201	fq.gz	37.0 MB	Report
EGAF00008097202	fq.gz	44.7 MB	Report
EGAF00008097203	fq.gz	32.8 MB	Report
EGAF00008097204	fq.gz	39.7 MB	Report
EGAF00008097205	fq.gz	14.6 MB	Report
EGAF00008097206	fq.gz	17.4 MB	Report
EGAF00008097207	fq.gz	20.4 MB	Report
EGAF00008097208	fq.gz	24.4 MB	Report
EGAF00008097209	fq.gz	27.0 MB	Report
EGAF00008097210	fq.gz	32.2 MB	Report
EGAF00008097211	fq.gz	21.2 MB	Report
EGAF00008097212	fq.gz	25.7 MB	Report
EGAF00008097213	fq.gz	29.6 MB	Report
EGAF00008097214	fq.gz	35.8 MB	Report
EGAF00008097215	fq.gz	23.2 MB	Report
EGAF00008097216	fq.gz	27.9 MB	Report
EGAF00008097217	fq.gz	25.2 MB	Report
EGAF00008097218	fq.gz	30.6 MB	Report
EGAF00008097219	fq.gz	25.6 MB	Report
EGAF00008097220	fq.gz	31.2 MB	Report
EGAF00008097221	fq.gz	26.4 MB	Report
EGAF00008097222	fq.gz	32.3 MB	Report
EGAF00008097223	fq.gz	37.6 MB	Report
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EGAF00008097225	fq.gz	30.3 MB	Report
EGAF00008097226	fq.gz	36.2 MB	Report
EGAF00008097227	fq.gz	31.6 MB	Report
EGAF00008097228	fq.gz	38.0 MB	Report
EGAF00008097229	fq.gz	33.1 MB	Report
EGAF00008097230	fq.gz	39.7 MB	Report
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EGAF00008097232	fq.gz	41.4 MB	Report
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EGAF00008097237	fq.gz	20.6 MB	Report
EGAF00008097238	fq.gz	25.2 MB	Report
EGAF00008097239	fq.gz	27.2 MB	Report
EGAF00008097240	fq.gz	32.9 MB	Report
EGAF00008097241	fq.gz	32.6 MB	Report
EGAF00008097242	fq.gz	39.1 MB	Report
EGAF00008097243	fq.gz	31.1 MB	Report
EGAF00008097244	fq.gz	37.3 MB	Report
EGAF00008097245	fq.gz	43.7 MB	Report
EGAF00008097246	fq.gz	52.5 MB	Report
EGAF00008097247	fq.gz	37.6 MB	Report
EGAF00008097248	fq.gz	45.3 MB	Report
EGAF00008097249	fq.gz	45.4 MB	Report
EGAF00008097250	fq.gz	53.9 MB	Report
EGAF00008097251	fq.gz	32.1 MB	Report
EGAF00008097252	fq.gz	38.8 MB	Report
EGAF00008097253	fq.gz	43.3 MB	Report
EGAF00008097254	fq.gz	52.4 MB	Report
EGAF00008097255	fq.gz	43.6 MB	Report
EGAF00008097256	fq.gz	52.6 MB	Report
EGAF00008097257	fq.gz	39.7 MB	Report
EGAF00008097258	fq.gz	47.8 MB	Report
EGAF00008097259	fq.gz	36.9 MB	Report
EGAF00008097260	fq.gz	44.4 MB	Report
EGAF00008097261	fq.gz	43.8 MB	Report
EGAF00008097262	fq.gz	53.3 MB	Report
EGAF00008097263	fq.gz	39.6 MB	Report
EGAF00008097264	fq.gz	46.9 MB	Report
EGAF00008097265	fq.gz	39.6 MB	Report
EGAF00008097266	fq.gz	48.1 MB	Report
EGAF00008097267	fq.gz	38.8 MB	Report
EGAF00008097268	fq.gz	46.4 MB	Report
EGAF00008097269	fq.gz	39.8 MB	Report
EGAF00008097270	fq.gz	48.1 MB	Report
EGAF00008097271	fq.gz	48.0 MB	Report
EGAF00008097272	fq.gz	50.0 MB	Report
EGAF00008097273	fq.gz	51.5 MB	Report
EGAF00008097274	fq.gz	61.4 MB	Report
EGAF00008097275	fq.gz	52.8 MB	Report
EGAF00008097276	fq.gz	63.7 MB	Report
EGAF00008097277	fq.gz	39.7 MB	Report
EGAF00008097278	fq.gz	48.3 MB	Report
EGAF00008097279	fq.gz	40.0 MB	Report
EGAF00008097280	fq.gz	47.7 MB	Report
EGAF00008097281	fq.gz	37.1 MB	Report
EGAF00008097282	fq.gz	44.4 MB	Report
EGAF00008097283	fq.gz	37.2 MB	Report
EGAF00008097284	fq.gz	45.5 MB	Report
EGAF00008097285	fq.gz	45.6 MB	Report
EGAF00008097286	fq.gz	54.8 MB	Report
EGAF00008097287	fq.gz	48.2 MB	Report
EGAF00008097288	fq.gz	58.7 MB	Report
EGAF00008097289	fq.gz	53.4 MB	Report
EGAF00008097290	fq.gz	63.4 MB	Report
EGAF00008097291	fq.gz	41.6 MB	Report
EGAF00008097292	fq.gz	50.5 MB	Report
EGAF00008097293	fq.gz	14.8 MB	Report
EGAF00008097294	fq.gz	17.8 MB	Report
EGAF00008097295	fq.gz	40.7 MB	Report
EGAF00008097296	fq.gz	49.1 MB	Report
EGAF00008097297	fq.gz	44.8 MB	Report
EGAF00008097298	fq.gz	54.0 MB	Report
EGAF00008097299	fq.gz	39.2 MB	Report
EGAF00008097300	fq.gz	47.0 MB	Report
EGAF00008097301	fq.gz	39.4 MB	Report
EGAF00008097302	fq.gz	47.4 MB	Report
EGAF00008097303	fq.gz	32.9 MB	Report
EGAF00008097304	fq.gz	39.6 MB	Report
EGAF00008097305	fq.gz	40.3 MB	Report
EGAF00008097306	fq.gz	48.3 MB	Report
EGAF00008097307	fq.gz	49.5 MB	Report
EGAF00008097308	fq.gz	59.5 MB	Report
EGAF00008097309	fq.gz	50.5 MB	Report
EGAF00008097310	fq.gz	56.3 MB	Report
EGAF00008097311	fq.gz	38.9 MB	Report
EGAF00008097312	fq.gz	46.7 MB	Report
EGAF00008097313	fq.gz	46.9 MB	Report
EGAF00008097314	fq.gz	56.1 MB	Report
EGAF00008097315	fq.gz	35.5 MB	Report
EGAF00008097316	fq.gz	42.1 MB	Report
EGAF00008097317	fq.gz	41.9 MB	Report
EGAF00008097318	fq.gz	50.5 MB	Report
EGAF00008097319	fq.gz	33.8 MB	Report
EGAF00008097320	fq.gz	40.3 MB	Report
EGAF00008097321	fq.gz	54.0 MB	Report
EGAF00008097322	fq.gz	64.7 MB	Report
EGAF00008097323	fq.gz	41.9 MB	Report
EGAF00008097324	fq.gz	49.8 MB	Report
EGAF00008097325	fq.gz	36.8 MB	Report
EGAF00008097326	fq.gz	44.3 MB	Report
EGAF00008097327	fq.gz	37.0 MB	Report
EGAF00008097328	fq.gz	44.4 MB	Report
EGAF00008097329	fq.gz	35.6 MB	Report
EGAF00008097330	fq.gz	43.0 MB	Report
EGAF00008097331	fq.gz	44.4 MB	Report
EGAF00008097332	fq.gz	48.7 MB	Report
EGAF00008097333	fq.gz	37.6 MB	Report
EGAF00008097334	fq.gz	44.6 MB	Report
EGAF00008097335	fq.gz	39.9 MB	Report
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EGAF00008097338	fq.gz	59.2 MB	Report
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EGAF00008097340	fq.gz	50.0 MB	Report
EGAF00008097341	fq.gz	48.9 MB	Report
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EGAF00008097343	fq.gz	47.6 MB	Report
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EGAF00008097348	fq.gz	55.3 MB	Report
EGAF00008097349	fq.gz	42.3 MB	Report
EGAF00008097350	fq.gz	51.3 MB	Report
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EGAF00008104581	fq.gz	113.3 MB	Report
EGAF00008104582	fq.gz	70.0 MB	Report
EGAF00008104583	fq.gz	81.3 MB	Report
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EGAF00008104585	fq.gz	78.3 MB	Report
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EGAF00008104588	fq.gz	22.6 MB	Report
EGAF00008104589	fq.gz	25.5 MB	Report
EGAF00008104590	fq.gz	51.1 MB	Report
EGAF00008104591	fq.gz	58.4 MB	Report
EGAF00008104592	fq.gz	78.0 MB	Report
EGAF00008104593	fq.gz	86.9 MB	Report
EGAF00008104594	fq.gz	99.1 MB	Report
EGAF00008104595	fq.gz	112.9 MB	Report
EGAF00008104596	fq.gz	77.1 MB	Report
EGAF00008104597	fq.gz	86.0 MB	Report
EGAF00008104598	fq.gz	72.8 MB	Report
EGAF00008104599	fq.gz	80.4 MB	Report
EGAF00008104600	fq.gz	86.0 MB	Report
EGAF00008104601	fq.gz	94.8 MB	Report
EGAF00008104602	fq.gz	82.2 MB	Report
EGAF00008104603	fq.gz	89.6 MB	Report
6348 Files (389.2 GB)