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sWGS of HGSOC samples for fixative comparison study

Shallow whole-genome sequencing of samples from the study "Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples". DNA from each sample (100ng) was sheared on Covaris S220 (Covaris): duty cycle - 10%, intensity -5.0, bursts per sec - 200, duration - 300 sec, mode - frequency sweeping, power - 23V, temperature -5:5 C to 6 C, water level - 13. Libraries were prepared with the TruSeq Nano DNA LT Sample Prep Kit (Illumina) using a modi?ed protocol - Sample Puri?cation Beads were replaced by Agencourt AMPure XP beads (Beckman Coultier) and size selection after the End Repair was done to remove only the short fragments. Quality and quantity for contructed libraries were assessed with DNA 7500 kit on Agilent 2100 Bioanalyzer and with Kapa Quanti?cation kit (KAPA Biosystems) on 7900HT Fast Real-Time PCR System (Applied Biosystems) according to the supplier's recommendations, respectively. Libraries from 18 barcoded samples were pooled together in equimolar amounts and each pool was loaded on a single lane of a HiSeq Single End Flowcell (Illumina), followed by cluster generation on a cBot (Illumina) and sequencing on a HiSeq 2500 (Illumina) in a single-read 50bp mode. Reads were aligned using bwa-mem v0.7.12-r1039 to the 1000 genomes version of human genome build GRCh37. Picard (http://picard.sourceforge.net) was used to remove duplicate reads.

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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
EGAS00001001433 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
EGAF00001104480 bam 669.7 MB
EGAF00001104481 bam 715.9 MB
EGAF00001104482 bam 717.9 MB
EGAF00001104483 bam 771.8 MB
EGAF00001104484 bam 767.2 MB
EGAF00001104485 bam 485.1 MB
EGAF00001104486 bam 866.3 MB
EGAF00001104487 bam 809.0 MB
EGAF00001104488 bam 1.8 GB
EGAF00001104489 bam 714.9 MB
EGAF00001104490 bam 755.8 MB
EGAF00001104491 bam 854.8 kB
EGAF00001104492 bam 661.3 MB
EGAF00001104493 bam 725.8 MB
EGAF00001104494 bam 1.0 GB
EGAF00001104495 bam 787.8 MB
EGAF00001104496 bam 770.9 MB
EGAF00001104497 bam 627.0 MB
EGAF00001104498 bam 731.4 MB
EGAF00001104499 bam 859.5 MB
EGAF00001104500 bam 847.2 MB
EGAF00001104501 bam 891.9 MB
EGAF00001104502 bam 766.0 MB
EGAF00001104503 bam 785.7 MB
EGAF00001104504 bam 732.6 MB
EGAF00001104505 bam 703.6 MB
EGAF00001104506 bam 952.8 MB
EGAF00001104507 bam 859.6 MB
EGAF00001104508 bam 786.4 MB
EGAF00001104509 bam 911.2 MB
EGAF00001104510 bam 771.4 MB
EGAF00001104511 bam 553.5 MB
EGAF00001104512 bam 792.3 MB
EGAF00001104597 bam 822.8 MB
EGAF00001104598 bam 437.2 MB
EGAF00001104599 bam 415.9 MB
EGAF00001104600 bam 382.8 MB
EGAF00001104601 bam 1.0 GB
EGAF00001104602 bam 1.0 GB
EGAF00001104603 bam 908.2 MB
EGAF00001104604 bam 482.2 MB
EGAF00001104605 bam 1.0 GB
EGAF00001104606 bam 1.1 GB
EGAF00001104607 bam 892.2 MB
EGAF00001104608 bam 640.3 MB
EGAF00001104609 bam 733.5 MB
EGAF00001104610 bam 743.4 MB
EGAF00001104611 bam 812.1 MB
EGAF00001104612 bam 881.2 MB
EGAF00001104613 bam 675.5 MB
EGAF00001104614 bam 662.4 MB
EGAF00001104615 bam 440.1 MB
EGAF00001104616 bam 829.1 MB
EGAF00001104617 bam 716.6 MB
EGAF00001104622 bam 649.9 MB
EGAF00001104661 bam 613.4 MB
EGAF00001104662 bam 806.6 MB
EGAF00001104687 bam 755.3 MB
EGAF00001104688 bam 315.0 MB
EGAF00001104689 bam 1.0 GB
60 Files (45.4 GB)