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Genetic investigation of 12q-amplified osteosarcomas

Further investigation and characterisation of 12q-amplified low- and high-grade osteosarcomas with MDM2 and/or CDK4 amplification focusing on SV, copy number and gene fusion analyses. In total, 25 cases (33 samples total due to multi-sampling) were included, with some form of sequencing data available for 27 samples. Mate-pair whole genome sequencing (Illumina) is available for 19 samples, longread whole genome sequencing (PacBio HiFi) on 10 samples and RNA-sequencing (Illumina Truseq) on 21 samples. Data is available as BAM files.

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Data access to Genetic investigation of 12q-amplified ostesarcomas

DATA ACCESS AGREEMENT between Lund University, P. O. Box 117, SE-221 00 Lund, Sweden, (hereinafter referred to as the “University”); and [name], [address], (hereinafter referred to as the “Recipient”); each a ‘Party’ and together the ‘Parties’. This agreement (the “Agreement”) is made on the last day of signature here below (the “Agreement Date”). BACKGROUND (A) The University’s Department of Laboratory Medicine, Division of Clinical Genetics is the owner of human genetic data relating to the research article by Saba et al. regarding genetic transposition of TP53 regulatory elements in osteosarcoma, for which the University has received approval from the Regional Ethics Committee (Regionala Etikprövningsnämnden) under the permission number Dnr 2011/289. (B) Pursuant to the request by the Recipient, the University has agreed to make the Data available to it for research purposes. OPERATIVE TERMS 1 Definitions and Interpretation 1.1 “User” means a researcher (or an individual conducting Research under the supervision of a researcher) who is employed by the Recipient and is bound by the terms and conditions of this Agreement. For the avoidance of doubt, “User” may also include students, visiting academics, contractors, sub-contractors or independent consultants provided that any such individual is bound by obligations no less onerous then those binding the Recipient’s employees. 1.2 ‘”Data” means the human genetic data obtained by the University. 1.3 “Data Subjects” means the individual to whom Data refers. 2 Access to Data 2.1 In consideration of the University agreeing to supply the Data to the Recipient, the Recipient agrees to be bound by the terms and conditions of this Agreement. The Recipient shall ensure that all Users are aware of and comply with the terms of the Agreement. 2.2 Recipient shall only use Data for the advancement of non-commercial biomedical research as specified in the data application form provided by the University and attached hereto as Appendix 1. 2.3 The Recipient agrees to only give access to Data, in whole or part, or any identifiable material derived from the Data, to Users. The Recipient agrees that before it gives any User access to Data, it shall first show the User a copy of this Agreement and shall inform the User that he or she must comply with the obligations contained in this Agreement and sign up to the provisions of this Agreement in the form set out at the end of this Agreement. 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Recipient further agrees to not attempt to identify the Data Subjects, redistribute the Data, or any subset or derivative of the Data, that could be used to identify the Data Subject, or in any other way compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy. 3.2 Where required under applicable laws regulating cross-border transfers of Personal Data, including European data protection laws, the parties, or their affiliates, will execute any further agreements or undertakings required to enable the lawful transfer of Personal Data, including where appropriate the EU standard contractual clauses for transfers of Personal Data to non-EU data processors set out in European Commission Decision 2010/87/EC of 5 February 2010 available at: http://eurlex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2010:039:0005:0018:EN:PDF or such standard contractual clauses as are then in force. 3.3 The Recipient agrees that it shall take all reasonable security precautions to keep the Data confidential, such precautions to be no less onerous than those applied in respect of the Recipient’s own confidential information. 4 Errors The Recipient agrees to notify the University of any errors detected in the Data. 5 Ownership of the Data 5.1 The Data and all intellectual property in them shall at all times remain the property of the University. 5.2 The Recipient and its Users shall have the right to develop Intellectual Property based on comparisons with their own data. 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The University makes no representation and gives no warranty or undertaking in relation to them whatsoever and excludes all implied warranties to the fullest extent permitted by law; 7.2 In particular, the University makes no representations or warranties, express or implied: • as to title, quality or fitness for a particular purpose or use of the Data; or • that the supply by the University or the use by the Recipient of the Data will not infringe the intellectual property rights of any third party. 7.3 The Recipient warrants that, in relation to the Data and their use: • they will comply with all relevant legislation and regulations; and • they have obtained all necessary consents and ethical approvals. 8 Liability 8.1 The University accepts no liability for loss of data, loss of profit, business or goodwill and all other indirect or consequential loss or damage suffered or incurred by the Recipient or by any other person arising from the supply of the Data or the use, keeping, or disposal of the Data. 8.2 The Recipient shall defend, indemnify and hold the University, its officers, employees and agents harmless against any loss, claim, damage or liability including reasonable legal costs and fees (of whatsoever kind or nature) which may arise in connection with the Recipient’s breach of this Agreement or the use, keeping, production or disposal of the Recipient or on its behalf, unless caused by the University’s gross negligence or wilful act or omission. 9 Termination 9.1 This Agreement shall take effect from the Agreement Date and will terminate on a Party giving 30 days’ prior written notice to the other; or upon breach by the Recipient or Users of any of the terms of this Agreement. 9.2 Upon termination of this Agreement or upon service of notice of termination by a Party for any reason whatsoever, the Recipient shall discontinue its use of the Data and shall, in accordance with the directions of the University, at its own cost and expense destroy the Data or return it to the University. 10 Notices 10.1 The Recipient will do all such acts and execute such documents as are required by the University to give effect to the terms of this Agreement or to enable the University to enjoy the full benefit of this Agreement (including but not limited to ownership of the Data and the arising intellectual property). 10.2 Recipient accepts that it may be necessary for the University or its appointed agent to alter the terms of this Agreement from time to time in order to address new concerns. In this event, the University or its appointed agent will contact Recipient to inform Recipient of any changes and Recipient agrees that Recipient’s continued use of the Data shall be dependent on the parties entering into a new version of the Agreement. 10.3 The Recipient may not assign or transfer all or any of its rights or obligations under this Agreement without the prior written consent of the University. 10.4 This Agreement is subject to Swedish substantive law. 10.5 Any dispute, controversy or claim arising out of or in connection with this Agreement, or the breach, termination or invalidity thereof, shall be solved by Swedish courts. This Agreement has been drawn up in two (2) original copies, each Party receiving one duly signed copy thereof. Signed …………………………….. Signed ……………………………… Authorised signature for and on behalf of Lund University Authorised signature for and on behalf of Recipient [please fill in the name of recipient] Name Name Position Position Dated Dated For the User (s):I acknowledge that I have read and understand the terms of this Agreement Signed ……………………………… Name Position Dated

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
EGAS50000000493 Whole Genome Sequencing
EGAS50000000494 RNASeq
EGAS50000000495 Whole Genome Sequencing

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
EGAF00008506053 bam 3.1 GB
EGAF00008506054 bam 3.7 GB
EGAF00008506055 bam 3.6 GB
EGAF00008506056 bam 3.7 GB
EGAF00008506057 bam 3.9 GB
EGAF00008506058 bam 3.7 GB
EGAF00008506059 bam 5.9 GB
EGAF00008506060 bam 4.3 GB
EGAF00008506061 bam 3.7 GB
EGAF00008506062 bam 6.4 GB
EGAF00008506063 bam 3.8 GB
EGAF00008506064 bam 6.3 GB
EGAF00008506065 bam 7.0 GB
EGAF00008506066 bam 7.3 GB
EGAF00008506067 bam 3.7 GB
EGAF00008506068 bam 3.1 GB
EGAF00008506069 bam 7.3 GB
EGAF00008506070 bam 4.4 GB
EGAF00008506071 bam 3.0 GB
EGAF00008506072 bam 6.5 GB
EGAF00008506073 bam 7.2 GB
EGAF00008506074 bam 8.3 GB
EGAF00008506075 bam 40.9 GB
EGAF00008506076 bam 38.9 GB
EGAF00008506077 bam 40.0 GB
EGAF00008506078 bam 40.3 GB
EGAF00008506079 bam 46.4 GB
EGAF00008506080 bam 7.5 GB
EGAF00008506081 bam 42.9 GB
EGAF00008506082 bam 45.5 GB
EGAF00008506083 bam 51.3 GB
EGAF00008506084 bam 6.5 GB
EGAF00008506085 bam 49.0 GB
EGAF00008506086 bam 3.4 GB
EGAF00008506087 bam 5.5 GB
EGAF00008506088 bam 7.1 GB
EGAF00008506089 bam 48.7 GB
EGAF00008506090 bam 6.1 GB
38 Files (590.0 GB)