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PGDx elio plasma resolve analytical validation

This dataset consists of 39 noncancerous donor and 62 cancer patient plasma samples (including 29 patients with CRC across a total of 13 tumor types) that were analyzed with the PGDx elio plasma resolve assay. The PGDx elio plasma resolve assay is a hybrid capture approach targeting 33 genes with sequencing performed using the Illumina NextSeq with 150bp paired-end reads. The bam files provided have been adapter masked and contain duplicate reads.

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PGDx EGA Data Access Policy

DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom PGDx grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: PGDx and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data.   1. The User Institution agrees to only use these Data for the purpose of the Project and only for Research Purposes. 2. 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. 3. 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. 4. 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. 5. 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. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. 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. 7. 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). This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution agrees to follow the Publication Policy. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. 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. 10. 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 ). 11. 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. 12. The User Institution will notify PGDx within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify PGDx prior to any significant changes to the protocol for the Project. 14. The User Institution will notify PGDx as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. PGDx may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than PGDx. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of the United States and shall be subject to the exclusive jurisdiction of the United States courts. Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for PGDx Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY   APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) This dataset consists of 39 noncancerous donor and 62 cancer patient plasma samples analyzed with the PGDx elio plasma resolve assay. The PGDx elio plasma resolve assay is a hybrid capture approach targeting 33 genes with sequencing performed using the Illumina NextSeq with 150bp paired-end reads. The bam files provided have been adapter masked and contain duplicate reads. Name of project that created the dataset PGDx elio plasma resolve analytical validation Names of other data producers/collaborators Not applicable Specific limitations on areas of research For research use only Minimum protection measures required File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted.   APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (500 words max) All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* All Individuals that should have an account created at the EGA Name of Registered User Email Job Title   APPENDIX III – PUBLICATION POLICY 1. PGDx intends to publish the results of analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. PGDx anticipates that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. 2. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until 12 months after these data were first made available on the relevant hosting database, unless PGDx has provided written consent to earlier submission. 3. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with PGDx.

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
EGAS00001006695 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
EGAF00007692908 bam 6.6 GB
EGAF00007692909 bam 4.5 GB
EGAF00007692910 bam 5.0 GB
EGAF00007692911 bam 5.1 GB
EGAF00007692912 bam 4.6 GB
EGAF00007692913 bam 5.7 GB
EGAF00007692914 bam 5.4 GB
EGAF00007692915 bam 6.4 GB
EGAF00007692916 bam 6.3 GB
EGAF00007692917 bam 5.4 GB
EGAF00007692918 bam 6.0 GB
EGAF00007692919 bam 5.8 GB
EGAF00007692920 bam 3.3 GB
EGAF00007692921 bam 6.3 GB
EGAF00007692922 bam 5.4 GB
EGAF00007692923 bam 7.2 GB
EGAF00007692924 bam 5.3 GB
EGAF00007692925 bam 5.5 GB
EGAF00007692926 bam 5.9 GB
EGAF00007692927 bam 4.9 GB
EGAF00007692928 bam 4.9 GB
EGAF00007692929 bam 6.6 GB
EGAF00007692930 bam 4.8 GB
EGAF00007692931 bam 5.4 GB
EGAF00007692932 bam 5.3 GB
EGAF00007692933 bam 6.3 GB
EGAF00007692934 bam 6.0 GB
EGAF00007692935 bam 8.3 GB
EGAF00007692936 bam 6.6 GB
EGAF00007692937 bam 3.0 GB
EGAF00007692938 bam 4.7 GB
EGAF00007692939 bam 4.0 GB
EGAF00007692940 bam 6.5 GB
EGAF00007692941 bam 8.7 GB
EGAF00007692942 bam 6.5 GB
EGAF00007692943 bam 6.2 GB
EGAF00007692944 bam 8.3 GB
EGAF00007692945 bam 4.6 GB
EGAF00007692946 bam 4.7 GB
EGAF00007692947 bam 6.0 GB
EGAF00007692948 bam 5.6 GB
EGAF00007692949 bam 3.6 GB
EGAF00007692950 bam 1.0 GB
EGAF00007692951 bam 6.1 GB
EGAF00007692952 bam 5.6 GB
EGAF00007692953 bam 5.8 GB
EGAF00007692954 bam 7.2 GB
EGAF00007692955 bam 5.7 GB
EGAF00007692956 bam 5.2 GB
EGAF00007692957 bam 9.0 GB
EGAF00007692958 bam 5.3 GB
EGAF00007692959 bam 5.9 GB
EGAF00007692960 bam 6.5 GB
EGAF00007692961 bam 6.6 GB
EGAF00007692962 bam 6.1 GB
EGAF00007692963 bam 4.6 GB
EGAF00007692964 bam 6.1 GB
EGAF00007692965 bam 6.3 GB
EGAF00007692966 bam 4.6 GB
EGAF00007692967 bam 5.5 GB
EGAF00007692968 bam 4.6 GB
EGAF00007692969 bam 5.6 GB
EGAF00007692970 bam 4.4 GB
EGAF00007692971 bam 5.7 GB
EGAF00007692972 bam 5.0 GB
EGAF00007692973 bam 5.4 GB
EGAF00007692974 bam 5.5 GB
EGAF00007692975 bam 5.2 GB
EGAF00007692976 bam 4.2 GB
EGAF00007692977 bam 5.5 GB
EGAF00007692978 bam 5.1 GB
EGAF00007692979 bam 6.5 GB
EGAF00007692980 bam 6.5 GB
EGAF00007692981 bam 6.2 GB
EGAF00007692982 bam 5.7 GB
EGAF00007692983 bam 5.4 GB
EGAF00007692984 bam 5.5 GB
EGAF00007692985 bam 5.2 GB
EGAF00007692986 bam 5.2 GB
EGAF00007692987 bam 4.6 GB
EGAF00007692988 bam 5.9 GB
EGAF00007692989 bam 5.6 GB
EGAF00007692990 bam 5.7 GB
EGAF00007692991 bam 6.0 GB
EGAF00007692992 bam 5.9 GB
EGAF00007692993 bam 7.2 GB
EGAF00007692994 bam 6.0 GB
EGAF00007692995 bam 6.0 GB
EGAF00007692996 bam 4.6 GB
EGAF00007692997 bam 5.7 GB
EGAF00007692998 bam 6.0 GB
EGAF00007692999 bam 5.7 GB
EGAF00007693000 bam 7.2 GB
EGAF00007693001 bam 4.4 GB
EGAF00007693002 bam 5.4 GB
EGAF00007693003 bam 6.7 GB
EGAF00007693004 bam 5.8 GB
EGAF00007693005 bam 6.0 GB
EGAF00007693006 bam 6.0 GB
EGAF00007693007 bam 4.8 GB
EGAF00007693008 bam 3.4 GB
101 Files (567.2 GB)