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Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients

Molecular cancer paper ( This dataset contain shallow whole-genome sequencing (sWGS) of plasma cell-free DNA from cancer patients and healthy subjects, obtained with both Nanopore and Illumina technology. A total of 6 cancer patients and 5 healthy subjects have been sequenced with Nanopore; 4 of the cancer patients have been also sequenced with Illumina. In addition, genomic DNA from white blood cells of one healthy subjects, genomic and 160bp DNA from HEK cells have been sequenced with Nanopore. Genome Biology paper: 3 additional healthy samples have been sequenced (HU), two different bioinformatic pipeline were applied. 2019: Fastqs from the molecular cancer paper were re-demultiplexed and adapter-trimmed (using guppy for multiplex samples, and porechop for singleplex) preserving 5' ends to allow fragmentomics analysis. HAC: All the samples were basecalled with the same updated High Accuracy model (the latest at the time of the analysis) and post-processed as the 2019 dataset. Raw FAST5 are currently available upon request, but will be uploaded soon.

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Nanopore Liquid Biopsy policy

Researchers which are interested in accessing the data of this project need to fill and submit a “Data access agreement” form. These terms and conditions govern access to the managed access datasets 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 CNR-IFC grants access to the Data. This includes the User, other individuals (listed in Appendix II of the data access agreement which will be submitted by the User) and any other individuals for whom the User Institution subsequently requests access to the Data. Data: The managed access datasets to which the User Institution has requested access. Data Producers: Dr. Silvestro Conticello 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 of the data access agreement. 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. CNR-IFC: 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 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. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 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 ( ) and the Toronto Statement ( 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 in Appendix III. 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) ( ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) ( ). 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 Dr. Silvestro Conticello within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Dr. Silvestro Conticello prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Dr. Silvestro Conticello as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Dr. Silvestro Conticello 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 Dr. Silvestro Conticello. 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 England and Wales and shall be subject to the exclusive jurisdiction of the English courts. 20. 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

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
EGAS00001004975 Cancer Genomics

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
EGAF00004974854 fastq.gz 1.2 GB
EGAF00004974855 fastq.gz 1.3 GB
EGAF00004974856 fastq.gz 1.7 GB
EGAF00004974857 fastq.gz 1.8 GB
EGAF00004974858 fastq.gz 1.6 GB
EGAF00004974859 fastq.gz 1.6 GB
EGAF00004974860 fastq.gz 1.6 GB
EGAF00004974861 fastq.gz 1.7 GB
EGAF00004974862 fastq.gz 870.5 MB
EGAF00004974863 fastq.gz 1.0 GB
EGAF00004974864 fastq.gz 2.1 GB
EGAF00004974865 fastq.gz 2.2 GB
EGAF00004974866 fastq.gz 2.2 GB
EGAF00004974867 fastq.gz 95.8 MB
EGAF00004974868 fastq.gz 1.0 GB
EGAF00004974869 fastq.gz 886.7 MB
EGAF00004974870 fastq.gz 919.7 MB
EGAF00004974871 fastq.gz 1.0 GB
EGAF00004975262 fastq.gz 2.0 GB
EGAF00004975263 fastq.gz 5.8 GB
EGAF00004975264 fastq.gz 6.5 GB
EGAF00004975265 fastq.gz 4.2 GB
EGAF00006460418 fastq.gz 6.5 GB
EGAF00006460419 fastq.gz 7.0 GB
EGAF00006460420 fastq.gz 4.6 GB
EGAF00006460421 fastq.gz 4.0 GB
EGAF00006460422 fastq.gz 981.4 MB
EGAF00006460423 fastq.gz 849.1 MB
EGAF00006460424 fastq.gz 1.0 GB
EGAF00006460425 fastq.gz 880.0 MB
EGAF00006460426 fastq.gz 1.2 GB
EGAF00006460427 fastq.gz 1.0 GB
EGAF00006460428 fastq.gz 2.4 GB
EGAF00006460429 fastq.gz 2.1 GB
EGAF00006460430 fastq.gz 1.2 GB
EGAF00006460431 fastq.gz 1.1 GB
EGAF00006460432 fastq.gz 999.5 MB
EGAF00006460433 fastq.gz 897.7 MB
EGAF00006460434 fastq.gz 1.2 GB
EGAF00006460435 fastq.gz 1.1 GB
EGAF00006460436 fastq.gz 2.5 GB
EGAF00006460437 fastq.gz 2.2 GB
EGAF00006460438 fastq.gz 606.0 MB
EGAF00006460439 fastq.gz 753.2 MB
EGAF00006460440 fastq.gz 526.2 MB
45 Files (88.8 GB)