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Lowpass whole genome sequencing of single circulating tumor cells (CTCs) in ALK-rearranged non-small-cell lung cancer resistant to ALK inhibitors

Lowpass whole genome sequencing of 43 single CTCs and one tumor biopsy

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Gatekeeper mutations are identified in only 50% of the cases at resistance to Anaplastic Lymphoma Kinase (ALK)-tyrosine kinase inhibitors (TKIs). Circulating tumor cells (CTCs) are relevant tools to identify additional resistance mechanisms and can be sequenced at the single-cell level. Here, we provide in-depth investigation of copy number alteration (CNA) heterogeneity in phenotypically characterized CTCs at resistance to ALK-TKIs in ALK-positive non-small cell lung cancer. CTCs showed wide CNA heterogeneity and elevated CIN at resistance to ALK-TKIs.

DATA ACCESS AGREEMENT 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 Françoise Farace at Gustave Roussy within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Dr Françoise Farace at Gustave Roussy prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Dr Françoise Farace at Gustave Roussy as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Dr Françoise Farace at Gustave Roussy 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 Françoise Farace at Gustave Roussy. 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.

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
EGAS00001005301 Other
ID File Type Size Located in
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EGAF00005299769 fastq.gz 136.9 MB
EGAF00005299770 fastq.gz 88.4 MB
EGAF00005299771 fastq.gz 121.0 MB
EGAF00005299772 fastq.gz 126.9 MB
EGAF00005299773 fastq.gz 130.4 MB
EGAF00005299774 fastq.gz 127.1 MB
EGAF00005299775 fastq.gz 111.9 MB
EGAF00005299776 fastq.gz 105.5 MB
EGAF00005299777 fastq.gz 116.3 MB
EGAF00005299778 fastq.gz 117.1 MB
EGAF00005299779 fastq.gz 82.5 MB
EGAF00005299780 fastq.gz 84.4 MB
EGAF00005299781 fastq.gz 91.8 MB
EGAF00005299782 fastq.gz 74.4 MB
EGAF00005299783 fastq.gz 85.1 MB
EGAF00005299784 fastq.gz 135.9 MB
EGAF00005299785 fastq.gz 86.0 MB
EGAF00005299786 fastq.gz 81.4 MB
EGAF00005299787 fastq.gz 71.2 MB
EGAF00005299788 fastq.gz 65.0 MB
EGAF00005299789 fastq.gz 92.2 MB
EGAF00005299790 fastq.gz 89.0 MB
EGAF00005299791 fastq.gz 72.3 MB
EGAF00005299792 fastq.gz 77.9 MB
EGAF00005299793 fastq.gz 69.0 MB
EGAF00005299794 fastq.gz 68.0 MB
EGAF00005299795 fastq.gz 63.0 MB
EGAF00005299796 fastq.gz 53.7 MB
EGAF00005299797 fastq.gz 76.8 MB
EGAF00005299798 fastq.gz 81.9 MB
EGAF00005299799 fastq.gz 92.8 MB
EGAF00005299800 fastq.gz 98.8 MB
EGAF00005299801 fastq.gz 64.3 MB
EGAF00005299802 fastq.gz 69.3 MB
EGAF00005299803 fastq.gz 86.4 MB
EGAF00005299804 fastq.gz 91.6 MB
EGAF00005299805 fastq.gz 86.8 MB
EGAF00005299806 fastq.gz 102.5 MB
EGAF00005299807 fastq.gz 107.4 MB
EGAF00005299808 fastq.gz 35.6 MB
EGAF00005299809 fastq.gz 56.7 MB
EGAF00005299810 fastq.gz 71.1 MB
EGAF00005299811 fastq.gz 109.8 MB
44 Files (3.9 GB)