Whole genome sequencing of multifocal ileal neuroendocrine tumors
This dataset includes whole genome sequences of 75 synchronous primary tumors, 15 metastases, and corresponding normal samples from 13 patients with multifocal ileal neuroendocrine tumors. The whole genomes were sequenced on Illumina HiSeq X Ten to generate 151-bp paired-end reads, which were aligned to GRCh38/hg38 reference assembly using BWA–MEM and duplicate-marked with Picard tools. GATK was utilized for base score recalibration and local indel re-alignments. The whole genomes are provided as CRAM files.
- 108 samples
- DAC: EGAC00001002701
- Technology: HiSeq X Ten
Dana-Farber Cancer Institute's outbound data use agreement (DUA)
These terms and conditions are an example of the data use agreement to the managed access datasets to which the Recipient Institution has requested access. DATA USE AGREEMENT – DEIDENTIFIED PATIENT DATA Dana-Farber Cancer Institute, Inc. [INSERT NAME HERE] ("Recipient Institution"), having an address at [INSERT ADDRESS HERE], whose investigator is [INSERT NAME HERE] (“Recipient Investigator”), who, with Recipient Institution is hereinafter collectively referred to as “Recipient”, in consideration of the receipt of de-identified patient data from [INSERT NAME HERE] (“Providing Scientist”) of the Dana Farber Cancer Institute, Inc. ("DFCI"), hereby agree to the following terms and conditions: 1. The de-identified patient data (“Data”) provided to Recipient are collected under DFCI Protocol number _____. 2. The Data are to be used only under Recipient’s immediate and direct control for the purposes of ________________(hereinafter the “Project”). The Data shall not be transferred to any third party or used for any purposes other than the Project, including, without limitation, in any research involving human subjects, in any product for commercial use or distribution, for screening purposes, or for the purpose of producing any product or providing any service, which product or service is sold or otherwise made commercially available. No other right or license, to a patent or otherwise, is granted to Recipient for the use of the Data as a result of DFCI’s transmission of them to Recipient. 3. It is understood that DFCI shall not provide to Recipient any patient identifying information or “personal data” (as defined in Massachusetts Law, c. 66A), including medical records and peer review data (“Information”). However, if in the performance of the Project Recipient is provided, obtains or has access to such Information, Recipient shall not use, publish or disclose such Information in any manner whatsoever. Recipient shall comply with the laws and regulations of the Commonwealth of Massachusetts and applicable federal laws and regulations relating to the confidentiality and privacy of such Information. Recipient agrees to notify DFCI and its investigators orally and in writing within twenty-four (24) hours of its discovery of any Information in its possession which is improperly used, copied, or removed by anyone except an authorized representative of DFCI or Recipient. Recipient shall cooperate with DFCI and DFCI investigators in taking such steps as are deemed appropriate by DFCI to enjoin the misuse, regain possession of the Information, and otherwise protect DFCI’s rights and patients’ privacy. 4. The Data are the property of DFCI. 5. This agreement is not assignable. 6. DFCI has, or may, make the Data available to others, both profit and non-profit. 7. Recipient will acknowledge DFCI as the source of the Data in all publications containing any analysis or information about the Data unless DFCI indicates otherwise. 8. Recipient will arrange the return to DFCI or destruction of all Data whenever investigation for which it has been supplied discontinues or is terminated. In the event investigator(s) transfer to another institution, a new Data Use Agreement is to be executed. 9. The Data are transferred AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, INCLUDING SAFETY. DFCI MAKES NO REPRESENTATION OR WARRANTY THAT THE USE OF THE DATA WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT. 10. To the extent allowable under applicable laws, Recipient agrees to indemnify, defend, and hold harmless DFCI and its trustees, officers, staff, representatives and agents against all damages, expenses (including without limitation legal expenses), claims, demands, suits or other actions arising from Recipient's acceptance, use and disposal of the Data and their progeny or derivatives. This Agreement may be executed in multiple counterparts, each of which shall be deemed to be an original, and all of which together shall constitute one and the same agreement. Each party acknowledges and agrees that such Agreement may be executed and delivered in hard copy or by facsimile or electronic means, any one of which shall be deemed to be original, valid and binding upon the parties. This Agreement is effective as of the date of the last signature below. SIGNATURE BY RECIPIENT’S INSTITUTIONAL OFFICIAL, BY ORIGINAL OR SCAN, ACKNOWLEDGES THAT SUCH OFFICIAL IS AUTHORIZED TO BIND THE RECIPIENT INSTITUTION, HAS READ THIS MTA, UNDERSTANDS IT, AND THAT THE INSTITUTION AND ITS RECIPIENT INVESTIGATOR AGREE TO BE BOUND BY AND ACCEPT ALL THE TERMS AND CONDITIONS HEREIN. 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 that are named as registered users by the Recipient Institution 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
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 |
---|---|---|
EGAS00001006294 | 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 | |
---|---|---|---|---|
EGAF00006173882 | cram | 29.6 GB | ||
EGAF00006173883 | cram | 27.9 GB | ||
EGAF00006173884 | cram | 34.5 GB | ||
EGAF00006173885 | cram | 40.8 GB | ||
EGAF00006173886 | cram | 37.2 GB | ||
EGAF00006173887 | cram | 32.9 GB | ||
EGAF00006173888 | cram | 27.7 GB | ||
EGAF00006173889 | cram | 33.2 GB | ||
EGAF00006173890 | cram | 22.5 GB | ||
EGAF00006173891 | cram | 34.2 GB | ||
EGAF00006173892 | cram | 37.2 GB | ||
EGAF00006173893 | cram | 16.3 GB | ||
EGAF00006173894 | cram | 40.6 GB | ||
EGAF00006173895 | cram | 42.4 GB | ||
EGAF00006173896 | cram | 17.2 GB | ||
EGAF00006173897 | cram | 43.9 GB | ||
EGAF00006173898 | cram | 29.0 GB | ||
EGAF00006173899 | cram | 13.7 GB | ||
EGAF00006173900 | cram | 32.5 GB | ||
EGAF00006173901 | cram | 31.5 GB | ||
EGAF00006173902 | cram | 12.7 GB | ||
EGAF00006173903 | cram | 30.8 GB | ||
EGAF00006173904 | cram | 29.2 GB | ||
EGAF00006173905 | cram | 30.6 GB | ||
EGAF00006173906 | cram | 27.0 GB | ||
EGAF00006173907 | cram | 46.3 GB | ||
EGAF00006173908 | cram | 14.5 GB | ||
EGAF00006173909 | cram | 46.0 GB | ||
EGAF00006173910 | cram | 37.3 GB | ||
EGAF00006173911 | cram | 27.4 GB | ||
EGAF00006173912 | cram | 15.1 GB | ||
EGAF00006173913 | cram | 29.0 GB | ||
EGAF00006173914 | cram | 34.7 GB | ||
EGAF00006173915 | cram | 28.4 GB | ||
EGAF00006173916 | cram | 25.7 GB | ||
EGAF00006173917 | cram | 24.2 GB | ||
EGAF00006173918 | cram | 13.0 GB | ||
EGAF00006173919 | cram | 25.0 GB | ||
EGAF00006173920 | cram | 32.7 GB | ||
EGAF00006173921 | cram | 27.8 GB | ||
EGAF00006173922 | cram | 30.3 GB | ||
EGAF00006173923 | cram | 27.2 GB | ||
EGAF00006173924 | cram | 69.7 GB | ||
EGAF00006173925 | cram | 31.6 GB | ||
EGAF00006173926 | cram | 32.2 GB | ||
EGAF00006173927 | cram | 32.8 GB | ||
EGAF00006173928 | cram | 38.4 GB | ||
EGAF00006173929 | cram | 27.0 GB | ||
EGAF00006173930 | cram | 28.2 GB | ||
EGAF00006173931 | cram | 34.8 GB | ||
EGAF00006173932 | cram | 30.8 GB | ||
EGAF00006173933 | cram | 28.1 GB | ||
EGAF00006173934 | cram | 38.0 GB | ||
EGAF00006173935 | cram | 30.3 GB | ||
EGAF00006173936 | cram | 25.7 GB | ||
EGAF00006173937 | cram | 34.3 GB | ||
EGAF00006173938 | cram | 36.9 GB | ||
EGAF00006173939 | cram | 37.2 GB | ||
EGAF00006173940 | cram | 14.2 GB | ||
EGAF00006173941 | cram | 12.6 GB | ||
EGAF00006173942 | cram | 28.5 GB | ||
EGAF00006173943 | cram | 33.9 GB | ||
EGAF00006173944 | cram | 29.2 GB | ||
EGAF00006173945 | cram | 38.3 GB | ||
EGAF00006173946 | cram | 43.8 GB | ||
EGAF00006173947 | cram | 31.5 GB | ||
EGAF00006173948 | cram | 30.1 GB | ||
EGAF00006173949 | cram | 41.3 GB | ||
EGAF00006173950 | cram | 38.7 GB | ||
EGAF00006173951 | cram | 27.5 GB | ||
EGAF00006173952 | cram | 29.3 GB | ||
EGAF00006173953 | cram | 35.5 GB | ||
EGAF00006173954 | cram | 28.3 GB | ||
EGAF00006173955 | cram | 29.0 GB | ||
EGAF00006173956 | cram | 27.9 GB | ||
EGAF00006173957 | cram | 13.7 GB | ||
EGAF00006173958 | cram | 26.2 GB | ||
EGAF00006173959 | cram | 27.3 GB | ||
EGAF00006173961 | cram | 34.7 GB | ||
EGAF00006173962 | cram | 38.1 GB | ||
EGAF00006173963 | cram | 30.3 GB | ||
EGAF00006173964 | cram | 39.1 GB | ||
EGAF00006173965 | cram | 26.0 GB | ||
EGAF00006173966 | cram | 38.3 GB | ||
EGAF00006173967 | cram | 28.3 GB | ||
EGAF00006173968 | cram | 27.0 GB | ||
EGAF00006173969 | cram | 35.0 GB | ||
EGAF00006173970 | cram | 31.2 GB | ||
EGAF00006173971 | cram | 44.7 GB | ||
EGAF00006173972 | cram | 44.7 GB | ||
EGAF00006173973 | cram | 32.2 GB | ||
EGAF00006173974 | cram | 44.1 GB | ||
EGAF00006173975 | cram | 15.5 GB | ||
EGAF00006173976 | cram | 33.4 GB | ||
EGAF00006173977 | cram | 36.2 GB | ||
EGAF00006173978 | cram | 26.8 GB | ||
EGAF00006173979 | cram | 43.5 GB | ||
EGAF00006173980 | cram | 33.6 GB | ||
EGAF00006173981 | cram | 31.8 GB | ||
EGAF00006173982 | cram | 41.3 GB | ||
EGAF00006173983 | cram | 35.8 GB | ||
EGAF00006173984 | cram | 30.8 GB | ||
EGAF00006173985 | cram | 34.1 GB | ||
EGAF00006173986 | cram | 34.4 GB | ||
EGAF00006173987 | cram | 33.1 GB | ||
EGAF00006173988 | cram | 35.7 GB | ||
EGAF00006173989 | cram | 15.3 GB | ||
107 Files (3.4 TB) |