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Whole Exome and RNA-Sequencing of Germline, Small Bowel Carcinoid Primary Tumor, and Liver Metastasis Trios

This dataset includes trios of germline/constitutional, primary tumor (small bowel carcinoid), and metastatic tumor (liver) trios for 5 patients (i.e. 15 samples total). Constitutional, primary tumor, and metastatic tumor samples all underwent whole exome sequencing (WES or WXS). Primary and metastatic tumor samples underwent RNA sequencing (RNA-seq).

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The Hoag Family Cancer Institute Carcinoid Multiomic Study Data Access Committee (DAC)'s Access Policy.

DATA ACCESS POLICY A. Data Recipient Information List information for Institution receiving the Data Set (“Institution”) and Principal Investigator (“Principal Investigator”) and include any co-investigators, staff, or students (collectively, “Other Users”) that will be provided access to the Data Set at Institution. Effective Date Name of Institution Institution Address Name of Principal Investigator Title Department Address 1 Address 2 City, State, Zip Phone Fax Email Title of Project Name(s) of Other Users Project Summary (Limit to this space) Data Set Analysis Plan (“Study”) 1. Introduction (Rationale and Background) 2. Research Aims 3. Hypotheses. 4. Analytical plan. 5. References. B. Hoag Principal Investigator Contact Information Name: Michael J. Demeure, MD, MBA, FACS, FACE Title: Director, Hoag Center for Applied Genomic Technologies Address: Hoag Family Cancer Institute, One Hoag Drive, P.O. Box 6100, Newport Beach, CA, 92663, USA Tel: +1 (949) 764-6263 Email: Michael.demeure@hoag.org DATA ACCESS AGREEMENT This Data Access Agreement (“Agreement”) is between the Data Access Committee (DAC), on behalf of the Hoag Family Cancer Institute, and the Institution (as defined in Section A) and is effective as of the “Effective Date”, indicated in Section A. Institution and Principal Investigator, as defined in Section A, are collectively referred to herein as “Data Recipient”. This Agreement governs the terms of access to the de-identified dataset – generated under the direction of Michael J. Demeure, M.D. (Hoag Principal Investigator, DAC member) – entitled: “Multiomic Sequencing of Paired Primary and Metastatic Small Bowel Carcinoids.” 1. Responsibility of Hoag The Data Set was collected in accordance with applicable laws, regulations, patient consent forms and authorizations pursuant to Institutional Review Board (IRB) approval and was de-identified in accordance with the Health Insurance Portability and Accountability Act (HIPAA). 2. Responsibility of Data Recipient Data Recipient agrees that: a. the Data Set shall be used solely for the Study described in Section A; b. any additional uses of the Data Set by the Data Recipient shall be covered under a separate agreement; c. the Data Set shall be used in compliance with all applicable local, state and federal statutes and regulations; d. the Data Set shall be used only at the Institution by the Principal Investigator and the Other Users working under his/her direct supervision; Principal Investigator will notify the DAC of any departures of the Principal Investigator or Other Users within 30 days of the changes made. e. the Data Set shall not be transferred, in whole or in part, to anyone outside the Institution without prior written consent of the DAC. f. Data Recipient will not contact or make any effort to identify individuals who are or may be included in the Data Set. 3. Confidentiality Data Recipient shall not disclose the Data Set to anyone except the Principal Investigator and the Other Users for the purposes of the Study. The Data Recipient will use the Data Set only in the conduct of the Study and evaluation of its results. Data Recipient agrees to preserve, at all times, the confidentiality of the Data Set. Data Recipient will use the Data Set in a secure manner using appropriate administrative, physical storage and technical safeguards to prevent use or disclosure of the data other than as provided for in this Agreement. Data Recipient agrees to notify the DAC within 5 days of becoming aware of any use or disclosure of the Data Set in violation of this Agreement. 4. Publication Data Recipient agrees to acknowledge the DAC in any publication, presentation, abstract or other work based in whole or in part on the Data Set. Data Recipient will cite the Hoag Cancer Institute Metastatic Small Bowel Carcinoid Study Dataset as the source of the data in the methods. 5. Intellectual Property Inventorship of inventions invented by Data Recipient in the performance of the Study (“Inventions”) shall be determined according to U.S. patent law and ownership will vest in the party to whom the inventor has an obligation to assign all right, title and interest in the Invention. Nothing in this Agreement grants Data Recipient any rights to use the Data Set for commercial purposes. The DAC explicitly retains ownership of the Data Set and this Agreement does not restrict the DAC’s right to distribute the Data Set to other entities. Notwithstanding the foregoing, Data Recipient shall not pursue intellectual property rights which occur as a result of the use of the Data Set in the performance of the Study without first notifying the DAC so that the DAC can assert claims to legal inventorship under U.S. law. Data Recipient agrees not to make intellectual property claims on the Data Set and not to use intellectual property protection in ways that would prevent or block access to the Data Set. This Agreement in no way alters any rights or interests of the U.S. government. 6. Limitation of Liability THE DATA SET IS EXPERIMENTAL IN NATURE AND IS BEING MADE AVAILABLE TO RECIPIENT WITH NO WARRANTIES, EXPRESS OR IMPLIED, OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR OTHERWISE. IN PARTICULAR, HOAG DOES NOT REPRESENT OR WARRANT THAT THE USE OF THE DATA SET WILL NOT INFRINGE OR VIOLATE ANY PATENT OR PROPRIETARY RIGHTS OF THIRD PARTIES. To the extent permitted by law, Institution assumes all liability for damages which may arise from the use, storage or disposal of the Data Set by Data Recipient. Hoag (including, but not limited to, its directors, trustees, officers employees, students and agents, as applicable), will not be liable to the Data Recipient for any loss, claim or demand made by or against the Data Recipient or Other Users, due to or arising from the use of the Data Set by the Data Recipient or Other Users or due to unavailability of or interruption in Data Set access for whatever reason, except to the extent caused by the gross negligence or willful misconduct of Hoag. To the extent allowable under applicable laws, Institution agrees to indemnify, defend and hold harmless Hoag 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 Data Recipient’s acceptance, storage, use and disposal of the Data Set, but only in proportion to and to the extent such are caused by or result from the negligent or intentional acts or omissions of Data Recipient, Other Users, or Institution’s officers, agents or employees. 7. Assignment. This agreement is not assignable by Institution. 8. Term and Termination The term of this agreement shall commence on the Effective Date and shall continue for as long as the Data Recipient retains the Data Set, unless terminated sooner as set forth in this Agreement. The Data Recipient may terminate this Agreement at any time by notifying the DAC. The DAC may terminate this Agreement at any time upon breach of this Agreement by Data Recipient. In the event of termination, Data Recipient shall destroy the Data Set and all copies in its possession, including all documents created by Data Recipient where portions of the Data Set are reproduced. 9. Agreement If Data Recipient agrees to the above terms and conditions for access to the Data Set, please so indicate by returning one copy of this Agreement signed by a duly authorized representative of Institution and by Principal Investigator. Upon receipt of signed Agreement by Institution and Principal Investigator, access to the Data Set will be provided to the Principal Investigator. Principal Investigator agrees to distribute a copy of this agreement and explain its content to any Other Users, and will ensure that they acknowledge their obligations to abide by the terms of this Agreement in their use of the Data Set. Agreed: __________________________ Signature for Institution __________________________ Title for Official Read and Understood by: __________________________ Print Name Date Michael J Demeure MD Electronically signed by: Michael J Demeure MD Reason: I have reviewed and approve this __________________________ Signature of Principal Investigator __________________________ Print Name Date document. Date: Feb 6, 2023 16:06 PST Michael J Demeure MD Feb 6, 2023 __________________ __________________ Data_access_agreement_ver2 Final Audit Report "Data_access_agreement_ver2" History Document created by Vikki Flaskerud (vikki.flaskerud@hoag.org) 2023-02-07 - 0:04:30 AM GMT- IP address: 75.48.98.2 Document emailed to michael.demeure@hoag.org for signature 2023-02-07 - 0:05:25 AM GMT Email viewed by michael.demeure@hoag.org 2023-02-07 - 0:05:41 AM GMT- IP address: 75.48.98.2 2023-02-07 Created: By: Status: Transaction ID: 2023-02-07 Vikki Flaskerud (vikki.flaskerud@hoag.org) Signed CBJCHBCAABAAgn9DFfyBAxIx6um1wP06oHyewFg_bE9z Signer michael.demeure@hoag.org entered name at signing as Michael J Demeure MD 2023-02-07 - 0:06:36 AM GMT- IP address: 75.48.98.2 Document e-signed by Michael J Demeure MD (michael.demeure@hoag.org) Signing reason: I have reviewed and approve this document. Signature Date: 2023-02-07 - 0:06:38 AM GMT - Time Source: server- IP address: 75.48.98.2 Agreement completed. 2023-02-07 - 0:06:38 AM GMT

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
EGAS00001006988 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
EGAF00007919085 fastq.gz 3.4 GB
EGAF00007919086 fastq.gz 3.6 GB
EGAF00007919087 fastq.gz 3.5 GB
EGAF00007919088 fastq.gz 3.7 GB
EGAF00007919089 fastq.gz 1.8 GB
EGAF00007919090 fastq.gz 2.0 GB
EGAF00007919091 fastq.gz 2.7 GB
EGAF00007919092 fastq.gz 2.8 GB
EGAF00007919093 fastq.gz 1.6 GB
EGAF00007919094 fastq.gz 1.7 GB
EGAF00007919095 fastq.gz 1.6 GB
EGAF00007919096 fastq.gz 1.6 GB
EGAF00007919097 fastq.gz 761.5 MB
EGAF00007919098 fastq.gz 777.1 MB
EGAF00007919099 fastq.gz 3.8 GB
EGAF00007919100 fastq.gz 4.0 GB
EGAF00007919101 fastq.gz 3.8 GB
EGAF00007919102 fastq.gz 4.1 GB
EGAF00007919103 fastq.gz 2.0 GB
EGAF00007919104 fastq.gz 2.1 GB
EGAF00007919105 fastq.gz 5.1 GB
EGAF00007919106 fastq.gz 5.2 GB
EGAF00007919107 fastq.gz 1.0 GB
EGAF00007919108 fastq.gz 1.1 GB
EGAF00007919109 fastq.gz 1.0 GB
EGAF00007919110 fastq.gz 1.1 GB
EGAF00007919111 fastq.gz 438.6 MB
EGAF00007919112 fastq.gz 445.4 MB
EGAF00007919113 fastq.gz 4.0 GB
EGAF00007919114 fastq.gz 4.2 GB
EGAF00007919115 fastq.gz 4.0 GB
EGAF00007919116 fastq.gz 4.2 GB
EGAF00007919117 fastq.gz 2.2 GB
EGAF00007919118 fastq.gz 2.3 GB
EGAF00007919119 fastq.gz 4.1 GB
EGAF00007919120 fastq.gz 4.3 GB
EGAF00007919121 fastq.gz 4.1 GB
EGAF00007919122 fastq.gz 4.3 GB
EGAF00007919123 fastq.gz 2.2 GB
EGAF00007919124 fastq.gz 2.3 GB
EGAF00007919125 fastq.gz 5.2 GB
EGAF00007919126 fastq.gz 5.3 GB
EGAF00007919127 fastq.gz 1.7 GB
EGAF00007919128 fastq.gz 1.8 GB
EGAF00007919129 fastq.gz 1.7 GB
EGAF00007919130 fastq.gz 1.8 GB
EGAF00007919131 fastq.gz 661.8 MB
EGAF00007919132 fastq.gz 670.6 MB
EGAF00007919133 fastq.gz 3.3 GB
EGAF00007919134 fastq.gz 3.4 GB
EGAF00007919135 fastq.gz 3.3 GB
EGAF00007919136 fastq.gz 3.5 GB
EGAF00007919137 fastq.gz 1.8 GB
EGAF00007919138 fastq.gz 1.9 GB
EGAF00007919139 fastq.gz 3.8 GB
EGAF00007919140 fastq.gz 3.8 GB
EGAF00007919141 fastq.gz 1.5 GB
EGAF00007919142 fastq.gz 1.5 GB
EGAF00007919143 fastq.gz 1.5 GB
EGAF00007919144 fastq.gz 1.5 GB
EGAF00007919145 fastq.gz 602.2 MB
EGAF00007919146 fastq.gz 617.1 MB
EGAF00007919147 fastq.gz 5.2 GB
EGAF00007919148 fastq.gz 5.5 GB
EGAF00007919149 fastq.gz 5.3 GB
EGAF00007919150 fastq.gz 5.6 GB
EGAF00007919151 fastq.gz 2.6 GB
EGAF00007919152 fastq.gz 2.8 GB
EGAF00007919153 fastq.gz 6.9 GB
EGAF00007919154 fastq.gz 7.2 GB
EGAF00007919155 fastq.gz 6.8 GB
EGAF00007919156 fastq.gz 7.1 GB
EGAF00007919157 fastq.gz 7.3 GB
EGAF00007919158 fastq.gz 7.6 GB
EGAF00007919159 fastq.gz 7.2 GB
EGAF00007919160 fastq.gz 7.5 GB
EGAF00007919161 fastq.gz 1.5 GB
EGAF00007919162 fastq.gz 1.6 GB
EGAF00007919163 fastq.gz 1.5 GB
EGAF00007919164 fastq.gz 1.6 GB
EGAF00007919165 fastq.gz 598.4 MB
EGAF00007919166 fastq.gz 644.3 MB
EGAF00007919167 fastq.gz 645.4 MB
EGAF00007919168 fastq.gz 660.4 MB
EGAF00007919169 fastq.gz 6.3 GB
EGAF00007919170 fastq.gz 6.5 GB
EGAF00007919171 fastq.gz 6.3 GB
EGAF00007919172 fastq.gz 6.5 GB
EGAF00007919173 fastq.gz 1.1 GB
EGAF00007919174 fastq.gz 1.2 GB
EGAF00007919175 fastq.gz 1.1 GB
EGAF00007919176 fastq.gz 1.2 GB
EGAF00007919177 fastq.gz 441.4 MB
EGAF00007919178 fastq.gz 469.2 MB
EGAF00007919179 fastq.gz 688.3 MB
EGAF00007919180 fastq.gz 698.8 MB
EGAF00007919181 fastq.gz 2.7 GB
EGAF00007919182 fastq.gz 2.9 GB
EGAF00007919183 fastq.gz 2.8 GB
EGAF00007919184 fastq.gz 2.9 GB
EGAF00007919185 fastq.gz 1.4 GB
EGAF00007919186 fastq.gz 1.4 GB
EGAF00007919187 fastq.gz 4.6 GB
EGAF00007919188 fastq.gz 4.8 GB
EGAF00007919189 fastq.gz 2.1 GB
EGAF00007919190 fastq.gz 2.2 GB
EGAF00007919191 fastq.gz 2.1 GB
EGAF00007919192 fastq.gz 2.2 GB
EGAF00007919193 fastq.gz 807.7 MB
EGAF00007919194 fastq.gz 857.3 MB
EGAF00007919195 fastq.gz 6.3 GB
EGAF00007919196 fastq.gz 6.5 GB
EGAF00007919197 fastq.gz 6.2 GB
EGAF00007919198 fastq.gz 6.4 GB
EGAF00007919199 fastq.gz 2.3 GB
EGAF00007919200 fastq.gz 2.5 GB
EGAF00007919201 fastq.gz 2.3 GB
EGAF00007919202 fastq.gz 2.5 GB
EGAF00007919203 fastq.gz 887.7 MB
EGAF00007919204 fastq.gz 940.8 MB
EGAF00007919205 fastq.gz 2.0 GB
EGAF00007919206 fastq.gz 2.0 GB
EGAF00007919207 fastq.gz 14.3 GB
EGAF00007919208 fastq.gz 14.8 GB
EGAF00007919209 fastq.gz 3.2 GB
EGAF00007919210 fastq.gz 3.3 GB
EGAF00007919211 fastq.gz 13.3 GB
EGAF00007919212 fastq.gz 14.0 GB
EGAF00007919213 fastq.gz 12.7 GB
EGAF00007919214 fastq.gz 13.3 GB
130 Files (449.0 GB)