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Genomic alterations in MM - BAM

Tumor DNA was extracted from 100 bone marrow aspirate samples where CD138+ selection had been performed to enrich plasma cells from patients with multiple myeloma. Patient matched control DNA from either peripheral blood leukocytes or CD34+ stem cell harvests was also isolated. Both tumor and control DNA underwent library preparation using the Hyperplus kit (KAPA Biosystems) and were hybridized to baits for a targeted SeqCap myeloma panel (Nimblegen) encompassing 129 genes, regions for SNPs for copy number determination, and the IGH, IGK, IGL loci, as well as approximately 5 Mb surrounding the MYC locus. Samples were sequenced on a HiSeq2500 using 100 bp paired end reads. Resulting BAM files were returned along with annotations for somatic events including single nucleotide mutations, indels and structural rearrangements.

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UAMS - Deidentified Data Transfer Agreement 2016

Terms subject to change based on each transfer 2016 Data Transfer Agreement This Data Transfer Agreement (this "Agreement") is entered into effective as of the last signature date of this Agreement (“Effective Date”) by and between [company] ("Recipient"),and the Board of Trustees of the University of Arkansas acting for and on behalf of the University of Arkansas for Medical Sciences ("Provider") in order to document the transferof certain de-identified data, as defined below and the mutual covenants and promises hereinafter set forth as agreed to by Recipient and Provider. Provider and Recipient maybe referred to herein individually as a "Party" or collectively as the "Parties".WHEREAS, the Parties agree that this Agreement shall govern only the transfer of the Study Data, as defined herein, if the Parties agree in writing to same. 1. "Study Data" shall be defined to mean de-identified data collected under informed consent related to the research study entitled [please insert title]. 2. Provider certifies that the Study Data shall be provided in a de-identified fashion. Under no circumstances shall Provider provide Recipient with the name, address, social security number, or any other identifier which would permit Recipient to identify the research subjects from whom such Study Data was collected. The Recipient, through [recipient scientist name], certifies that they neither have nor will seek to obtain information from Provider that identifies or can be used to identify or link de-identified data to any research subject, and in the event that either receives any PHI, such PHI shall be kept confidential, not used or disclosed, and shall be immediately returned to Provider. 3. Subject to, and in accordance with terms set in this Agreement, Recipient shall use Study Data for the following research purposes only (and for no other purpose): [indicate purpose/research/reference number if applicable] 4. Recipient shall only disclose Study Data to Recipient’s employees who have a need to know and who are directly responsible for the activities related to the Purpose. The Recipient, through [recipient scientist name], who shall serve as the Principal Investigator of the research study utilizing the Study Data, will ensure that all such parties are informed of the terms and conditions under this Agreement. 5. Recipient shall not use or further disclose the Study Data other than as permitted or required by this Agreement or as otherwise required by law. Recipient shall report to Provider immediately within upon Recipient’s discovery of any unauthorized use or disclosure of the Study Data not provided for by this Agreement. Recipient shall provide the following information: (1) the nature of the use or disclosure; (2) the information used or disclosed; (3) who made the use or disclosure; and (4) what corrective action will be taken by Recipient as a result of the use or disclosure. Recipient shall take any other actions available to it to mitigate any detrimental effects of the use or disclosure. 6. Recipient and its employees shall not identify or attempt to identify the individual(s) to whom the Study Data pertains or contact or attempt to contact the individual(s) who Recipient believes to be the subject of any Study Data. The obligations set forth in this Section 6 shall survive the termination or expiration of this Agreement for any reason. 7. As principal investigator, [recipient scientist name] has agreed to provide any results gained from the analysis of the Study Data with Provider. Provider Institution shall maintain these results in confidence pending publication and/or presentation of the results of the analysis being conducted on the Study Data. However, if Recipient has not published within six (6) months of the completion of the Study at Recipient’s institution, Provider shall have the right to publish or present independently any results from its work at Provider’s institution. [this term will change to joint publication if that is what is agreed]. 8. Subject to Applicable Laws, none of Provider, Principal Investigator, or Recipient shall use the name, trademark, trade name or logo of the other in any publication, press release, or promotional material with respect to the Study without the prior written approval of the other party; provided, however, that Recipient shall have the right to identify Provider as the site at which the Study Data was generated and to identify those individuals responsible for conducting the Study. Provider retains the right to use Recipient’s name, and a non-confidential descriptor, on any and all funding applications it may seek in the future. 9. This Agreement may be terminated by either Party, for any reason, upon thirty (30) days' advance written notice to the other Party, and this Agreement may be terminated upon mutual written agreement signed by the authorized representatives of both of the Parties. Notwithstanding anything to the contrary, Recipient and [recipient scientist name] shall not use or disclose any information provided by Provider except in accordance with the terms of this Agreement and applicable law. This obligation shall extend in perpetuity. Recipient agrees that upon termination of this Agreement, Recipient shall, at its expense, (a) return or destroy all Study Data received from Provider and retain no copies of such Study Data. 10. Any notice required or permitted hereunder shall be in writing and shall be deemed given as of the date it is: (i) delivered by hand; (ii) received by registered or certified mail, postage prepaid, return receipt requested; (iii) confirmed as received if by facsimile; or (iv) received by nationally recognized, overnight courier, and addressed to the party to receive such notice at the address set forth below, or such other address as is subsequently specified in writing. If to Recipient: [ please provide ] If to Provider: University of Arkansas for Medical Sciences By Post: 4301 West Markham Drive, MS#860 Little Rock, AR 72205 By Courier: Ed II, 5th Floor, Suite 104 Little Rock, AR 72205 Attn: Sr. Research Contracts Attorney 11. Recipient and Provider shall not assign or transfer any rights or obligations hereunder, or any part hereof, without the prior written consent of the other Party. 12. Entire Agreement. This Agreement constitutes the entire agreement and understanding between the Parties and supersedes any prior or contemporaneous negotiations, agreements, understandings, or arrangements of any nature or kind with respect to the subject matter herein. 13. This Agreement may be executed simultaneously in any number of counterparts (including scanned copies of signature in portable document format “pdf” and delivered via electronic mail), each of which shall be deemed an original and all of which taken together shall constitute one and the same instrument. IN WITNESS WHEREOF, the parties have executed this Data Transfer Agreement as of the [Effective Date] Board of Trustees of the University of Arkansas [Name of Recpient] Acting For And On Behalf Of The University of Arkansas for Medical Sciences By: ___________________________________ By: ________________________ Name: Suzanne Alstadt Name: Title: Director, Office of Research and Title: Sponsored Programs Date: _________________________________ Date: ______________________ READ AND UNDERSTOOD BY PRINCIPAL INVESTIGATOR By: ________________________________ Date: _______________________________

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
EGAS00001002859 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
EGAF00002008216 bam 2.0 GB
EGAF00002008217 bam 2.4 GB
EGAF00002008218 bam 2.0 GB
EGAF00002008219 bam 1.5 GB
EGAF00002008220 bam 1.5 GB
EGAF00002008221 bam 1.7 GB
EGAF00002008222 bam 5.2 GB
EGAF00002008223 bam 2.1 GB
EGAF00002008224 bam 1.4 GB
EGAF00002008225 bam 2.4 GB
EGAF00002008226 bam 1.9 GB
EGAF00002008227 bam 2.7 GB
EGAF00002008228 bam 2.0 GB
EGAF00002008229 bam 2.0 GB
EGAF00002008230 bam 1.9 GB
EGAF00002008231 bam 1.8 GB
EGAF00002008232 bam 1.9 GB
EGAF00002008233 bam 1.9 GB
EGAF00002008234 bam 1.8 GB
EGAF00002008235 bam 1.4 GB
EGAF00002008236 bam 3.0 GB
EGAF00002008237 bam 2.1 GB
EGAF00002008238 bam 2.1 GB
EGAF00002008239 bam 2.2 GB
EGAF00002008240 bam 2.6 GB
EGAF00002008241 bam 2.2 GB
EGAF00002008242 bam 1.7 GB
EGAF00002008243 bam 2.3 GB
EGAF00002008244 bam 2.1 GB
EGAF00002008245 bam 1.5 GB
EGAF00002008246 bam 1.5 GB
EGAF00002008247 bam 2.1 GB
EGAF00002008248 bam 1.7 GB
EGAF00002008249 bam 2.2 GB
EGAF00002008250 bam 2.0 GB
EGAF00002008251 bam 1.4 GB
EGAF00002008252 bam 1.5 GB
EGAF00002008253 bam 1.6 GB
EGAF00002008254 bam 1.3 GB
EGAF00002008255 bam 2.4 GB
EGAF00002008256 bam 2.1 GB
EGAF00002008257 bam 2.4 GB
EGAF00002008258 bam 1.9 GB
EGAF00002008259 bam 2.2 GB
EGAF00002008260 bam 1.8 GB
EGAF00002008261 bam 2.2 GB
EGAF00002008262 bam 2.1 GB
EGAF00002008263 bam 2.6 GB
EGAF00002008264 bam 1.9 GB
EGAF00002008265 bam 2.3 GB
EGAF00002008266 bam 2.2 GB
EGAF00002008267 bam 2.0 GB
EGAF00002008268 bam 1.6 GB
EGAF00002008269 bam 2.2 GB
EGAF00002008270 bam 2.1 GB
EGAF00002008271 bam 2.1 GB
EGAF00002008272 bam 2.0 GB
EGAF00002008273 bam 2.2 GB
EGAF00002008274 bam 1.9 GB
EGAF00002008275 bam 2.4 GB
EGAF00002008276 bam 2.1 GB
EGAF00002008277 bam 1.5 GB
EGAF00002008278 bam 1.5 GB
EGAF00002008279 bam 2.6 GB
EGAF00002008280 bam 2.1 GB
EGAF00002008281 bam 2.0 GB
EGAF00002008282 bam 1.8 GB
EGAF00002008283 bam 3.6 GB
EGAF00002008284 bam 2.7 GB
EGAF00002008285 bam 2.9 GB
EGAF00002008286 bam 2.8 GB
EGAF00002008287 bam 2.3 GB
EGAF00002008288 bam 1.7 GB
EGAF00002008289 bam 2.1 GB
EGAF00002008290 bam 1.7 GB
EGAF00002008291 bam 2.8 GB
EGAF00002008292 bam 1.9 GB
EGAF00002008293 bam 3.0 GB
EGAF00002008294 bam 2.6 GB
EGAF00002008295 bam 2.3 GB
EGAF00002008296 bam 1.7 GB
EGAF00002008297 bam 2.5 GB
EGAF00002008298 bam 1.9 GB
EGAF00002008299 bam 1.9 GB
EGAF00002008300 bam 1.8 GB
EGAF00002008301 bam 2.9 GB
EGAF00002008302 bam 2.0 GB
EGAF00002008303 bam 3.9 GB
EGAF00002008304 bam 2.5 GB
EGAF00002008305 bam 1.8 GB
EGAF00002008306 bam 1.8 GB
EGAF00002008307 bam 2.1 GB
EGAF00002008308 bam 2.3 GB
EGAF00002008309 bam 2.2 GB
EGAF00002008310 bam 1.9 GB
EGAF00002008311 bam 2.7 GB
EGAF00002008312 bam 2.6 GB
EGAF00002008313 bam 1.7 GB
EGAF00002008314 bam 1.6 GB
EGAF00002008315 bam 2.4 GB
EGAF00002008316 bam 2.4 GB
EGAF00002008317 bam 3.0 GB
EGAF00002008318 bam 2.5 GB
EGAF00002008319 bam 2.4 GB
EGAF00002008320 bam 2.0 GB
EGAF00002008321 bam 2.7 GB
EGAF00002008322 bam 2.6 GB
EGAF00002008323 bam 1.7 GB
EGAF00002008324 bam 1.9 GB
EGAF00002008325 bam 2.1 GB
EGAF00002008326 bam 2.6 GB
EGAF00002008327 bam 2.1 GB
EGAF00002008328 bam 2.3 GB
EGAF00002008329 bam 3.4 GB
EGAF00002008330 bam 2.5 GB
EGAF00002008331 bam 2.8 GB
EGAF00002008332 bam 2.1 GB
EGAF00002008333 bam 2.4 GB
EGAF00002008334 bam 2.2 GB
EGAF00002008335 bam 2.1 GB
EGAF00002008336 bam 2.1 GB
EGAF00002008337 bam 2.4 GB
EGAF00002008338 bam 2.3 GB
EGAF00002008339 bam 1.8 GB
EGAF00002008340 bam 1.9 GB
EGAF00002008341 bam 1.9 GB
EGAF00002008342 bam 1.9 GB
EGAF00002008343 bam 2.0 GB
EGAF00002008344 bam 1.8 GB
EGAF00002008345 bam 2.5 GB
EGAF00002008346 bam 2.6 GB
EGAF00002008347 bam 3.1 GB
EGAF00002008348 bam 2.5 GB
EGAF00002008349 bam 3.5 GB
EGAF00002008350 bam 3.5 GB
EGAF00002008351 bam 2.6 GB
EGAF00002008352 bam 2.7 GB
EGAF00002008353 bam 2.3 GB
EGAF00002008354 bam 2.2 GB
EGAF00002008355 bam 2.9 GB
EGAF00002008356 bam 2.7 GB
EGAF00002008357 bam 3.1 GB
EGAF00002008358 bam 2.6 GB
EGAF00002008359 bam 2.6 GB
EGAF00002008360 bam 2.8 GB
EGAF00002008361 bam 1.8 GB
EGAF00002008362 bam 1.7 GB
EGAF00002008363 bam 2.2 GB
EGAF00002008364 bam 2.1 GB
EGAF00002008365 bam 2.5 GB
EGAF00002008366 bam 2.4 GB
EGAF00002008367 bam 1.9 GB
EGAF00002008368 bam 1.8 GB
EGAF00002008369 bam 2.0 GB
EGAF00002008370 bam 2.0 GB
EGAF00002008371 bam 1.6 GB
EGAF00002008372 bam 1.6 GB
EGAF00002008373 bam 2.8 GB
EGAF00002008374 bam 2.8 GB
EGAF00002008375 bam 2.0 GB
EGAF00002008376 bam 1.9 GB
EGAF00002008377 bam 1.9 GB
EGAF00002008378 bam 1.9 GB
EGAF00002008379 bam 2.6 GB
EGAF00002008380 bam 2.8 GB
EGAF00002008381 bam 1.7 GB
EGAF00002008382 bam 1.5 GB
EGAF00002008383 bam 2.0 GB
EGAF00002008384 bam 1.8 GB
EGAF00002008385 bam 2.0 GB
EGAF00002008386 bam 2.0 GB
EGAF00002008387 bam 2.2 GB
EGAF00002008388 bam 1.8 GB
EGAF00002008389 bam 2.0 GB
EGAF00002008390 bam 1.8 GB
EGAF00002008391 bam 2.8 GB
EGAF00002008392 bam 2.4 GB
EGAF00002008393 bam 3.5 GB
EGAF00002008394 bam 3.2 GB
EGAF00002008395 bam 1.8 GB
EGAF00002008396 bam 1.5 GB
EGAF00002008397 bam 1.7 GB
EGAF00002008398 bam 1.6 GB
EGAF00002008399 bam 2.4 GB
EGAF00002008400 bam 2.7 GB
EGAF00002008401 bam 2.2 GB
EGAF00002008402 bam 1.9 GB
EGAF00002008403 bam 2.2 GB
EGAF00002008404 bam 1.8 GB
EGAF00002008405 bam 1.8 GB
EGAF00002008406 bam 1.9 GB
EGAF00002008407 bam 2.3 GB
EGAF00002008408 bam 2.0 GB
EGAF00002008409 bam 2.3 GB
EGAF00002008410 bam 2.1 GB
EGAF00002008411 bam 2.2 GB
EGAF00002008412 bam 1.8 GB
EGAF00002008413 bam 2.3 GB
EGAF00002008414 bam 2.0 GB
EGAF00002008415 bam 2.3 GB
200 Files (439.3 GB)