Whole genome sequencing of 198 epileptic individuals.
This dataset includes whole genome sequencing of 198 epileptic individuals. Libraries preparation and whole-genome sequencing: gDNA was cleaned up using ZR-96 DNA Clean & ConcentratorTM-5 Kit (Zymo) prior to being quantified using the Quant-iTTM PicoGreen dsDNA Assay Kit (Life Technologies) and its integrity assessed on agarose gels. Libraries were generated using the TruSeq DNA PCR-Free Library Preparation Kit (Illumina) according to the manufacturer’s recommendations. Libraries were quantified using the Quant-iTTM PicoGreen dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were denatured in 0.05N NaOH and diluted to 8pM using HT1 buffer. The clustering was done on a Illumina cBot and the flowcell was ran on a HiSeq 2500 for 2x125 cycles (paired-end mode) using v4 chemistry and following the manufacturer's instructions. A phiX library was used as a control and mixed with libraries at 0.01 level. Bioinformatics: The Illumina control software was HCS 2.2.58, the real-time analysis program was RTA v. 1.18.64. Program bcl2fastq v1.8.4 was used to demultiplex samples and generate fastq reads. The filtered reads were aligned to reference Homo_sapiens assembly b37. Each readset was aligned to creates a Binary Alignment Map file (.bam).
- 16/04/2018
- 198 samples
- DAC: EGAC00001000827
- Technology: Illumina HiSeq 2500
Data access agreement for CENET data.
DATA ACCES AGREEMENT This data transfer agreement (the "Agreement") is made and entered into effective as of the date of signature of the last Party to sign below (the "Effective Date"). BETWEEN: Centre Hospitalier de l'Université de Montréal (CHUM), a constituted corporation under An Act Respecting Health Services and Social Services, CQLR c S-4.2, a law of Quebec, Canada, having its head office at 850 St-Denis St, S Pavilion, Montréal, Quebec, H2X 0A9, Canada; (the "Disclosing Institution") -and- Dr. Patrick Cossette, a researcher having research status at the Receiving Institution, having an address at Centre Hospitalier de l'Université de Montréal (CHUM), CRCHUM - Pavilion R, 900 St. Denis St., Suite R04-482, Montréal, Québec H2X 0A9 Canada; (the "Disclosing Investigator") (the Receiving Institution and, together with Receiving Investigator, "Disclosing Party") -and- , having its principal place of business at , Canada; (the "Receiving Institution") -and- Dr. , a researcher having research privileges at the Disclosing Institution, having his/her address at ; (the " ("Receiving Investigator") (the Disclosing Institution and, together with Disclosing Investigator, the "Receiving Party") The Receiving Institution, Receiving Investigator, Disclosing Institution and Disclosing Investigator shall all be considered separately as a "Party" and together as the "Parties WHEREAS, the Receiving Investigator has created a study entitled " " (the "Study") as fully described in the Protocol, as such Protocol may be amended from time to time, attached to this Agreement as Schedule "B" ("Protocol"); WHEREAS, the Disclosing Party has agreed to share some data with the Receiving Party; NOW THEREFORE THIS AGREEMENT WITNESSETH that in consideration of the covenants and obligations herein contained the Parties hereto covenant and agree with each other as follows: 1 Scope and Purpose The purpose of this Agreement is to provide Receiving Party with the data described in the Schedule "A" ("Data") for use in the Study. The Parties shall comply with all applicable laws, regulations, guidelines and policies ("Applicable Law"). The Disclosing Party will prepare and furnish the Data in accordance with Applicable Law including without limitation obtaining all appropriate consents. 2 Subject Confidentiality a. The Parties (i) shall comply with applicable health information and privacy legislation relating to the use, protection, disclosure, return or disposal of any individual's identifying health information ("Health Information"); (ii) use Health Information only for the purpose of conducting the Study; (iii) not publish the Health Information in a form that could reasonably enable the identity of an individual who is the subject of the information to be readily ascertained; (iv) be liable for the actions of its employees, agents, consultants or other persons for whom they are in law responsible respecting the collection, use or disclosure of Health Information and for ensuring compliance with applicable legislation by these persons; and (v) ensure that Health Information will not be disclosed to any third parties, except where such disclosure is required by law. b. The provisions of this section 5 shall survive the completion or earlier termination of this Agreement. Each Party shall be liable for the actions of its/his employees, agents, consultants or other persons for whom it/he/she is in law responsible respecting the collection, use or disclosure of personal information and for ensuring compliance with applicable legislation by such persons. 3 Safeguards and Notification. The Receiving Party shall use appropriate safeguards (including without limitation with respect to encrypting identifying numbers, linking files, storing and retrieving files from secured locations) to prevent any unauthorized use or disclosure of the Data and shall promptly report to Disclosing Party any unauthorized use or disclosure of which Receiving Party becomes aware. 4 Data use limitation The Receiving Party acknowledges and agrees to only use the Data for the Study and only for epilepsy research purposes. 5 Contact with Subjects/Individuals. The Receiving Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify any individual, even if access to that data has been formally granted to the Receiving Party or is freely available without restriction. The Receiving Party shall not make contact or attempt to make contact with an individual unless the Disclosing Party first obtains the individual's consent to be contacted, except to the extent that the Receiving Party is otherwise the individual's health information custodian. 6 Intellectual Property. Except as expressly provided herein, no right, title or interest in and to the Data is granted to the Receiving Party or implied hereunder. The Receiving Party 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. 7 Publication a. Disclosing Party intends to publish the results of its analysis of the Data and do not consider its deposition into public databases to be the equivalent of such publications. Disclosing Party anticipate that the Data could be useful to other qualified researchers for research on epilepsy. However, work on epilepsy is subject to a publication moratorium. b. The publication moratorium covers any publications (including oral communications) that describe the use of the Data. For research papers, submission for publication should not occur until 12 months after the signature of this Agreement, unless Disclosing Party has provided written consent to earlier submission. c. Subject to section 7(b), receiving Party shall have the right to use a) the analyzed, de-identified data derived from the use of the Data; and b) information and results arising out of analysis of the Data, as part of a publication or presentation of the results of the Study. Disclosing Party's investigator's contribution to the Study shall be acknowledged appropriately in any such publication or presentation in accordance with academic standards. d. In any publications based on Data, Receiving Party shall describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (EGAS00001002825). 8 Indemnification a. Each Party assumes its/his/her own liability for any costs, damages, suits or claims (Claim) to the extent that such Claim arise out of its/his/her activities in the course of this Agreement or the activities of those for whom in law it/he/she is responsible; 9 Term and Termination. a. The term of this Agreement will commence on the Effective Date of this Agreement and shall, unless sooner terminated in accordance with this Agreement, continue in full force and effect until the end of the Study, unless otherwise extended, renewed, or amended by mutual written consent or unless terminated earlier in accordance with the provisions hereof. b. The Dislcosing Party reserves the right to terminate the Study and this Agreement at any time upon thirty (30) days written notice. . If this agreement terminates for any reason, the Receiving Party will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the Receiving Party from retaining these data for archival purpose in conformity with audit or legal requirements. c. Termination shall not relieve any Party of any obligation accrued prior thereto. d. Termination of this Agreement will not affect the validity of any provisions that are, expressly or by implication, to survive or to take effect after such termination. No termination hereunder shall constitute a waiver of any rights or causes of action that any Party may have based upon events occurring prior to the termination date. 10. Notices. Any notice, request, demand or communication required or permitted to be given or made hereunder shall be in writing and shall be well and sufficiently given or made if i) delivered in person during normal business hours on a business day and left with the addressee or a receptionist or other responsible employee at the relevant addresses or; ii) sent by email or either means of recorded electronic communication: Disclosing Institution : Centre Hospitalier de l'Université de Montréal (CHUM) Director of Research - CHUM, Scientific Director - CRCHUM CRCHUM - Pavilion R 900 St. Denis St., Suite R05.406 Montréal, Quebec H2X 0A9 Canada (With a copy to Receiving Investigator) Disclosing Investigator: Dr Patrick Cossette Centre Hospitalier de l'Université de Montréal (CHUM) CRCHUM - Pavilion R 900 St. Denis St., Suite R04-482 Montréal, Québec H2X 0A9 Canada Receiving Institution: (Address of Disclosing Institution) Receiving Investigator: [Name of Disclosing Investigator] [Address of Disclosing Investigator] 11. Independent Contractor The relationship between the Parties is that of independent contractors and nothing in this Agreement shall constitute an agency relationship, employment relationship, partnership or a joint-venture between the Parties or any two of them. No Party shall have the authority to act on behalf of any other Party or to bind another Party in any manner. 12. Waiver No failure or delay by other Parties in exercising any right or remedies shall operate as a waiver thereof nor shall any single or partial exercise or waiver of any right or remedy preclude its further exercise or the exercise of any other right or remedy. 13. Entire Agreement and Amendments This Agreement including any attachments contains the entire understanding among the Parties hereto and supersedes all previously executed negotiations and agreements relating to the subject matter, including any confidential disclosure agreements. In the event that there is a conflict between the terms of this Agreement and any attachments or appendices to this Agreement, the terms of this Agreement shall govern. This Agreement shall not be amended, modified, varied or supplemented except in writing signed by each of the Parties or their duly authorized representatives. 14. Severability Any provision hereof that is prohibited or unenforceable in any jurisdiction will, as to such jurisdiction, be ineffective to the extent of such prohibition or unenforceability without invalidating the remaining provisions hereof, and any such prohibition or unenforceability in any jurisdiction will not invalidate or render unenforceable such provision in any other jurisdiction and the Parties shall in good faith negotiate a substitute for any provision declared unenforceable, which shall most nearly approximate the intent of the Parties in entering into this Agreement. 15. Headings The headings herein are inserted for convenience of reference only and shall not be used in interpreting or construing this Agreement. 16. Assignment Neither Disclosing Investigator nor Disclosing Institution may assign or subcontract its obligations under this Agreement, in whole or in part, without the prior written consent of Receiving Investigator and Receiving Institution. 17. Execution This Agreement may be executed in any number of counterparts, each of which shall be deemed an original and all of which shall together be deemed to constitute one and the same Agreement. Each Party acknowledges that an original signature or a copy thereof, including a "portable document format" or PDF copy, or a signature generated by industry standard electronic signature software, which is transmitted by facsimile or by email shall constitute an original signature for purposes of this Agreement and shall have the same legal force and effect as the exchange of original signatures, and that in any proceeding arising under or relating to this Agreement, each Party hereby waives any right to raise any defense or waiver based upon execution of this Agreement by means of such electronic signatures or maintenance of the executed Agreement electronically. 18. Force Majeure No Party shall be responsible to another for any delay in the performance of, or failure to perform, this Agreement where such delay or failure is caused by circumstances beyond the reasonable control of the affected Party including, without limitation, causes including strikes, lockouts or any other labour disruptions, war, natural disaster, disease or epidemic, or acts of God. In the event of any such delay or failure in performance, the affected Party shall be granted an extension of time for performance that is equitable in light of the cause of the delay. 19. Governing Law This Agreement shall be governed by and interpreted in accordance with the laws of the Province of Quebec. The Parties hereby agree that any dispute arising out of or relating to this Agreement will be subject to the exclusive jurisdiction of the courts of Quebec. [Signature Page Follows] IN WITNESS WHEREOF, the Parties hereto have executed this Agreement as of the Effective Date. Centre Hospitalier de l'Université de Montréal (CHUM) ___________________________ Vincent Poitout Director of Research, CHUM Scientific Director, CRCHUM Date: ____________________ __________________________ Jocelyn Boucher Executive Vice President, Administrative Affaires - CHUM Date: ______________________ DISCLOSING INVESTIGATOR ___________________________ Dr Patrick Cossette Date: ______________________ RECEIVING INSTITUTION: Date: _______________________ RECEIVING INVESTIGATOR: _____________________________ Date: ________________________ Schedule A Data Bam files of whole genome sequencing of 198 individuals with epilepsy. Schedule B Protocol
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 |
---|---|---|
EGAS00001002825 | 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.