PKD1 capture-by-hybridization resequencing for genetic diagnostics of polycystic kidney disease
We established and validated a sequence capture based NGS testing approach for PKD1. The presence of six PKD1 pseudogenes and tremendous allelic heterogeneity make molecular genetic testing of PKD1 variants challenging. In the publication accompaying this dataset (An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease, Eisenberger et.al., PLoS one), we demonstrate that the applied standard mapping algorithm specifically aligns reads to the PKD1 locus and overcomes the complication of unspecific capture of pseudogenes. This dataset contains the raw PKD1 reads of all patients from the publication.
- 27/05/2015
- 55 samples
- DAC: EGAC00001000271
- Technology: Illumina HiSeq 1500
Bioscientia Human Genetics Data Access Agreement for the ADPKD Sequencing Project
Bioscientia Molecular Genetics DACHuman genetic data access agreementBetween:(1) Bioscientia, Center for Human Genetics, Konrad Adenauer-Str. 17, 55218 Ingelheim, Germany(2) [INSERT INSTITUTION DETAILS] (the “Recipient”).This agreement governs the terms on which access will be granted to the genotype data generated by the Bioscientia Center for Human Genetics. In signing this agreement the recipient agrees to be bound by the terms and conditions of access set out in this agreement. For the sake of clarity, the terms of access set out in this agreement apply both to the User and the User’s Institution (as defined below). In response to the Recipient's request for access to the Data (as defined below), Bioscientia Center for Human Genetics and the Recipient agree as follows:1 Definitions1.1 “ADPKD sequencing project” (“ADPKD-SP”) shall mean the project undertakenat the Bioscientia Center for Human Genetics to identify genetic sequencevariants and mutations relevant to the development of autosomal dominant polycystic kidney disease.1.2 “Data” shall mean all and any human genetic data obtained from theADPKD-SP. Explicitly, Data does not include samples or biological materials;1.3 “Data Subject” shall mean the person (irrespective of state of health) towhom Data refers and who has been informed of the purpose for which the Data is held and has given his/her informed consent thereto;1.4 “Intellectual Property” means (i) patents, designs, trade marks and tradenames (whether registered or unregistered), copyright and related rights,database rights, know-how and confidential information; (ii) all other intellectualproperty rights and similar or equivalent rights anywhere in the world whichcurrently exist or are recognised in the future; and (iii) applications, extensionsand renewals in relation to any such rights;1.5 “Registered User” shall mean a Researcher (or an individual conductingResearch under the supervision of a Researcher) that is employed by theRecipient and is bound by confidentiality and non-use obligations in respect ofData and who has signed this Agreement and has received acknowledgementof its acceptance. For the avoidance of doubt, “Registered User” may alsoinclude students, visiting academics, contractors, sub-contractors or independent consultants provided that any such individual is bound by confidentiality and nonuse obligations no less onerous then those binding the Recipient’s employees;1.6 “Research” shall mean research that is seeking to advance theunderstanding and treatment of ADPKD and closely related diseases, and work on statistical methods that may be applied to such research;1.7 Publications means, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research.1.8 User Institution means the organisation at which the User is employed, affiliated or enrolled.2 PurposeThe Recipient agrees to use Data only for the Research. The Recipient agrees to use the Data only for the advancement of medical research, according to the consent obtained from sample donors. The Recipient agrees to use the data for the approved purpose and project described in your application; use of the data for a new purpose or project will require a new application and approval. 3 ConfidentialityThe Recipient agrees to preserve, at all times, the confidentiality of Datapertaining to identifiable Data Subjects. In particular, the Recipient undertakesnot to use, or attempt to use the Data to deliberately compromise or otherwiseinfringe the confidentiality of information on Data Subjects and their right toprivacy.4 Data Protection4.1 The Recipient agrees that it, and its Registered Users, are covered byand shall comply with the obligations contained in the German Data Protection laws as amended from time to time, or equivalent national provisions no less onerous than those contained in the German Data Protection law. In particular, the Recipient and its Registered Users understand their duties under such legislation in relation to the handling of Data and the rights of Data Subjects.4.2 The Recipient agrees that it, and its Registered Users, shall not analyseor make any use of the Data in such a way that has the potential to:(a) lead to the identification of any Data Subject; or(b) compromise the anonymity of any Data Subject in any way.5 Access and Governance5.1 The Recipient agrees that it shall take all reasonable security precautionsto keep the Data confidential, such precautions to be no less onerous than those applied in respect of the Recipient’s own confidential information.5.2 The Recipient agrees not to transfer or disclose the Data, in whole or part, or any identifiable material derived from the Data, to others, except as necessary for data/safety monitoring or programme management. Should the recipient wish to share the Data with a collaborator outwith the same Institution, the third party must make a separate application for access to the Data. 5.3 The Recipient agrees that it shall only give Registered Users that are notResearchers (including but not limited to students or new researchers to the field) access to the Data if they are supervised by a Researcher who will takeresponsibility for such Registered Users’ use of the Data.5.4 ADPKD-SP reserves the right to request and inspect data security andmanagement documentation to ensure the adequacy of data protectionmeasures in countries that have no national laws comparable to that pertainingin the European Economic Area (EEA).6 ErrorsThe Recipient agrees to notify the ADPKD-SP of any errors detected in the Data.7 Data reissueThe Recipient accepts that Data will be reissued from time to time, withsuitable versioning. If Data is reissued at the request of sample donors and/or asthe result of other ethical scrutiny, the Recipient agrees to destroy all earlierversions of the Data.8 Intellectual Property8.1 The Recipient recognises that nothing in this Agreement shall operate totransfer to the Recipient or its Registered Users any Intellectual Property rights inor relating to the Data.8.2 The Recipient and its Registered Users shall have the right to developIntellectual Property based on comparisons with their own data.9 PublicationsThe Recipient agrees to acknowledge in any work based in whole or parton the Data, the published paper from which the Data derives, the version of theData, and the role of the ADPKD-SP and its funders in its distribution. The Recipientagrees to use the acknowledgement wording provided for the relevant Data in itspublication. The Recipient will also declare in any such work that those whocarried out the original analysis and collection of the Data bear no responsibilityfor the further analysis or interpretation of it by the Recipient.10 Termination of Agreement10.1 This Agreement will terminate immediately upon any breach of theprovisions of this Agreement by the Recipient or by the Recipient’s RegisteredUsers.10.2 The Recipient accepts that the changing ethical framework of humangenetic research may lead to: (i) alteration to the provisions of this Agreement, in which case the Recipient may accept such alterations or terminate thisAgreement; or (ii) the withdrawal of this Agreement in extreme circumstances.10.3 Either party shall have the right to terminate this Agreement withimmediate effect upon giving written notice of termination to the other party.10.4 In the event that this Agreement is terminated in accordance with thisClause 10 the Recipient shall return or destroy all Data at the direction of ADPKD-SP.11 CostsThe Recipient acknowledges that ADPKD-SP shall incur costs in providing theData to the Recipient, including but not limited to administrative costs and thecost of obtaining appropriate data storage devices. The Recipient agrees to pay,on the request of ADPKD-SP, such reasonable costs as ADPKD-SP may incur in providing the Data, within thirty (30) days of ADPKD-SP making such a request for payment.12 Legal statement12.1 The Recipient acknowledges that ADPKD-SP and all other parties involved inthe creation, funding or protection of the Data:(a) make no warranty or representation, express or implied asto the accuracy, quality or comprehensiveness of the Data; and(b) exclude to the fullest extent permitted by law all liability foractions, claims, proceedings, demands, losses (including but not limited toloss of profit), costs, awards damages and payments made by theRecipient that may arise (whether directly or indirectly) in any waywhatsoever from the Recipient’s use of the Data, or from the unavailabilityof, or break in access to the Data for whatever reason.12.2 The Recipient understands that all the Data is protected by copyright andother intellectual property rights, such that duplication or sale of all of or part ofthe Data on any media is not permitted under any circumstances, except with the prior written consent of ADPKD-SP.13 Governing LawThis Agreement (and any dispute, controversy, proceedings or claim ofwhatever nature arising out of this Agreement or its formation) shall beconstrued, interpreted and governed by the laws of Germany and shallbe subject to the exclusive jurisdiction of the German courts. Place of jurisdiction shall be Mainz, Germany.AGREED by the parties through their authorised signatoriesBioscientia ADPDK-SPAuthorisedSignature:Name: Carsten BergmannTitle: Prof.Date:Recipient:Recipient Name:Address:Telephone No:Email:AuthorisedSignature:Name:Title:Date:Registered Users:The Registered Users acknowledge the contents of this Agreement and agree to comply with the obligations herein. For the avoidance of doubt the Registered Users are not a party to this Agreement.Signature:Name:Title:Date:Email:Signature:Name:Title:Date:Email:Please send completed forms to:Bioscientia complies with the requirements of the German Data Protection laws with regard to the collection, storage, processing and disclosure of personal information and is committed to upholding the core Data Protection Principles.Information collected under the Agreement will be used for the purposes of maintaining the Agreement.
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 |
|---|---|---|
| EGAS00001001003 | 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 | |
|---|---|---|---|---|
| EGAF00000690874 | fastq.gz | 83.2 MB | ||
| EGAF00000690875 | fastq.gz | 87.2 MB | ||
| EGAF00000690876 | fastq.gz | 47.3 MB | ||
| EGAF00000690877 | fastq.gz | 49.4 MB | ||
| EGAF00000690878 | fastq.gz | 51.0 MB | ||
| EGAF00000690879 | fastq.gz | 53.6 MB | ||
| EGAF00000690880 | fastq.gz | 73.2 MB | ||
| EGAF00000690881 | fastq.gz | 78.2 MB | ||
| EGAF00000690882 | fastq.gz | 141.8 MB | ||
| EGAF00000690883 | fastq.gz | 151.2 MB | ||
| EGAF00000690884 | fastq.gz | 162.1 MB | ||
| EGAF00000690885 | fastq.gz | 169.7 MB | ||
| EGAF00000690886 | fastq.gz | 196.4 MB | ||
| EGAF00000690887 | fastq.gz | 205.7 MB | ||
| EGAF00000690888 | fastq.gz | 155.2 MB | ||
| EGAF00000690889 | fastq.gz | 163.5 MB | ||
| EGAF00000690890 | fastq.gz | 178.8 MB | ||
| EGAF00000690891 | fastq.gz | 186.9 MB | ||
| EGAF00000690892 | fastq.gz | 131.7 MB | ||
| EGAF00000690893 | fastq.gz | 137.2 MB | ||
| EGAF00000690894 | fastq.gz | 203.0 MB | ||
| EGAF00000690895 | fastq.gz | 214.5 MB | ||
| EGAF00000690896 | fastq.gz | 110.3 MB | ||
| EGAF00000690897 | fastq.gz | 116.3 MB | ||
| EGAF00000690898 | fastq.gz | 150.5 MB | ||
| EGAF00000690899 | fastq.gz | 159.3 MB | ||
| EGAF00000690900 | fastq.gz | 142.2 MB | ||
| EGAF00000690901 | fastq.gz | 151.2 MB | ||
| EGAF00000690902 | fastq.gz | 159.1 MB | ||
| EGAF00000690903 | fastq.gz | 167.6 MB | ||
| EGAF00000690904 | fastq.gz | 209.3 MB | ||
| EGAF00000690905 | fastq.gz | 219.2 MB | ||
| EGAF00000690906 | fastq.gz | 146.8 MB | ||
| EGAF00000690907 | fastq.gz | 156.5 MB | ||
| EGAF00000690908 | fastq.gz | 131.5 MB | ||
| EGAF00000690909 | fastq.gz | 140.5 MB | ||
| EGAF00000690910 | fastq.gz | 183.8 MB | ||
| EGAF00000690911 | fastq.gz | 193.0 MB | ||
| EGAF00000690912 | fastq.gz | 100.5 MB | ||
| EGAF00000690913 | fastq.gz | 105.6 MB | ||
| EGAF00000690914 | fastq.gz | 142.2 MB | ||
| EGAF00000690915 | fastq.gz | 151.4 MB | ||
| EGAF00000690916 | fastq.gz | 163.1 MB | ||
| EGAF00000690917 | fastq.gz | 174.0 MB | ||
| EGAF00000690918 | fastq.gz | 161.7 MB | ||
| EGAF00000690919 | fastq.gz | 171.3 MB | ||
| EGAF00000690920 | fastq.gz | 191.7 MB | ||
| EGAF00000690921 | fastq.gz | 202.2 MB | ||
| EGAF00000691000 | fastq.gz | 90.3 MB | ||
| EGAF00000691001 | fastq.gz | 96.5 MB | ||
| EGAF00000691002 | fastq.gz | 113.5 MB | ||
| EGAF00000691003 | fastq.gz | 120.8 MB | ||
| EGAF00000691004 | fastq.gz | 171.9 MB | ||
| EGAF00000691005 | fastq.gz | 180.8 MB | ||
| EGAF00000691006 | fastq.gz | 164.6 MB | ||
| EGAF00000691007 | fastq.gz | 173.1 MB | ||
| EGAF00000691008 | fastq.gz | 137.3 MB | ||
| EGAF00000691009 | fastq.gz | 144.7 MB | ||
| EGAF00000691049 | fastq.gz | 43.1 MB | ||
| EGAF00000691050 | fastq.gz | 45.9 MB | ||
| EGAF00000691051 | fastq.gz | 55.4 MB | ||
| EGAF00000691052 | fastq.gz | 58.5 MB | ||
| EGAF00000691053 | fastq.gz | 42.0 MB | ||
| EGAF00000691054 | fastq.gz | 43.8 MB | ||
| EGAF00000691055 | fastq.gz | 56.7 MB | ||
| EGAF00000691056 | fastq.gz | 59.7 MB | ||
| EGAF00000691057 | fastq.gz | 71.2 MB | ||
| EGAF00000691058 | fastq.gz | 77.1 MB | ||
| EGAF00000691059 | fastq.gz | 186.7 MB | ||
| EGAF00000691060 | fastq.gz | 193.6 MB | ||
| EGAF00000691061 | fastq.gz | 112.5 MB | ||
| EGAF00000691062 | fastq.gz | 117.8 MB | ||
| EGAF00000691063 | fastq.gz | 152.7 MB | ||
| EGAF00000691064 | fastq.gz | 160.3 MB | ||
| EGAF00000691065 | fastq.gz | 204.8 MB | ||
| EGAF00000691066 | fastq.gz | 217.4 MB | ||
| EGAF00000691067 | fastq.gz | 164.2 MB | ||
| EGAF00000691068 | fastq.gz | 174.1 MB | ||
| EGAF00000691069 | fastq.gz | 168.6 MB | ||
| EGAF00000691070 | fastq.gz | 177.9 MB | ||
| EGAF00000691071 | fastq.gz | 141.6 MB | ||
| EGAF00000691072 | fastq.gz | 149.5 MB | ||
| EGAF00000691073 | fastq.gz | 168.5 MB | ||
| EGAF00000691074 | fastq.gz | 176.6 MB | ||
| EGAF00000691075 | fastq.gz | 65.7 MB | ||
| EGAF00000691076 | fastq.gz | 70.1 MB | ||
| EGAF00000691077 | fastq.gz | 136.2 MB | ||
| EGAF00000691078 | fastq.gz | 143.3 MB | ||
| EGAF00000691079 | fastq.gz | 120.9 MB | ||
| EGAF00000691080 | fastq.gz | 126.2 MB | ||
| EGAF00000691081 | fastq.gz | 146.5 MB | ||
| EGAF00000691082 | fastq.gz | 154.2 MB | ||
| EGAF00000691083 | fastq.gz | 115.3 MB | ||
| EGAF00000691084 | fastq.gz | 123.4 MB | ||
| EGAF00000691085 | fastq.gz | 129.9 MB | ||
| EGAF00000691086 | fastq.gz | 136.2 MB | ||
| EGAF00000691087 | fastq.gz | 76.6 MB | ||
| EGAF00000691088 | fastq.gz | 82.4 MB | ||
| EGAF00000691089 | fastq.gz | 129.9 MB | ||
| EGAF00000691090 | fastq.gz | 137.6 MB | ||
| EGAF00000691091 | fastq.gz | 223.0 MB | ||
| EGAF00000691092 | fastq.gz | 235.3 MB | ||
| EGAF00000691093 | fastq.gz | 178.4 MB | ||
| EGAF00000691094 | fastq.gz | 187.7 MB | ||
| EGAF00000691095 | fastq.gz | 56.2 MB | ||
| EGAF00000691096 | fastq.gz | 59.5 MB | ||
| EGAF00000691097 | fastq.gz | 137.2 MB | ||
| EGAF00000691098 | fastq.gz | 145.6 MB | ||
| EGAF00000691099 | fastq.gz | 191.5 MB | ||
| EGAF00000691100 | fastq.gz | 201.2 MB | ||
| 110 Files (15.1 GB) | ||||