Need Help?

Benchmarking dataset for ProSolo, a probabilistic single nucleotide caller for single cell DNA sequencing data

This is the dataset used in the benchmarking of ProSolo, a new probabilistic single nucleotide variant caller for single cell DNA sequencing data that provides control over the false discovery rate of different single cell events at genomic sites (e.g. alternative allele presence or allele dropout). It provides the whole exome sequencing data used in assessing ProSolo's performance that is not available elsewhere, namely bulk whole exome sequencing data of a patient with a constitutional mismatch repair defect (MSH6-) and their parents and siblings, a bulk whole exome sample of granulocytes from that patient and 5 single granulocytes whole exome sequenced after whole genome amplification.

Request Access

Data Access Policy for the data used in the benchmarking of ProSolo

DATA ACCESS AGREEMENT This agreement governs the terms on which access will be granted through the Data Access Committee (DAC) to ProSolo benchmarking data available in the European Genome-phenome Archive (EGA) by the European Bioinformatics Institute, the UK Outstation of the European Molecular Biology Laboratory for and mandated by the ProSolo benchmarking DAC of the Clinic of Pediatric Oncology, Hematology and Immunology, University Hospital Duesseldorf, Germany. In signing this agreement, you are agreeing 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). User institution and user are referred to within the agreement as “You” and “Your” shall be construed accordingly. Definitions: ProSolo benchmarking DAC means the Data Access Committee appointed by the Clinic of Pediatric Oncology, Hematology and Immunology (University Hospital Duesseldorf, Germany) to manage access to all data submitted to the EGA for the benchmarking publication of the software ProSolo. EGA means the European Genome-phenome Archive, a permanent archive of controlled access data generated for biomedical research and deposited to enable data sharing. The EGA is described on the website Data means all and any human genetic or phenotype data obtained from the EGA. Data Subject means a person, who has been informed of the purpose for which the data is held and has given his/her informed consent thereto. User means a researcher whose user institution has previously completed this Data Access Agreement and has received acknowledgement of its acceptance. Publications means, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. User Institution means the organisation at which the user is employed, affiliated or enrolled. Terms and Conditions: In signing this agreement: 1. You agree to use the data only for the advancement of medical research, according to the consent obtained from sample donors. 2. You agree to preserve, at all times, the confidentiality of information and data pertaining to data subjects. In particular, you undertake not to use, or attempt to use the data to compromise or otherwise infringe the confidentiality of information on data subjects and their right to privacy. 3. You agree not to attempt to link the data provided under this agreement to other information or archive data available for the data sets provided, even if access to that data has been formally granted to you, or it is freely available without restriction, without specific permission being sought from the relevant access committees. 4. You agree 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 you 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. You agree 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. 6. You accept that data will be updated from time to time, with suitable versioning. If the reissue is at the request of sample donors and/or other ethical scrutiny, you will destroy earlier versions of the Data. 7. You accept that the ProSolo benchmarking DAC, the Clinic of Pediatric Oncology, Hematology and Immunology (University Hospital Duesseldorf, Germany) or the funders of the data or any part of the data supplied: a) bear no legal responsibility for the accuracy or comprehensiveness of the data; and b) accept no liability for indirect, consequential, or incidental, damages or losses arising from use of the data, or from the unavailability of, or break in access to, the data for whatever reason. 8. You understand and acknowledge that the data may be protected by copyright and other intellectual property rights, and that duplication, except as reasonably required to carry out your research with the data, or sale of all or part of the data on any media may not be permitted. Users of the data are solely responsible for establishing the nature of and complying with any such intellectual property restrictions. 9. You recognise that nothing in this agreement shall operate to transfer to the user institution any intellectual property rights relating to the data. The user institution has the right to develop intellectual property based on comparisons with their own data. 10. You accept that this agreement will terminate immediately upon any breach of this agreement by you and you will be required to destroy any data held. 11. You accept that it may be necessary for the Clinic of Pediatric Oncology, Hematology and Immunology (University Hospital Duesseldorf, Germany) or its appointed agent to alter the terms of this agreement from time to time in order to address new concerns. In this event, the EGA or its appointed agent will contact you to inform you of any changes and you agree that your continued use of the data shall be dependent on the parties entering into a new version of the agreement. 12. You agree that you will submit a report to the ProSolo benchmarking DAC, if requested, on completion of the agreed purpose. The ProSolo benchmarking DAC agrees to treat the report and all information, data, results, and conclusions contained within such report as confidential information belonging to the User Institution. 13. You accept that the data may be protected by and subject to international laws, including but not limited to applicable laws on the protection of personal data, and that you are responsible for ensuring compliance with any such applicable law. You undertake to implement or have implemented adequate technical and organisational security measures to protect data. The ProSolo benchmarking DAC reserves the right to request and inspect data security and management documentation to ensure the adequacy of data protection measures, particularly in countries that have no national laws comparable to those which pertain in the EEA. For and on behalf of User: Name of Applicant(s): _____________________________________ _____________________________________ _____________________________________ _____________________________________ Signature of Applicant(s): _____________________________________ _____________________________________ _____________________________________ _____________________________________ Date: _____________________________________ For and on behalf of User Institution: Signature of Institutional or Administrative Authority: ______________________________________ Print name: ______________________________________ User Institution: ______________________________________ Date: ¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬______________________________________ WHEN SUBMITTING THIS DOCUMENT, PLEASE INCLUDE ALL PAGES OF THE AGREEMENT WITH THIS SIGNATURE PAGE APPENDIX 1 Publications Policy Authors who use data from the project must cite the upcoming ProSolo benchmarking article. If the whole exome sequencing data of the family pedigree is used, they must also cite: Hoell, Jessica, Michael Gombert, S. Ginzel, S. Loth, Pablo Landgraf, V. Käfer, M. Streiter, et al. 2014. “Constitutional Mismatch Repair-deficiency and Whole-exome Sequencing as the Means of the Rapid Detection of the Causative MSH6 Defect.” Klinische Pädiatrie 226 (06/07): 357–61.

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
EGAS00001004123 Other
ID File Type Size Located in
EGAF00003296478 fastq.gz 5.5 GB
EGAF00003296479 fastq.gz 5.6 GB
EGAF00003296480 fastq.gz 4.2 GB
EGAF00003296481 fastq.gz 4.2 GB
EGAF00003296482 fastq.gz 5.3 GB
EGAF00003296483 fastq.gz 5.4 GB
EGAF00003296484 fastq.gz 5.4 GB
EGAF00003296485 fastq.gz 5.5 GB
EGAF00003296486 fastq.gz 5.6 GB
EGAF00003296487 fastq.gz 5.7 GB
EGAF00003296488 fastq.gz 7.1 GB
EGAF00003296489 fastq.gz 7.1 GB
EGAF00003296490 fastq.gz 6.5 GB
EGAF00003296491 fastq.gz 6.4 GB
EGAF00003296492 fastq.gz 6.5 GB
EGAF00003296493 fastq.gz 6.4 GB
EGAF00003296494 fastq.gz 5.6 GB
EGAF00003296495 fastq.gz 5.6 GB
EGAF00003296496 fastq.gz 6.7 GB
EGAF00003296497 fastq.gz 6.6 GB
EGAF00003296498 fastq.gz 5.6 GB
EGAF00003296499 fastq.gz 5.5 GB
EGAF00003296500 fastq.gz 6.1 GB
EGAF00003296501 fastq.gz 6.1 GB
24 Files (139.9 GB)