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59 CLPD-NK cases WGS & WTS data

For the cohort of 59 samples, we performed TruSeq DNA PCR-Free whole-genome sequencing library preparation according to manufacturer’s instructions (llumina, ILMN, San Diego, CA) on the automated NGS Star liquid handling platform (Hamilton, Bonaduz, Switzerland) followed by 2x150 bp paired-end sequencing on the HiSeqX or NovaSeq6000 (ILMN). An average coverage of >100x was achieved. For whole transcriptome analysis, the TruSeq Total Stranded RNA kit was used, starting with 250 ng of total RNA, to generate RNA libraries following the manufacturer’s recommendations (ILMN). 2x100bp paired-end reads were sequenced on the NovaSeq 6000 with a median of 50 mio. reads per sample (ILMN).

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MLL Munich Leukemia Laboratory Data Access Policy

MLL Munich Leukemia Laboratory Data Access Policy This policy describes how the Munich Leukemia Laboratory’s (MLL) Data Access Committee (DAC) will process requests for datasets stored in the European Genome-phenome Archive (EGA), when those datasets are made available by manuscripts that specifically reference this policy. Purpose 1. To ensure that applicants are qualified investigators, affiliated with an academic, non- profit, or government research organization. 2. To ensure that users of the data agree to comply with applicable laws, including requirements as outlined in any governing consent and appropriate ethical approvals, along with any restrictions for the data in question. General principles The DAC will consider applications for access to datasets stored in the EGA when authorized to do so in accordance with this policy. Access to de-identified and anonymized genomic sequence data will be granted to qualified researchers for appropriate use. A qualified researcher refers to a scientist who is employed, or legitimately affiliated with an academic, non-profit, or government research organization. The data will be deposited in the European Genome-Phenome Archive (EGA) and access will be by application to the MLL Data Access Committee (MLL DAC). Access to data will be granted to researchers for appropriate use and will be governed by the provisions in the associated informed consent for each cohort or collection, and the terms contained in the Data Access Agreement. The MLL DAC is concerned with access to de-identified anonymized genomic data generated by MLL, and associated phenotypic information published by MLL in reports of the analyses of each tumor subtype. The Committee will not consider requests for more detailed phenotypic information which is held by the principal investigators for the individual case collections. Access to this data should be by arrangement with the relevant principal investigator. Access is conditional upon availability of data and signed agreement by the researcher(s) and the responsible employing Institution to abide by policies related to publication, data disposal, ethical approval, confidentiality, and security. Application procedure Applicants requesting access to data from MLL will be asked to complete a basic application form and to agree to the terms and conditions laid out in the Data Access Agreement (DAA). Applications must be made by a Laboratory Head, Principal Investigator, or Departmental Chair. Both the applicant and an authorized representative of the applicant’s institution, e.g., the relevant Head of Department, Head of Institute, or equivalent, must sign the DAA. Successful applicants who have access to data will be designated "Registered Users" and will be issued a username and password by the EGA to enable access to the database. The MLL DAC will consider applications that include named collaborators, but each Institution must sign a separate Data Access Agreement. Should you wish to share the data with additional collaborators not previously approved, they must make a separate application for access to the Data. Applicants agree to use the data for the approved purpose and project described in the application; use of the data for a new purpose or project will require a new application and approval. Membership of Consortium Data Access Committee Prof. Dr. med. Dr. phil. Torsten Haferlach CEO MLL Munich Leukemia Laboratory and MHP Munich Hematology Practice; Head of the Cytomorphology Department, Munich Germany Prof. Dr. med. Claudia Haferlach Head of the Cytogenetics and Fluorescence In-situ Hybridization Department, MLL Munich Leukemia Laboratory, Munich, Germany Prof. Dr. med. Wolfgang Kern Head of the Immunophenotyping Department, MLL Munich Leukemia Laboratory, Munich Germany Dr. rer. nat. Manja Meggendorfer, MBA Head of Molecular genetics & Head of Research and development, MLL Munich Leukemia Laboratory, Munich Germany Assessment Criteria Each application will be assessed to determine if: • it has been submitted by a qualified researcher or researchers, embedded in a recognized research institution that can provide institutional responsibility for appropriate research governance • the project described constitutes “biomedical research” in the context of the consent process, and is likely to be understood as such by the sample donors • it does not breach any of the ethical permissions or restrictions in the consent forms for any component cohort or collection; • it does not have the potential to produce information that will enable identification of individual participants or other individually identifiable information The DAC will use these practices in its assessment: • The MLL DAC does NOT attempt to peer review the scientific quality of proposals. However, it does ask for a brief summary of the research to be undertaken, to judge whether it falls within the scope of the consents. It also considers whether the research is grossly inadequate or ethically questionable, and reserves the right to require clarification for those requests that do not appear to attain even a minimal standard of competence; • the use of data by commercial companies for commercial purposes is prohibited; and use of de-identified and anonymized data is permissible

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
EGAS00001006009 Other
ID File Type Size Located in
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EGAF00005797650 bam 139.4 GB
EGAF00005797651 bam 5.4 GB
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EGAF00005800335 bam 6.5 GB
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EGAF00005800337 bam 6.6 GB
EGAF00005800338 bam 143.5 GB
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EGAF00005800343 bam 164.3 GB
EGAF00005800344 bam 141.9 GB
EGAF00005800345 bam 161.6 GB
EGAF00005800346 bam 5.7 GB
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EGAF00005800352 bam 123.4 GB
EGAF00005800353 bam 126.7 GB
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EGAF00005800356 bam 97.5 GB
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EGAF00005800361 bam 147.3 GB
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EGAF00005800364 bam 152.8 GB
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EGAF00005800369 bam 120.1 GB
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EGAF00005800371 bam 4.7 GB
EGAF00005800372 bam 139.2 GB
EGAF00005800373 bam 122.9 GB
EGAF00005800374 bam 139.0 GB
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EGAF00005800377 bam 165.5 GB
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EGAF00005800394 bam 6.8 GB
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EGAF00005800396 bam 120.5 GB
EGAF00005800397 bam 7.2 GB
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EGAF00005800431 bai 8.7 MB
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EGAF00005800491 bai 7.3 MB
235 Files (8.7 TB)