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Genomic Data of Pediatric MDS

The dataset consists of - 126 whole exome sequencings (SAMD9/9Lmut: 64; GATA2mut 24, MDS wildtype 38/471) performed using SureSelect Human All Exon V6 enrichment (Agilent, cat# 5190-8863). The generated libraries were sequenced on the Illumina Hiseq 2500 with 150bp paired-end reads. FASTQ files were processed using SeqNext platform (JSI medical system, Germany), with gene-based alignment to a virtual panel of 300 genes (including 28 MDS-associated genes, SAMD9, and SAMD9L), consisting of genes relevant to bone marrow failure, MDS predisposition, and hematological cancers as per the Pan-Cancer studies with cohorts of >10,000 cancers. The respective BAM files are provided. - Custom panel targeting SAMD9, SAMD9L, and 22 single nucleotide polymorphisms (SNP) on chromosome 7q (allele frequency >35% in all ethnic sub-populations in gnomAD) (Ampliseq #IAD104171) were performed in 666/669 cases. And Custom panel targeting 28 MDS-associated genes (GATA2, RUNX1, HOXA9, CEBPA, GATA1, KRAS, NRAS, CBL, PTPN11, ASXL1, EZH2, SETBP1, FLT3, KIT, JAK2, JAK3, CSF3R, MPL, SH2, BCOR, BCORL1; RAD21, STAG2, CTCF, TP53, PTEN, CALR, VPS45) was performed in 544 cases (Ampliseq #IAD51150). Both custom panel libraries were prepared using NEBNext Ultra II DNA library prep kit (New England BioLabs, cat#E7645S/L) per manufacturer’s instruction and samples were sequenced on an Illumina Miseq 2000 with 2 x 150 bp reads. The respective BAM files are provided - 4 SAMD9/9L patients were subjected to MissionBio custom single-cell panel (CO-112) targeting 250 heterozygous gnomAD population polymorphisms on 7q arm and 69 amplicons in SAMD9/9L and other cancer genes. All libraries were sequenced on an Illumina NovaSeq6000 with 150 base-paired ending multiplexed runs. Fastq files were processed using the Tapestri Pipeline V2 and python-based Mosaic package (multi-omics analysis, data visualization). The derived BAM and loom files are provided.

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Data Submission for The Genetic Landscape of SAMD9/9L Syndromes in Pediatric MDS

DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom DAC for Genomics of MDS Freiburg Germany grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: University Children’s Hospital Freiburg Germany and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. The User Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. The User Institution 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. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (http://www.oecd.org/science/biotech/36198812.pdf ). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify DAC for Genomics of MDS Freiburg Germany within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify DAC for Genomics of MDS Freiburg Germany prior to any significant changes to the protocol for the Project. 14. The User Institution will notify DAC for Genomics of MDS Freiburg Germany as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. DAC for Genomics of MDS Freiburg Germany may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than University Children’s Hospital Freiburg Germany. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of Germany and shall be subject to the exclusive jurisdiction of the German courts.

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
EGAS00001005431 Other
EGAS00001005432 Other
EGAS00001005433 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
EGAF00005335386 bam 4.1 MB
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EGAF00005335388 bam 19.2 MB
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EGAF00005335391 bam 7.1 MB
EGAF00005337000 bam 22.5 MB
EGAF00005337001 bam 56.7 MB
EGAF00005337002 bam 51.3 MB
EGAF00005337003 bam 7.7 MB
EGAF00005337004 bam 23.6 MB
EGAF00005337005 bam 27.2 MB
EGAF00005337006 bam 20.4 MB
EGAF00005337007 bam 18.9 MB
EGAF00005337008 bam 21.7 MB
EGAF00005337009 bam 38.6 MB
EGAF00005337010 bam 33.7 MB
EGAF00005337011 bam 29.3 MB
EGAF00005337012 bam 11.3 MB
EGAF00005337013 bam 10.9 MB
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EGAF00005337015 bam 9.1 MB
EGAF00005337016 bam 17.6 MB
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EGAF00005337018 bam 10.5 MB
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EGAF00005337022 bam 41.3 MB
EGAF00005337023 bam 23.2 MB
EGAF00005337024 bam 20.0 MB
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EGAF00005337027 bam 24.3 MB
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EGAF00005337030 bam 12.0 MB
EGAF00005337031 bam 16.7 MB
EGAF00005337032 bam 25.8 MB
EGAF00005337033 bam 6.8 MB
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EGAF00005337035 bam 7.1 MB
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EGAF00005337038 bam 30.7 MB
EGAF00005337039 bam 18.5 MB
EGAF00005337040 bam 15.8 MB
EGAF00005337041 bam 13.6 MB
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EGAF00005337043 bam 13.3 MB
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EGAF00005337050 bam 11.5 MB
EGAF00005337051 bam 14.7 MB
EGAF00005337052 bam 13.1 MB
EGAF00005337053 bam 14.0 MB
EGAF00005337054 bam 8.1 MB
EGAF00005337055 bam 20.6 MB
EGAF00005337056 bam 18.9 MB
EGAF00005337057 bam 12.8 MB
EGAF00005337058 bam 19.1 MB
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EGAF00005337063 bam 21.0 MB
EGAF00005337064 bam 4.1 GB
EGAF00005337065 bam 6.8 GB
EGAF00005337066 bam 7.7 GB
EGAF00005337067 bam 17.7 MB
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EGAF00005337069 bam 14.5 MB
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EGAF00005337071 bam 3.9 MB
EGAF00005337072 bam 62.0 MB
EGAF00005337073 bam 42.7 MB
EGAF00005337074 bam 20.6 MB
EGAF00005337075 bam 25.2 MB
EGAF00005337076 bam 2.4 MB
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EGAF00005337078 bam 1.5 MB
EGAF00005337079 bam 8.0 MB
EGAF00005337080 bam 3.7 MB
EGAF00005337081 bam 2.4 MB
EGAF00005337082 bam 852.5 kB
EGAF00005337083 bam 7.3 MB
EGAF00005337084 bam 25.0 MB
EGAF00005337085 bam 4.8 MB
EGAF00005337086 bam 14.3 MB
EGAF00005337087 bam 36.8 MB
EGAF00005337088 bam 1.7 MB
EGAF00005337089 bam 142.3 MB
EGAF00005337090 bam 17.4 MB
EGAF00005337091 bam 27.2 MB
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EGAF00005337098 bam 11.9 MB
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EGAF00005337102 bam 19.2 MB
EGAF00005337103 bam 26.1 MB
EGAF00005337104 bam 1.1 MB
EGAF00005337105 bam 18.3 MB
EGAF00005337106 bam 13.8 MB
EGAF00005337107 bam 12.6 MB
EGAF00005337108 bam 1.5 MB
EGAF00005337109 bam 1.3 MB
EGAF00005337110 bam 30.3 MB
EGAF00005337111 bam 2.4 MB
EGAF00005337112 bam 2.3 MB
EGAF00005337113 bam 1.5 MB
EGAF00005337114 bam 26.8 MB
EGAF00005337115 bam 12.5 MB
EGAF00005337116 bam 7.1 MB
EGAF00005337117 bam 21.7 MB
EGAF00005337118 bam 27.0 MB
EGAF00005337119 bam 31.5 MB
EGAF00005337120 bam 15.0 MB
EGAF00005337121 bam 1.8 MB
EGAF00005337122 bam 1.1 MB
EGAF00005337123 bam 3.4 MB
EGAF00005337124 bam 20.4 MB
EGAF00005337125 bam 14.4 MB
EGAF00005337126 bam 18.4 MB
EGAF00005337127 bam 9.6 MB
EGAF00005337128 bam 10.7 MB
EGAF00005337129 bam 14.8 MB
EGAF00005337130 bam 14.0 MB
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EGAF00005337134 bam 21.6 MB
EGAF00005337135 bam 25.7 MB
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EGAF00005337138 bam 7.7 MB
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EGAF00005337145 bam 28.6 MB
EGAF00005337146 bam 18.3 MB
EGAF00005337147 bam 21.8 MB
EGAF00005337148 bam 17.1 MB
EGAF00005337149 bam 20.6 MB
EGAF00005337150 bam 19.6 MB
EGAF00005337151 bam 13.7 MB
EGAF00005337152 bam 9.2 MB
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EGAF00005337154 bam 28.2 MB
EGAF00005337155 bam 17.0 MB
EGAF00005337156 bam 24.6 MB
EGAF00005337157 bam 10.7 MB
EGAF00005337158 bam 8.7 MB
EGAF00005337159 bam 20.8 MB
EGAF00005337160 bam 19.2 MB
EGAF00005337161 bam 18.2 MB
EGAF00005337162 bam 17.2 MB
EGAF00005337163 bam 20.3 MB
EGAF00005337164 bam 12.8 MB
EGAF00005337165 bam 20.4 MB
EGAF00005337166 bam 14.9 MB
EGAF00005337167 bam 17.9 MB
EGAF00005337168 bam 2.7 MB
EGAF00005337169 bam 12.1 MB
EGAF00005337170 bam 16.2 MB
EGAF00005337171 bam 22.7 MB
EGAF00005337172 bam 19.9 MB
EGAF00005337173 bam 19.6 MB
EGAF00005337174 bam 181.0 kB
EGAF00005337175 bam 11.0 MB
EGAF00005337176 bam 487.8 kB
EGAF00005337177 bam 10.8 MB
EGAF00005337178 bam 26.0 MB
EGAF00005337179 bam 7.8 MB
EGAF00005337180 bam 7.5 MB
EGAF00005337181 bam 25.1 MB
EGAF00005337182 bam 16.2 MB
EGAF00005337183 bam 8.5 MB
EGAF00005337184 bam 15.7 MB
EGAF00005337185 bam 17.9 MB
EGAF00005337186 bam 18.4 MB
EGAF00005337187 bam 105.7 MB
EGAF00005337188 bam 25.4 MB
EGAF00005337189 bam 16.0 MB
EGAF00005337190 bam 26.0 MB
EGAF00005337191 bam 15.1 MB
EGAF00005337192 bam 24.8 MB
EGAF00005337193 bam 19.1 MB
EGAF00005337194 bam 19.1 MB
EGAF00005337195 bam 23.3 MB
EGAF00005337196 bam 17.7 MB
EGAF00005337197 bam 15.0 MB
EGAF00005337198 bam 20.8 MB
EGAF00005337199 bam 16.1 MB
EGAF00005337200 bam 1.4 MB
EGAF00005337201 bam 16.6 MB
EGAF00005337202 bam 20.6 MB
EGAF00005337203 bam 23.9 MB
EGAF00005337204 bam 12.7 MB
EGAF00005337205 bam 33.9 MB
EGAF00005337206 bam 17.6 MB
EGAF00005337207 bam 39.0 MB
EGAF00005337208 bam 14.3 MB
EGAF00005337209 bam 9.9 MB
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EGAF00005337211 bam 12.0 MB
EGAF00005337212 bam 18.1 MB
EGAF00005339788 bam 56.5 MB
EGAF00005339789 bam 56.4 MB
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EGAF00005339791 bam 31.9 MB
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EGAF00005339795 bam 22.8 MB
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EGAF00005339797 bam 63.3 MB
EGAF00005339798 bam 62.8 MB
EGAF00005339799 bam 67.5 MB
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EGAF00005339802 bam 72.4 MB
EGAF00005339803 bam 45.4 MB
EGAF00005339804 bam 71.0 MB
EGAF00005339805 bam 58.7 MB
EGAF00005339806 bam 65.4 MB
EGAF00005339809 bam 51.9 MB
EGAF00005339810 bam 59.9 MB
EGAF00005339811 bam 84.1 MB
EGAF00005339812 bam 64.3 MB
EGAF00005339813 bam 56.9 MB
EGAF00005339814 bam 65.0 MB
EGAF00005339815 bam 38.8 MB
EGAF00005339816 bam 73.9 MB
EGAF00005339817 bam 49.8 MB
EGAF00005339818 bam 62.9 MB
EGAF00005339820 bam 64.9 MB
EGAF00005339821 bam 55.9 MB
EGAF00005339822 bam 50.4 MB
EGAF00005339823 bam 57.9 MB
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EGAF00005339825 bam 62.3 MB
EGAF00005339826 bam 48.0 MB
EGAF00005339827 bam 65.1 MB
EGAF00005339828 bam 45.3 MB
EGAF00005339829 bam 67.7 MB
EGAF00005340491 bam 66.1 MB
EGAF00005340492 bam 54.4 MB
EGAF00005340493 bam 73.2 MB
EGAF00005340494 bam 72.1 MB
EGAF00005340495 bam 55.0 MB
EGAF00005340496 bam 56.7 MB
EGAF00005340497 bam 63.1 MB
EGAF00005340498 bam 66.2 MB
EGAF00005340499 bam 55.6 MB
EGAF00005340500 bam 69.8 MB
EGAF00005340501 bam 51.6 MB
EGAF00005340502 bam 77.5 MB
EGAF00005340503 bam 138.0 MB
EGAF00005340504 bam 75.7 MB
EGAF00005340505 bam 69.9 MB
EGAF00005340506 bam 88.2 MB
EGAF00005340507 bam 58.0 MB
EGAF00005340508 bam 76.2 MB
EGAF00005340509 bam 53.2 MB
EGAF00005341081 bam 72.8 MB
EGAF00005341082 bam 41.5 MB
EGAF00005341083 bam 58.0 MB
EGAF00005341084 bam 78.9 MB
EGAF00005341085 bam 47.9 MB
EGAF00005341086 bam 57.2 MB
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EGAF00005341088 bam 72.9 MB
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EGAF00005341091 bam 60.0 MB
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EGAF00005341093 bam 36.5 MB
EGAF00005341094 bam 74.8 MB
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EGAF00005341096 bam 40.6 MB
EGAF00005341097 bam 75.6 MB
EGAF00005341098 bam 70.1 MB
EGAF00005341099 bam 67.2 MB
EGAF00005341100 bam 51.6 MB
EGAF00005341101 bam 59.1 MB
EGAF00005341102 bam 67.4 MB
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EGAF00005341118 bam 54.2 MB
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EGAF00005341126 bam 61.5 MB
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EGAF00005341129 bam 55.1 MB
EGAF00005341130 bam 55.4 MB
EGAF00005341131 bam 54.3 MB
EGAF00005341132 bam 54.4 MB
EGAF00005341133 bam 66.8 MB
EGAF00005341134 bam 65.0 MB
EGAF00005341135 bam 57.0 MB
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EGAF00005341137 bam 60.6 MB
EGAF00005341138 bam 52.5 MB
EGAF00005341139 bam 59.3 MB
EGAF00005341140 bam 46.3 MB
EGAF00005341141 bam 71.9 MB
EGAF00005341142 bam 51.0 MB
EGAF00005341143 bam 71.2 MB
EGAF00005341144 bam 66.5 MB
EGAF00005341145 bam 52.1 MB
EGAF00005341146 bam 62.7 MB
EGAF00005341147 bam 3.5 MB
EGAF00005341148 bam 68.7 MB
EGAF00005341149 bam 1.8 MB
EGAF00005341150 bam 3.3 MB
EGAF00005341151 bam 10.5 MB
EGAF00005341152 bam 15.1 MB
EGAF00005341153 bam 5.2 MB
EGAF00005341154 bam 11.0 MB
EGAF00005341155 bam 13.4 MB
EGAF00005341156 bam 13.3 MB
EGAF00005341157 bam 57.7 MB
EGAF00005341158 bam 21.3 MB
EGAF00005341159 bam 7.8 MB
EGAF00005341160 bam 151.2 MB
EGAF00005341161 bam 34.0 MB
EGAF00005341162 bam 558.6 kB
EGAF00005341163 bam 24.5 MB
EGAF00005341164 bam 15.1 MB
EGAF00005341165 bam 9.1 MB
EGAF00005341166 bam 73.0 MB
EGAF00005341167 bam 31.8 MB
EGAF00005341168 bam 5.9 MB
EGAF00005341169 bam 16.2 MB
EGAF00005341170 bam 4.1 MB
EGAF00005341171 bam 30.5 MB
EGAF00005341172 bam 7.1 MB
EGAF00005341173 bam 8.4 MB
EGAF00005341174 bam 13.8 MB
EGAF00005341175 bam 15.2 MB
EGAF00005341176 bam 33.2 MB
EGAF00005341177 bam 9.9 MB
EGAF00005341178 bam 8.9 MB
EGAF00005341179 bam 9.2 MB
EGAF00005341180 bam 17.3 MB
EGAF00005341181 bam 22.5 MB
EGAF00005341182 bam 16.6 MB
EGAF00005341183 bam 15.1 MB
EGAF00005341184 bam 8.1 MB
EGAF00005341185 bam 10.5 MB
EGAF00005341186 bam 32.3 MB
EGAF00005341187 bam 28.0 MB
EGAF00005341188 bam 4.0 MB
EGAF00005341189 bam 8.5 MB
EGAF00005341190 bam 15.1 MB
EGAF00005341191 bam 19.9 MB
EGAF00005341192 bam 26.1 MB
EGAF00005341193 bam 4.3 MB
EGAF00005341194 bam 1.8 MB
EGAF00005341195 bam 28.1 MB
EGAF00005341196 bam 10.1 MB
EGAF00005341197 bam 5.4 MB
EGAF00005341198 bam 39.0 MB
EGAF00005341199 bam 7.4 MB
EGAF00005341200 bam 6.9 MB
EGAF00005341201 bam 26.9 MB
EGAF00005341202 bam 28.2 MB
EGAF00005341203 bam 8.3 MB
EGAF00005341204 bam 24.5 MB
EGAF00005341205 bam 17.0 MB
EGAF00005341206 bam 21.9 MB
EGAF00005341207 bam 25.5 MB
EGAF00005341208 bam 54.8 MB
EGAF00005341209 bam 7.9 MB
EGAF00005341210 bam 30.1 MB
EGAF00005341211 bam 9.5 MB
EGAF00005341212 bam 8.7 MB
EGAF00005341213 bam 14.9 MB
EGAF00005341214 bam 51.9 MB
EGAF00005341215 bam 50.5 MB
EGAF00005341216 bam 25.3 MB
EGAF00005341217 bam 21.2 MB
EGAF00005341218 bam 4.9 MB
EGAF00005341219 bam 1.5 MB
EGAF00005341220 bam 14.9 MB
EGAF00005341221 bam 5.2 MB
EGAF00005341222 bam 4.5 MB
EGAF00005341223 bam 18.4 MB
EGAF00005341224 bam 12.9 MB
EGAF00005341225 bam 6.2 MB
EGAF00005341226 bam 24.8 MB
EGAF00005341227 bam 14.5 MB
EGAF00005341228 bam 18.5 MB
EGAF00005341229 bam 6.1 MB
EGAF00005341230 bam 41.0 MB
EGAF00005341231 bam 6.5 MB
EGAF00005341232 bam 95.5 MB
EGAF00005341233 bam 6.8 MB
EGAF00005341234 bam 15.8 MB
EGAF00005341235 bam 3.2 MB
EGAF00005341236 bam 44.3 MB
EGAF00005341237 bam 12.1 MB
EGAF00005341238 bam 33.3 MB
EGAF00005341239 bam 12.5 MB
EGAF00005341240 bam 53.0 MB
437 Files (31.9 GB)