Clinical response to nivolumab in an INI1-deficient pediatric chordoma correlates with immunogenic recognition of brachyury
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Data is generated as part of the Personal Oncogenomics (POG) project. For more information, please see personalizedoncogenomics.org. All data is described in the following publication, which should be cited with any data use:


Files available
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Patient 1 and patient 2 single nucleotide variants and indels:
patient1_snvs.vcf
patient2_snvs.vcf
patient1_indels.vcf
patient2_indels.vcf

Patient 1 and patient 2 expression matrix:
POG_chordoma_gene_expression.tsv

Patient 1 and patient 2 DNA methylation:
patient1_DNA_methylation.tsv.gz
patient2_DNA_methulation.tsv.gz


File information
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Mutation Data:
Coordinates are on hg19
Mutations were called using Stelka v.1.0.6
Annotations are from SNPEff v.3.2 based on Ensembl v69.

Expression Data:
Coordinates are on hg38
Expression data was generated using RSEM v.1.3.0
Ensembl 85 gene models. 

DNA methylation Data:
Coordinates are on hg19
Fractional methylation was assessed using novo5mC (0.8.9d) (https://svn.bcgsc.ca/bitbucket/projects/EDCC/repos/opencemt/browse/WGBS/QC)


Please contact Laura Williamson at lwilliamson@bcgsc.ca with any questions or requests for additional data.


Terms and Conditions for Data Use
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By accessing and downloading the somatic data made available by the Personalized OncoGenomics (POG) program, the user agrees to following terms of use:

- These data are for research purposes only. If data may or will be used for any commercial or non-research purpose, please contact poginfo@bcgsc.ca prior to proceeding.
- These data will be treated as controlled datasets. It is the user’s responsibility to maintain these data as anonymized and secure.
- No attempt will be made to identify or contact individual participants from whom these data were derived.
- These data will not be redistributed without express written permission from the POG coordinating center (poginfo@bcgsc.ca).

Failure to comply with any of the terms specified here may result in disqualification of the recipient from receiving additional data. BC Cancer shall have the right to institute and prosecute any proceeding at law or in equity against the recipient for violating or threatening to violate the confidentiality requirements of these terms, the limitations on the use of the data provided, or both. Proceedings may be initiated against the violating party, legal representatives, and assigns, for a restraining injunction, compensatory and punitive damages, mandamus, and/or any other proceeding in law or equity, including obtaining the proceeds from any intellectual property or other rights that are derived in whole or in part from the breach of the confidentiality requirements or use limitations of these terms. In addition, the recipient acknowledges and agrees that a breach or threatened breach of the confidentiality requirements or use limitations of these terms may subject the recipient to legal action on the part of study participants, their families, or both.

Anyone is free to copy, display, and make derivative data sets with this data for research purposes.

The POG program and funders must be acknowledged when publishing or presenting work using or referencing the POG dataset accessed here. The following sample text has been provided:

“This work would not be possible without the participation of our patients and families, the POG team, and the generous support of the BC Cancer Foundation and Genome British Columbia (project B20POG). We also acknowledge contributions towards equipment and infrastructure from Genome Canada and Genome BC (projects 202SEQ, 212SEQ, 12002), Canada Foundation for Innovation (projects 20070, 30981, 30198, 33408) and the BC Knowledge Development Fund. The results published here are in part based upon data generated by the following projects and obtained from dbGaP (http://www.ncbi.nlm.nih.gov/gap): The Cancer Genome Atlas managed by the NCI and NHGRI (http://cancergenome.nih.gov); Genotype-Tissue Expression (GTEx) Project, supported by the Common Fund of the Office of the Director of the National Institutes of Health (https://commonfund.nih.gov/GTEx). All data were generated and are maintained by the BC Cancer Genome Sciences Centre, a part of the Provincial Health Services Authority."