Xiaotu et al., Pan-cancer genome and transcriptome analyses of 1,699 pediatric leukemia’s and solid tumors, Nature 2018

[rmadupuri]

Please keep this checklist for curation of a new study.

• create a issue on datahub before curating a study (one issue per study) and copy this checklist to the issue tracker
• List information of the dataset/paper in the issue, e.g. pmid, paper link, suppl file link
• Document the curation process, e.g. how and by whom the data was transformed
• Follow the data checklist
• Create a pull request to datahub once the data is curated
• Push to triage portal
• Import into msk and public portal database
• Update cBioPortal news

[rmadupuri]

PMID: 29489755

• Does study name and study ID follow our convention? e.g. Tumor_Type (Institue, Journal Year); brca_mskcc_2015
• Is study meta data complete? e.g. pmid, group of PUBLIC
• Were all samples profiled with WES/WGS? If not, is gene panel file curated?
• Are oncotree codes of all samples curated; Cancer Type and Cancer Type Detailed needs to be added in addition to Oncotree Code
• Clinical sample and patient data with meta files
• Mutations data with meta files
• MAF is based on hg19
• MAF with 2 isoforms: uniprot and mskcc
• CNA data with meta files
• CNA segment data with meta files
• Expression data including z-scores with meta files
• Case-lists for all profiles
• Passes Validation
• Manual checking (Niki or JJ): Triage Portal

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.