OpenPedCan-analysis

release notes

current release

release-v15

Release date: 2024-03-01
Status: available
Overview of changes:
- This release fixes a bug in the TCGA and GTEX collapse script per issues #552 and #551.
- Files changed:
  - gtex_gene-counts-rsem-expected_count-collapsed.rds
  - gtex_gene-expression-rsem-tpm-collapsed.rds
  - tcga_gene-expression-rsem-tpm-collapsed.rds
- Files added:
  - tcga_gene-counts-rsem-expected_count-collapsed.rds

v15
├── 20038D-17Q6-01.regions.100bp_padded.bed
├── S0274956_Padded_HG38.merged.bed
├── S02972011_Covered_hg38_100.bed
├── S04380110_Regions_hg38_100.bed
├── S07604715_100bp_Padded.bed
├── SeqCap_EZ_Exome_v2_Padded_HG38.merged.bed
├── StrexomeLite_hg38_liftover_100bp_padded.bed
├── Strexome_targets_intersect_sorted_padded100.GRCh38.bed
├── TARGET_AML_NBL_WT_SeqVal79_attempt06_AllTracks_HG38_bed_expanded100.bed
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
├── WGS.hg38.vardict.100bp_padded.bed
├── agilent-v4-targets-ucsc.100bp_padded.bed
├── ashion_exome_v2_targets_hg38_padded100.bed
├── biospecimen_id_to_bed_map.tsv
├── cnv-cnvkit.seg.gz
├── cnv-consensus-gistic-only.seg.gz
├── cnv-consensus-gistic.zip
├── cnv-consensus.seg.gz
├── cnv-controlfreec-tumor-only.tsv.gz
├── cnv-controlfreec.tsv.gz
├── cnv-gatk.seg.gz
├── cnvkit_with_status.tsv
├── consensus_seg_with_status.tsv
├── consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_autosomes.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_x_and_y.tsv.gz
├── cptac-protein-imputed-phospho-expression-log2-ratio.tsv.gz
├── cptac-protein-imputed-prot-expression-abundance.tsv.gz
├── cptac-protein-imputed-prot-expression-log2-ratio.tsv.gz
├── efo-mondo-map.tsv
├── ensg-hugo-pmtl-mapping.tsv
├── fusion-annoFuse.tsv.gz
├── fusion-arriba.tsv.gz
├── fusion-dgd.tsv.gz
├── fusion-putative-oncogenic.tsv
├── fusion-starfusion.tsv.gz
├── fusion_summary_embryonal_foi.tsv
├── fusion_summary_ependymoma_foi.tsv
├── fusion_summary_ewings_foi.tsv
├── fusion_summary_lgg_hgg_foi.tsv
├── gbm-protein-imputed-phospho-expression-abundance.tsv.gz
├── gbm-protein-imputed-prot-expression-abundance.tsv.gz
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── gtex_gene-counts-rsem-expected_count-collapsed.rds
├── gtex_gene-expression-rsem-tpm-collapsed.rds
├── hg38_strelka.bed
├── histologies-base.tsv
├── histologies.tsv
├── hope-protein-imputed-phospho-expression-abundance.tsv.gz
├── hope-protein-imputed-prot-expression-abundance.tsv.gz
├── independent-specimens.methyl.primary-plus.eachcohort.tsv
├── independent-specimens.methyl.primary-plus.tsv
├── independent-specimens.methyl.primary.eachcohort.tsv
├── independent-specimens.methyl.primary.tsv
├── independent-specimens.methyl.relapse.eachcohort.tsv
├── independent-specimens.methyl.relapse.tsv
├── independent-specimens.rnaseq.primary-plus-pre-release.tsv
├── independent-specimens.rnaseq.primary-pre-release.tsv
├── independent-specimens.rnaseq.relapse-pre-release.tsv
├── independent-specimens.rnaseqpanel.primary-plus.eachcohort.tsv
├── independent-specimens.rnaseqpanel.primary-plus.tsv
├── independent-specimens.rnaseqpanel.primary.eachcohort.tsv
├── independent-specimens.rnaseqpanel.primary.tsv
├── independent-specimens.rnaseqpanel.relapse.eachcohort.tsv
├── independent-specimens.rnaseqpanel.relapse.tsv
├── independent-specimens.wgs.primary-plus.eachcohort.tsv
├── independent-specimens.wgs.primary-plus.tsv
├── independent-specimens.wgs.primary.eachcohort.tsv
├── independent-specimens.wgs.primary.tsv
├── independent-specimens.wgs.relapse.eachcohort.tsv
├── independent-specimens.wgs.relapse.tsv
├── independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary-plus.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary-plus.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv
├── infinium.gencode.v39.probe.annotations.tsv.gz
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── md5sum.txt
├── mirna-expression-counts.rds
├── nexterarapidcapture_exome_targetedregions_v1.2_hg38_100.bed
├── onco1500-v2-targets-ucsc.100bp_padded.bed
├── onco1500-v4-targets-ucsc.100bp_padded.bed
├── onco1500-v6-targets-ucsc.100bp_padded.bed
├── onco1500-v6a-targets-ucsc.100bp_padded.bed
├── release-notes.md
├── rna-dna-qc-stats.tsv
├── rna-isoform-expression-rsem-tpm.rds
├── snv-consensus-plus-hotspots.maf.tsv.gz
├── snv-mutation-tmb-all.tsv
├── snv-mutation-tmb-coding.tsv
├── snv-mutect2-tumor-only-plus-hotspots.maf.tsv.gz
├── splice-events-rmats.tsv.gz
├── sv-manta.tsv.gz
├── tcga_gene-counts-rsem-expected_count-collapsed.rds
├── tcga_gene-expression-rsem-tpm-collapsed.rds
├── truseq-exome-targeted-regions-manifest-v1-2_hg38_100.bed
├── uberon-map-gtex-group.tsv
├── uberon-map-gtex-subgroup.tsv
├── wgs_canonical_calling_regions.hg38.bed
└── xgen-exome-research-panel-targets_hg38_ucsc_liftover.100bp_padded.sort.merged.bed

previous release

release-v14

Release date: 2024-01-29
Status: available
Overview of changes:
- This release adds the following data:
  - 126 new methylation samples from PBTA
  - 262 new miRNA-Seq samples from PBTA
- Files changed:
  - Files added:
    - mirna-expression-counts.rds
- Analysis updates:
  - Adds DGD CNS tumors to PBTA cohort
  - Adds DGD composition as “Solid Tissue” for CNS tumors
  - Adds CNS_region for DGD CNS tumors
  - Fix extent_of_tumor_resection bug originating from DGD samples having “Not Reported” tumor resection - internal ticket
  - Fix C4118901-Tumor diagnosis from HGG–>LGG
  - Add new NIH Bethesda methylation v2 classifier columns to histology file
  - Use NIH classifier if unable to get high-confidence subtypes any other way for ATRT and HGG subtyping modules

release-v13

Release date: 2024-01-03
Status: available
Overview of changes:
- This release adds the following data:
  - Whole cell proteomic and phosphorylation data from HOPE and CPTAC
    - 218 Whole Cell Proteomics samples from CPTAC (cptac-protein-imputed-prot-expression.tsv)
    - 218 Phospho-Proteomics samples from CPTAC (cptac-protein-imputed-phospho-expression.tsv)
    - 90 Whole Cell Proteomics samples from HOPE (hope-protein-imputed-prot-expression.tsv)
    - 90 Phospho-Proteomics samples from HOPE (hope-protein-imputed-phospho-expression.tsv)
  - RNA-Seq data
    - 93 RNA-seq samples from PBTA
    - 40 RNA-seq samples from Maris
    - 243 RNA-seq samples from PPTC
    - 10 RNA-seq samples from DGD
  - Fusion panels
    - 1437 fusion panel samples from DGD
  - DNA data
    - 501 WGS samples from samples PBTA
    - 647 targeted sequencing samples from DGD
      - 323 normal samples
      - 324 tumor samples
Files changed
- files added
  - cptac-protein-imputed-phospho-expression-log2-ratio.tsv.gz
  - cptac-protein-imputed-prot-expression-abundance.tsv.gz
  - cptac-protein-imputed-prot-expression-log2-ratio.tsv.gz
  - cnv-controlfreec-tumor-only.tsv.gz
  - gbm-protein-imputed-phospho-expression-abundance.tsv.gz
  - gbm-protein-imputed-prot-expression-abundance.tsv.gz
  - gtex_gene-counts-rsem-expected_count-collapsed.rds
  - gtex_gene-expression-rsem-tpm-collapsed.rds
  - hope-cnv-controlfreec-tumor-only.tsv
  - hope-protein-imputed-phospho-expression-abundance.tsv.gz
  - hope-protein-imputed-prot-expression-abundance.tsv.gz
  - snv-mutect2-tumor-only-plus-hotspots.maf.tsv.gz
Analysis update
- Newly-added analysis modules
  - Add Pineoblastoma subtype module (https://github.com/d3b-center/OpenPedCan-analysis/pull/476)
  - Create copy_number_consensus_call_manta module for samples without GATK CNV (https://github.com/d3b-center/OpenPedCan-analysis/pull/410, (https://github.com/d3b-center/OpenPedCan-analysis/pull/419)
- Molecular subtyping update:
  - Add workflows to molecular subtyping modules (https://github.com/d3b-center/OpenPedCan-analysis/pull/467, https://github.com/d3b-center/OpenPedCan-analysis/pull/466, https://github.com/d3b-center/OpenPedCan-analysis/pull/465, https://github.com/d3b-center/OpenPedCan-analysis/pull/464, https://github.com/d3b-center/OpenPedCan-analysis/pull/463, https://github.com/d3b-center/OpenPedCan-analysis/pull/462, https://github.com/d3b-center/OpenPedCan-analysis/pull/461, https://github.com/d3b-center/OpenPedCan-analysis/pull/460, https://github.com/d3b-center/OpenPedCan-analysis/pull/458, https://github.com/d3b-center/OpenPedCan-analysis/pull/454)
  - Add DMG, EGFR to HGG methyl molecular subtype (https://github.com/d3b-center/OpenPedCan-analysis/pull/451)
  - Add PXA to HGG molecular subtype (https://github.com/d3b-center/OpenPedCan-analysis/pull/450)
  - Add K28I mutation into HGG molecular subtyping (https://github.com/d3b-center/OpenPedCan-analysis/pull/439)
  - Update LGG methylation subtyping (https://github.com/d3b-center/OpenPedCan-analysis/pull/433)
- Histologies update
  - Add match_id column (Kids_First_Participant_ID + sample_id + composition, tumor_descriptor + cell_line_composition + cell_line_passage) for matching experimental strategies per event in histologies-base file
- Others
  - Organize Dockerfile and reduce docker size (https://github.com/d3b-center/OpenPedCan-analysis/pull/447, https://github.com/d3b-center/OpenPedCan-analysis/pull/440)
  - Update readmes for deprecated modules and remove unused modules (https://github.com/d3b-center/OpenPedCan-analysis/pull/481)
  - Add script for methylation file download (https://github.com/d3b-center/OpenPedCan-analysis/pull/415)
  - RNA-seq and DNA samples QC (https://github.com/d3b-center/bixu-tracker/issues/2164)
    - = 20M total reads and 50% mapped for RNA-Seq
    - = 20X coverage for tumor DNA samples
  - Using NGSCheckmate and Somalier to identigy mismatched RNA-seq samples (https://github.com/d3b-center/bixu-tracker/issues/2157, https://github.com/d3b-center/bixu-tracker/issues/2163)

v13
├── 20038D-17Q6-01.regions.100bp_padded.bed
├── S0274956_Padded_HG38.merged.bed
├── S02972011_Covered_hg38_100.bed
├── S04380110_Regions_hg38_100.bed
├── S07604715_100bp_Padded.bed
├── SeqCap_EZ_Exome_v2_Padded_HG38.merged.bed
├── StrexomeLite_hg38_liftover_100bp_padded.bed
├── Strexome_targets_intersect_sorted_padded100.GRCh38.bed
├── TARGET_AML_NBL_WT_SeqVal79_attempt06_AllTracks_HG38_bed_expanded100.bed
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
├── WGS.hg38.vardict.100bp_padded.bed
├── agilent-v4-targets-ucsc.100bp_padded.bed
├── ashion_exome_v2_targets_hg38_padded100.bed
├── biospecimen_id_to_bed_map.tsv
├── cnv-cnvkit.seg.gz
├── cnv-consensus-gistic-only.seg.gz
├── cnv-consensus-gistic.zip
├── cnv-consensus.seg.gz
├── cnv-controlfreec-tumor-only.tsv.gz
├── cnv-controlfreec.tsv.gz
├── cnv-gatk.seg.gz
├── cnvkit_with_status.tsv
├── consensus_seg_with_status.tsv
├── consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_autosomes.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_x_and_y.tsv.gz
├── cptac-protein-imputed-phospho-expression-log2-ratio.tsv.gz
├── cptac-protein-imputed-prot-expression-abundance.tsv.gz
├── cptac-protein-imputed-prot-expression-log2-ratio.tsv.gz
├── efo-mondo-map.tsv
├── ensg-hugo-pmtl-mapping.tsv
├── fusion-annoFuse.tsv.gz
├── fusion-arriba.tsv.gz
├── fusion-dgd.tsv.gz
├── fusion-putative-oncogenic.tsv
├── fusion-starfusion.tsv.gz
├── fusion_summary_embryonal_foi.tsv
├── fusion_summary_ependymoma_foi.tsv
├── fusion_summary_ewings_foi.tsv
├── fusion_summary_lgg_hgg_foi.tsv
├── gbm-protein-imputed-phospho-expression-abundance.tsv.gz
├── gbm-protein-imputed-prot-expression-abundance.tsv.gz
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── gtex_gene-counts-rsem-expected_count-collapsed.rds
├── gtex_gene-expression-rsem-tpm-collapsed.rds
├── hg38_strelka.bed
├── histologies-base.tsv
├── histologies.tsv
├── hope-cnv-controlfreec-tumor-only.tsv
├── hope-protein-imputed-phospho-expression-abundance.tsv.gz
├── hope-protein-imputed-prot-expression-abundance.tsv.gz
├── independent-specimens.methyl.primary-plus.eachcohort.tsv
├── independent-specimens.methyl.primary-plus.tsv
├── independent-specimens.methyl.primary.eachcohort.tsv
├── independent-specimens.methyl.primary.tsv
├── independent-specimens.methyl.relapse.eachcohort.tsv
├── independent-specimens.methyl.relapse.tsv
├── independent-specimens.rnaseq.primary-plus-pre-release.tsv
├── independent-specimens.rnaseq.primary-pre-release.tsv
├── independent-specimens.rnaseq.relapse-pre-release.tsv
├── independent-specimens.rnaseqpanel.primary-plus.eachcohort.tsv
├── independent-specimens.rnaseqpanel.primary-plus.tsv
├── independent-specimens.rnaseqpanel.primary.eachcohort.tsv
├── independent-specimens.rnaseqpanel.primary.tsv
├── independent-specimens.rnaseqpanel.relapse.eachcohort.tsv
├── independent-specimens.rnaseqpanel.relapse.tsv
├── independent-specimens.wgs.primary-plus.eachcohort.tsv
├── independent-specimens.wgs.primary-plus.tsv
├── independent-specimens.wgs.primary.eachcohort.tsv
├── independent-specimens.wgs.primary.tsv
├── independent-specimens.wgs.relapse.eachcohort.tsv
├── independent-specimens.wgs.relapse.tsv
├── independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary-plus.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary-plus.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── md5sum.txt
├── nexterarapidcapture_exome_targetedregions_v1.2_hg38_100.bed
├── onco1500-v2-targets-ucsc.100bp_padded.bed
├── onco1500-v4-targets-ucsc.100bp_padded.bed
├── onco1500-v6-targets-ucsc.100bp_padded.bed
├── onco1500-v6a-targets-ucsc.100bp_padded.bed
├── release-notes.md
├── rna-dna-qc-stats.tsv
├── rna-isoform-expression-rsem-tpm.rds
├── snv-consensus-plus-hotspots.maf.tsv.gz
├── snv-mutation-tmb-all.tsv
├── snv-mutation-tmb-coding.tsv
├── snv-mutect2-tumor-only-plus-hotspots.maf.tsv.gz
├── splice-events-rmats.tsv.gz
├── sv-manta.tsv.gz
├── tcga-gene-expression-rsem-tpm-collapsed.rds
├── truseq-exome-targeted-regions-manifest-v1-2_hg38_100.bed
├── uberon-map-gtex-group.tsv
├── uberon-map-gtex-subgroup.tsv
├── wgs_canonical_calling_regions.hg38.bed
└── xgen-exome-research-panel-targets_hg38_ucsc_liftover.100bp_padded.sort.merged.bed

release-v12

release date: 2023-04-30
status: available
overview of changes (See Ticket 431 for additional details):
- MAJOR UPDATE
This release adds the following data:
- 744 methylation array data samples
  - 728 PBTA samples (17 normal, 711 tumor)
  - 16 TARGET samples (6 normal, 10 tumor)
- 1264 RNA-seq samples
  - 1264 PBTA samples (3 normal, 1261 tumor)
- 2762 WGS/WXS samples
  - 2444 PBTA WGS samples (1174 normal, 1270 tumor)
  - 315 PBTA WXS samples (160 normal, 155 tumor)
- This release reprocessed these data:
  - Harmonize PBTA X01 cohort using GENCODE v39 Ticket 427
- Harmonize TARGET and GMKF cohorts using GENCODE v39 Ticket 428
- Remap TCGA expression matrix to GENCODE v39 Ticket 521
- Remap GTEx TPM matrix to GENCODE v39 gene symbols Ticket 522
- files changed
  - files added
    - 20038D-17Q6-01.regions.100bp_padded.bed
    - S0274956_Padded_HG38.merged.bed
    - agilent-v4-targets-ucsc.100bp_padded.bed
    - cnv-gatk.seg.gz
    - fusion-annoFuse.tsv.gz
    - independent-specimens.methyl.primary-plus.eachcohort.tsv
    - independent-specimens.methyl.primary.eachcohort.tsv
    - independent-specimens.methyl.relapse.eachcohort.tsv
    - methyl-md5sum.txt
    - onco1500-v2-targets-ucsc.100bp_padded.bed
    - onco1500-v4-targets-ucsc.100bp_padded.bed
    - onco1500-v6-targets-ucsc.100bp_padded.bed
    - onco1500-v6a-targets-ucsc.100bp_padded.bed
  - files renamed
    - biospecimen_id_to_bed_map.txt renamed to biospecimen_id_to_bed_map.tsv
    - independent-specimens.rnaseqpanel.primary-plus.eachcohort.tsv renamed to independent-specimens.rnaseq.primary-plus-pre-release.tsv
    - independent-specimens.rnaseqpanel.primary.pre-release.tsv renamed to independent-specimens.rnaseq.primary-pre-release.tsv
    - independent-specimens.rnaseqpanel.relapse.pre-release.tsv to independent-specimens.rnaseq.relapse-pre-release.tsv
    - fusion_summary_lgat_foi.tsv renamed to fusion_summary_lgg_hgg_foi.tsv
  - files longer automatically downloaded
    - methyl-beta-values.rds
    - methyl-m-values.rds
  - files removed
    - tcga-gene-counts-rsem-expected_count-collapsed.rds
    - snv-dgd.maf.tsv.gz
- Updated data to use GENCODE v39 GDC
  - Update gene_match module GENCODE versions Ticket 400
  - Update analysis modules to use GENCODE 39 Tikcet 422
  - Update analysis modules to use GENCODE 39 Tikcet 423
  - Include updated gene symbol to gene_match module PMTL table Ticket 472
  - Update EPN analysis to pull new gene names using GENCODE v39 symbols Ticket 485
  - Fusion summary to use new gene symbols from GENCODE v39 Ticket 486
  - HGG subtyping to include GENCODE v39 gene symbols Ticket 487
  - LGG subtyping to take in new H3 gene symbols for GENCODE v39 update Ticket 488
  - Update DGD fusion file to match GENCODE v39 symbols + run FusionAnnotator on it Ticket 490
- Update histologies file - key changes noted here (other tickets can be found in OpenPedCan repo)
  - Corrected diagnosis for sample 7316-356 Ticket 366
  - Update histologies with the correct MYCN status from TARGET and GMKF clinical files Ticket 415
  - Add previously excluded methylation samples to the histologies file Ticket 421
  - Updated GTEx base histologies file to inclue gtex-group and getx_subgroup columns Ticket 435
  - Examine the latest base adapt histologies for updates Ticket 454
  - Create bixu-generated fields for v12 release Ticket 481
  - v12 WGS germline sex estimate Ticket 492
- Updates to help with creation and QC of histologies file
  - Histologies QC to check germline sex estimate Ticket 426
- Molecular subtyping updates
  - Update EPN fusions Ticket 287
  - Update gliomatosis cerebri term in LGAT subtyping Ticket 358
  - Manually add BS_YKEK4YWT fusion to DGD fusion file Ticket 392
  - fusion-summary: modify ependymoma gene pairs Ticket 440
  - Update Ependymoma subtyping to add K28M –> PFA Ticket 424
  - Ependymoma subyping - add spinal EPN type Ticket 425
  - Ependymoma subtyping– rename EPN, ST RELA subgroup to EPN, ST ZFTA Ticket 439
  - Neuroblastoma (NBL) molecular subtyping into MYCN amplified or MYCN non-amplified Ticket 417
  - Remove manual override of patient ID “PT_7E3V3JFX” subtying Ticket 449
  - Update EPN subtyping fusion pairs to include the YAP1--MAML2 fusion Ticket 451
  - Add Infant-Type Hemispheric Glioma to HGG subtyping module Ticket 474
  - Update ATRT subtyping to assign samples to one of 3 subtypes, ATRT, MYC, ATRT, SHH, or ATRT, TYR Ticket 496
  - Update modules using manta file for v12 release due to column name changes Ticket
  - Update mol subtyping integrate to include ATRT + NBL Ticket 504
  - Update embryonal subtyping TTYH1 fusion search Ticket 531
- Update EFO MONDO file
  - Updated EFO/MONDO mapping using OT custom EFO ontology Ticket 418 and Ticket 420
- methylation updates
  - Update methylation summary module Ticket 371
  - Add v12b6 CBTN methylation classifier results to data warehouse Ticket 391
  - Updated methylation arrays pre-processing module Ticket 404
  - Preprocess CBTN methylation arrays Ticket 430
  - Update methylation subtyping information for D3b warehouse import Ticket 434
  - Create methylation summary tables for display and download on the MTP portal Ticket 456 and Ticket 478
- v12 data release updates
  - Update gene_match module for v12 data release Ticket 525
  - Updated efo-mondo-mapping module for v12 data release Ticket 526
  - Update cnv-frequencies tables for v12 data release Ticket 527
  - Update fusion-frequencies tables for v12 data release Ticket 528
  - Update snv-frequencies tables for v12 data release Ticket 529
  - Update rna-seq-expression-summary-stats tables for v12 data release Ticket 530
- other changes
  - Remove metastatic secondary tumors from independent specimen lists Ticket 383
  - Update MTP tables filtering module Ticket 433
  - Resolved duplicate rows/different values in CNVkit consensus file Ticket 436
  - Update focal cn prep to resolve multiple locus status calls Ticket 437
  - Updated analyses modules to remove PMTL annotation process Ticket 447
  - Updated data pre-release QC module Ticket 450
  - Create Open Targets Platform approved targets and diseases identifiers Ticket 491
  - Update CI testing data to include methylation matrices Ticket 493
  - Update driver gene list Ticket 494
  - Fusion filtering (annoFuse) bug Ticket 503
  - Modify artifact column selection in fusion filtering for GTEx Ticket 507
  - Updated MTP tables datatypeId column Ticket 510

v12
├── 20038D-17Q6-01.regions.100bp_padded.bed
├── S0274956_Padded_HG38.merged.bed
├── S02972011_Covered_hg38_100.bed
├── S04380110_Regions_hg38_100.bed
├── S07604715_100bp_Padded.bed
├── SeqCap_EZ_Exome_v2_Padded_HG38.merged.bed
├── StrexomeLite_hg38_liftover_100bp_padded.bed
├── Strexome_targets_intersect_sorted_padded100.GRCh38.bed
├── TARGET_AML_NBL_WT_SeqVal79_attempt06_AllTracks_HG38_bed_expanded100.bed
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
├── WGS.hg38.vardict.100bp_padded.bed
├── agilent-v4-targets-ucsc.100bp_padded.bed
├── ashion_exome_v2_targets_hg38_padded100.bed
├── biospecimen_id_to_bed_map.tsv
├── cnv-cnvkit.seg.gz
├── cnv-consensus-gistic.zip
├── cnv-consensus.seg.gz
├── cnv-controlfreec.tsv.gz
├── cnv-gatk.seg.gz
├── cnvkit_with_status.tsv
├── consensus_seg_with_status.tsv
├── consensus_wgs_plus_cnvkit_wxs.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz
├── efo-mondo-map.tsv
├── ensg-hugo-pmtl-mapping.tsv
├── fusion-annoFuse.tsv.gz
├── fusion-arriba.tsv.gz
├── fusion-dgd.tsv.gz
├── fusion-putative-oncogenic.tsv
├── fusion-starfusion.tsv.gz
├── fusion_summary_embryonal_foi.tsv
├── fusion_summary_ependymoma_foi.tsv
├── fusion_summary_ewings_foi.tsv
├── fusion_summary_lgg_hgg_foi.tsv
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── hg38_strelka.bed
├── histologies-base.tsv
├── histologies.tsv
├── independent-specimens.methyl.primary-plus.eachcohort.tsv
├── independent-specimens.methyl.primary-plus.tsv
├── independent-specimens.methyl.primary.eachcohort.tsv
├── independent-specimens.methyl.primary.tsv
├── independent-specimens.methyl.relapse.eachcohort.tsv
├── independent-specimens.methyl.relapse.tsv
├── independent-specimens.rnaseq.primary-plus-pre-release.tsv
├── independent-specimens.rnaseq.primary-pre-release.tsv
├── independent-specimens.rnaseq.relapse-pre-release.tsv
├── independent-specimens.rnaseqpanel.primary-plus.eachcohort.tsv
├── independent-specimens.rnaseqpanel.primary-plus.tsv
├── independent-specimens.rnaseqpanel.primary.eachcohort.tsv
├── independent-specimens.rnaseqpanel.primary.tsv
├── independent-specimens.rnaseqpanel.relapse.eachcohort.tsv
├── independent-specimens.rnaseqpanel.relapse.tsv
├── independent-specimens.wgs.primary-plus.eachcohort.tsv
├── independent-specimens.wgs.primary-plus.tsv
├── independent-specimens.wgs.primary.eachcohort.tsv
├── independent-specimens.wgs.primary.tsv
├── independent-specimens.wgs.relapse.eachcohort.tsv
├── independent-specimens.wgs.relapse.tsv
├── independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary-plus.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary-plus.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── md5sum.txt
├── methyl-md5sum.txt
├── nexterarapidcapture_exome_targetedregions_v1.2_hg38_100.bed
├── onco1500-v2-targets-ucsc.100bp_padded.bed
├── onco1500-v4-targets-ucsc.100bp_padded.bed
├── onco1500-v6-targets-ucsc.100bp_padded.bed
├── onco1500-v6a-targets-ucsc.100bp_padded.bed
├── release-notes.md
├── rna-isoform-expression-rsem-tpm.rds
├── snv-consensus-plus-hotspots.maf.tsv.gz
├── snv-dgd.maf.tsv.gz
├── snv-mutation-tmb-all.tsv
├── snv-mutation-tmb-coding.tsv
├── sv-manta.tsv.gz
├── tcga-gene-expression-rsem-tpm-collapsed.rds
├── truseq-exome-targeted-regions-manifest-v1-2_hg38_100.bed
├── uberon-map-gtex-group.tsv
├── uberon-map-gtex-subgroup.tsv
├── wgs_canonical_calling_regions.hg38.bed
└── xgen-exome-research-panel-targets_hg38_ucsc_liftover.100bp_padded.sort.merged.bed

release-v11

release date: 2022-07-07
status: available
overview of changes (See PR 188 for additional details):
- This release adds the following data:
  - 11 RNA-Seq and WXS PBTA samples (plus 2 WXS PBTA results from previous release)
  - 1799 DGD tumor samples (929 DNA, 870 RNA)
  - methylation array data from
    - normal samples:
      - 5 PBTA samples
      - 12 TARGET samples
    - tumor samples: Ticket 278 and Ticket 269
      - 1146 PBTA samples
      - 751 TARGET samples
    - RNA isoform merged TPM samples
- Update TCGA RNA-Seq data to use GENCODE v36 GDC
  - Ticket 285
  - Ticket 308
- All additional changes as well as details about the above changes are as followed.
Add base histologies file to data release, see ticket 333
Update histologies file - key changes noted here (other tickets can be found in OpenPedCan repo)
- Change cancer_group of Metastatic secondary tumors;Neuroblastoma to Neuroblastoma - See discussion in ticket 232 - Ticket 234
- Update primary_site for some GMKF and TARGET NBL samples to resolve lumped together primary_site issues - Ticket 257
- Update histologies file to use pathology_diagnosis (when available) or cancer_group (when path dx not available) to fill in harmonized_diagnosis for non-PBTA samples - Ticket 259
- DGD histologies cleanup: ticket 325
- Fix short_histology for PBTA cohort: ticket 309
- Add extent of tumor resection: ticket 298
Update EFO MONDO file
- Create efo-mondo-map-prefill.tsv file based on cancer_group generated in molecular-subtyping-integrate: PR 176
- Update EFO MONDO map file to contain new cancer group in v10 histologies file: ticket 237
- Add NCIT column to the EFO MONDO map file: ticket 261
Update ensg-hugo-pmtl-mapping.tsv to remove NA line: ticket 231
Re-run independent samples module to accommodate new cancer groups and additional samples: ticket 370 and Ticket 370
Add pre-release RNA-Seq only independent specimens
Add concatenated DGD MAF files to data release as snv-dgd.maf.tsv.gz: ticket 248
Add concatenated DGD fusion files as fusion-dgd.tsv.gz: ticket 249
Update DNA and RNA delivery data files with new PBTA samples: ticket 253
Re-run fusion filtering: ticket 316
Update focal CN preparation module to fine tune ENSEMBL, gene symbol, and cytoband matching
- Ticket 320
- Ticket 318
Rerun focal-cn-preparation: ticket 254
Run molecular subtyping for all samples
- Ticket 299
- Ticket 303
- Updates:
  - Added DGD samples to medulloblastoma and craniopharyngioma subtyping
  - Modified EPN subtyping per Ticket 365
  - Add methylation bs_ids in neurocytoma subtyping
Update the download script to change from v10 to v11 and GENCODE file: ticket 270
Add bed files for TMB calculation and TMB results to data release
- Ticket 250
- Ticket 258
Run GISTIC module and upload zip file for data release: Ticket 302
Merge all RNA isoform files into one for data release and downstream analyses: Ticket 341
Add fusion summary files required for subtyping modules Ticket 239:
- fusion_summary_embryonal_foi.tsv
- fusion_summary_ependymoma_foi.tsv
- fusion_summary_ewings_foi.tsv
- fusion_summary_lgat_foi.tsv

v11
├── ashion_exome_v2_targets_hg38_padded100.bed
├── biospecimen_id_to_bed_map.txt
├── cnv-cnvkit.seg.gz
├── cnv-controlfreec.tsv.gz
├── cnv-consensus.seg.gz
├── cnv-consensus-gistic.zip
├── cnvkit_with_status.tsv
├── consensus_seg_with_status.tsv
├── consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs.tsv.gz
├── data-files-description.md
├── efo-mondo-map.tsv
├── ensg-hugo-pmtl-mapping.tsv
├── fusion-arriba.tsv.gz
├── fusion-starfusion.tsv.gz
├── fusion-putative-oncogenic.tsv
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── histologies.tsv
├── histologies-base.tsv
├── independent-specimens.methyl.primary-plus.tsv
├── independent-specimens.methyl.primary.tsv
├── independent-specimens.methyl.relapse.tsv
├── independent-specimens.rnaseq.primary-plus-pre-release.tsv
├── independent-specimens.rnaseq.primary-pre-release.tsv
├── independent-specimens.rnaseq.primary.eachcohort.tsv
├── independent-specimens.rnaseq.primary.tsv
├── independent-specimens.rnaseq.relapse-pre-release.tsv
├── independent-specimens.rnaseq.relapse.eachcohort.tsv
├── independent-specimens.rnaseq.relapse.tsv
├── independent-specimens.rnaseqpanel.primary-plus.eachcohort.tsv
├── independent-specimens.rnaseqpanel.primary-plus.pre-release.tsv
├── independent-specimens.rnaseqpanel.primary-plus.tsv
├── independent-specimens.rnaseqpanel.primary.eachcohort.tsv
├── independent-specimens.rnaseqpanel.primary.pre-release.tsv
├── independent-specimens.rnaseqpanel.primary.tsv
├── independent-specimens.rnaseqpanel.relapse.eachcohort.tsv
├── independent-specimens.rnaseqpanel.relapse.pre-release.tsv
├── independent-specimens.rnaseqpanel.relapse.tsv
├── independent-specimens.wgs.primary-plus.eachcohort.tsv
├── independent-specimens.wgs.primary-plus.tsv
├── independent-specimens.wgs.primary.eachcohort.tsv
├── independent-specimens.wgs.primary.tsv
├── independent-specimens.wgs.relapse.eachcohort.tsv
├── independent-specimens.wgs.relapse.tsv
├── independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary-plus.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary-plus.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.tsv
├── independent-specimens.wgswxspanel.primary.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.tsv
├── independent-specimens.wgswxspanel.relapse.prefer.wgs.tsv
├── independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.tsv
├── md5sum.txt
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── nexterarapidcapture_exome_targetedregions_v1.2_hg38_100.bed
├── release-notes.md
├── rna-isoform-expression-rsem-tpm.rds
├── S0274956_Padded_HG38.merged.bed
├── S02972011_Covered_hg38_100.bed
├── S04380110_Regions_hg38_100.bed
├── S07604715_100bp_Padded.bed
├── SeqCap_EZ_Exome_v2_Padded_HG38.merged.bed
├── StrexomeLite_hg38_liftover_100bp_padded.bed
├── Strexome_targets_intersect_sorted_padded100.GRCh38.bed
├── TARGET_AML_NBL_WT_SeqVal79_attempt06_AllTracks_HG38_bed_expanded100.bed
├── tcga-gene-counts-rsem-expected_count-collapsed.rds
├── tcga-gene-expression-rsem-tpm-collapsed.rds
├── truseq-exome-targeted-regions-manifest-v1-2_hg38_100.bed
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
├── WGS.hg38.vardict.100bp_padded.bed
├── snv-consensus-plus-hotspots.maf.tsv.gz
├── sv-manta.tsv.gz
├── methyl-beta-values.rds
├── methyl-m-values.rds
├── snv-dgd.maf.tsv.gz
├── fusion-dgd.tsv
├── snv-mutation-tmb-all.tsv
├── snv-mutation-tmb-coding.tsv
├── uberon-map-gtex-group.tsv
├── uberon-map-gtex-subgroup.tsv
├── wgs_canonical_calling_regions.hg38.bed
└── xgen-exome-research-panel-targets_hg38_ucsc_liftover.100bp_padded.sort.merged.bed

archived release

release-v10

release date: 2021-10-11
status: available
overview of changes:
- This particular releae added 438 tumor/nomral pairs of TARGET ALL WXS samples as well as a total of 144 samples (including WGS, WXS, RNA-Seq for both tumor and normal) from PNOC clinical trials.
- Usable TCGA RNA-Seq data from diseaseXpress with GDC clinical information are added to (n=10414) were added to the release
- cnv-consensus-gistic.zip from run-gistic module was added to the release
- ensg-hugo-rmtl-mapping.tsv is replaced with ensg-hugo-pmtl-mapping.tsv after we switch from RMTL v1.0 to PMTL v1.1
- All additional changes as well as details about the above 3 changes are as followed.
Update histologies file:
- Add 120 samples from PNOC_dataset_2 (40 WXS tumor, 40 WXS normal and 40 RNA-Seq from 40 patients) and additional 24 PNOC_dataset_1 tumor WGS from 18 samples to release
  - Details see ticket 174
  - After tp53-nf1-scores and run-gistic modules were ran with the base histology file, these samples then ran through molecular-subtyping-HGG, molecular-subtyping-pathology and molecular-subtyping-integrate modules to get their subtype (details also captured below)
  - See ticket 210 for details
- Add 438 tumor/normal pairs of TARGET ALL WXS samples
  - Details see ticket 158
- Change “Known” to “Unknown” in the histologies file since it was mis-coded before
  - Details see ticket 192
- Fixed TCGA and GMKF/TARGET OS_days in histology file - see ticket 199
  - For TCGA samples, OS_days column is now populated this way: days_to_death column is preferentially used for OS_days; when it is NA, days_to_last_follow_up is used as long as the value is not negative
  - For TARGET samples that are also present in GMKF cohort, OS_days in TARGET cohort are replaced with OS_days in GMKF cohort since GMKF has more up-to-date records
- Remove TCGA samples in histology file that is not in the expression matrix or does not have clinical information from GDC portal
  - Details see ticket 202
- Additional changes to TCGA histology file - RNA-library of poly-A and sample_type of Tumor (a total of 9551 samples) all have NA composition:
  - For these samples, composition is modified to Solid Tissue as long as primary_site is not NA or Bone Marrow
- Additionally, there are normal samples in TARGET cohort with broad_histology, short_histology, tumor_descriptor and cancer_group that are not NA
  - For those samples, these fields are changed to NA
Use PMTL v1.1 instead of RMTL v1.0 for gene annotation - ensg-hugo-pmtl-mapping.tsv will now be the included in the data release and ensg-hugo-rmtl-mapping.tsv will not longer be used. - Details see ticket 206
Run molecular subtyping for new PNOC clinical trials samples
- Use the merged snv-consensus-plus-hotspots.maf.tsv.gz, consensus_wgs_plus_cnvkit_wxs.tsv.gz, gene-expression-rsem-tpm-collapsed.rds and base histology file to re-run TP53-NF1 module
  - Details see ticket 209
- Use the new cnv-consensus.seg.gz and run through GISTIC module
  - Details see ticket 211
- Run molecular subtyping for new PNOC sample through HGG, pathology and integrate modules
  - Details see ticket 210
Update cnv-cnvkit.seg.gz, cnv-controlfreec.tsv.gz,consensus_wgs_plus_cnvkit_wxs.tsv.gz, snv-consensus-plus-hotspots.maf.tsv.gz and sv-manta.tsv to include 438 tumor/normal pairs of TARGET ALL WXS samples as well as a total of 144 samples (including WGS, WXS, RNA-Seq for both tumor and normal) from PNOC clinical samples.
- Details for merging PNOC clinical samples see ticket 174
- Details for merging 438 tumor/normal pairs of TARGET ALL WXS samples see ticket 194
Update EFO-MONDO mapped file to remove trailing white space that is causing error
- Details for merging 438 tumor/nomral pairs of TARGET ALL WXS samples see ticket 208
Update gene-counts-rsem-expected_count-collapsed.rds, gene-expression-rsem-tpm-collapsed.rds, fusion-arriba.tsv.gz and fusion-starfusion.tsv.gz with 40 RNA-Seq tumor sample from PNOC_dataset_2 results merged
- Details see ticket 203
Two TCGA gene expression files, tcga-gene-counts-rsem-expected_count-collapsed.rds and tcga-gene-expression-rsem-tpm-collapsed.rds, for all TCGA in diseaseXpress and has GDC clinical information (n=10414) were now include in data release
- Details see ticket 200
Update consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz, consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz and consensus_wgs_plus_cnvkit_wxs.tsv.gz files with the following changes:
- When annotating CNV status, for WXS samples, if WGS was performed on the same sample, we use the germline_sex_estimate from the WGS as the germline_sex_estimate for the WXS samples. Details see ticket 177
- When matching WGS samples were not available, gender is used as `germline_sex_estimate. Details see ticket 177
- Additionally, focal-cn-file-preparation module was re-run to include 438 tumor/normal pairs of TARGET ALL WXS samples as well as a total of 144 samples (including WGS, WXS, RNA-Seq for both tumor and normal) from PNOC clinical samples. Details see ticket 196
cnv-consensus-gistic.zip will now be added to data release after 24 WGS PNOC tumor samples were merged and the module re-run
- Details see ticket 218
Independent sample lists were re-generated with the following changes:
- In addition to what are currently in data release, we added scripts to preferentially select WXS tumor when available and the following files will now be added to data release for use by snv-frequencies module - Details see ticket 193
  - independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
  - independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
  - independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
  - independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv
- The independent lists are re-generated with 438 tumor/normal pairs of TARGET ALL WXS samples as well as a total of 144 samples (including WGS, WXS, RNA-Seq for both tumor and normal) from PNOC clinical samples added to the histology file
  - Details see ticket 215
Regenerate fusion-putative-oncogenic.tsv to include results from 40 RNA-Seq tumor samples from PNOC clinical trials - Details see ticket 214

v10
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
├── WGS.hg38.vardict.100bp_padded.bed
├── cnv-cnvkit.seg.gz
├── cnv-controlfreec.tsv.gz
├── cnv-consensus.seg.gz
├── cnv-consensus-gistic.zip
├── consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs.tsv.gz
├── data-files-description.md
├── efo-mondo-map.tsv
├── ensg-hugo-pmtl-mapping.tsv
├── fusion-arriba.tsv.gz
├── fusion-starfusion.tsv.gz
├── fusion-putative-oncogenic.tsv
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── tcga-gene-counts-rsem-expected_count-collapsed.rds
├── tcga-gene-expression-rsem-tpm-collapsed.rds
├── histologies.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.tsv
├── independent-specimens.rnaseq.primary.eachcohort.tsv
├── independent-specimens.rnaseq.relapse.eachcohort.tsv
├── independent-specimens.wgswxspanel.primary.tsv
├── independent-specimens.wgswxspanel.relapse.tsv
├── independent-specimens.rnaseq.primary.tsv
├── independent-specimens.rnaseq.relapse.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── release-notes.md
├── snv-consensus-plus-hotspots.maf.tsv.gz
├── sv-manta.tsv.gz
├── uberon-map-gtex-group.tsv
└── uberon-map-gtex-subgroup.tsv

release-v9

release date: 2021-09-01
status: available
overview of changes:
- This particular release is just an update of efo-mondo-map.tsv per discussion in ticket 182.
- MONDO and EFO codes were manually reviewed and assigned to cancer_group in OpenPedCan.

v9
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
├── WGS.hg38.vardict.100bp_padded.bed
├── cnv-cnvkit.seg.gz
├── cnv-controlfreec.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs.tsv.gz
├── data-files-description.md
├── efo-mondo-map.tsv
├── ensg-hugo-rmtl-mapping.tsv
├── fusion-arriba.tsv.gz
├── fusion-starfusion.tsv.gz
├── fusion-putative-oncogenic.tsv
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── histologies.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.tsv
├── independent-specimens.rnaseq.primary.eachcohort.tsv
├── independent-specimens.rnaseq.relapse.eachcohort.tsv
├── independent-specimens.wgswxspanel.primary.tsv
├── independent-specimens.wgswxspanel.relapse.tsv
├── independent-specimens.rnaseq.primary.tsv
├── independent-specimens.rnaseq.relapse.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── release-notes.md
├── snv-consensus-plus-hotspots.maf.tsv.gz
├── sv-manta.tsv.gz
├── uberon-map-gtex-group.tsv
└── uberon-map-gtex-subgroup.tsv

archived release

release-v8

release date: 2021-08-20
status: available
overview of changes:
- This particular release is mainly to include 412 tumor/normal pairs of TARGET WXS samples as listed in ticket 111. Detailed changes see below.
detailed changes:
- Histology file updates - the master ticket is d3b center ticket 43:
  - 412 tumor/normal TARGET WXS samples were included in the histologies.tsv file per ticket 111v
  - sample_id and aliquot_id for some TARGET samples were miscoded before. This release fixed the issue per ticket 145
  - sample_id and aliquot_id were updated using the GTEx coding nomenclature GTEX-[donor ID]-[tissue site ID]-SM-[aliquot ID] (https://www.gtexportal.org/home/faq#sampleIdFormat)
  - primary_site for GTEx samples were updated to match gtex_subgroup column, changing Whole Blood to Blood and Brain - Cerebellar Hemisphere to Brain - Cerebellum
  - broad_histology for TARGET samples were updated as following: Acute Lymphoblastic Leukemia and Acute Myeloid Leukemia were merged to Hematologic malignancy; Clear cell sarcoma of the kidney, Rhabdoid tumor, and Wilms tumor were combined as Renal tumor; Osteosarcoma is changed to Mesenchymal non-meningothelial tumor and Neuroblastoma is converted to Embryonal tumor. See ticket 136 and [ticket 176] (https://github.com/PediatricOpenTargets/ticket-tracker/issues/176)
  - For gtex_group == "Cells", the composition column is changed from Solid Tissue to Derived Cell Line per discussion in d3b center ticket 43
  - For short_histology, neuroblastoma samples previously annotated as NBL or Embryonal tumor are converted to Neuroblastoma to be consistent with other samples
  - Updated MB subtypes in the histologies file per ticket 148
  - Some GMKF WGS samples does not have germline_sex_estimate as indicated in ticket 168. Added using the file in the discussion of ticket 159
  - Some TARGET WXS samples miss tumor_ploidy that are actually available - and those samples now have updated ploidy using the file in the discussion session of ticket 160
- Update DNA related files to include TARGET WXS DNA (412 tumor/normal pairs):
  - cnv-cnvkit.seg.gz ticket 156
  - cnv-controlfreec.tsv.gz ticket 156
  - snv-consensus-plus-hotspots.maf.tsv.gz ticket 156
- Update method to call CNV consensus (WGS) as described in ticket 134 and ticket 149. Briefly, CNV called by MantaSV were filtered to contain only filter == "PASS" before going into the consensus calling workflow. In the subsequent step, instead of only retaining CNV calls that have 50% reciprocal overlap between callers (which was too stringent), the criteria is expanded to include small CNV regions that are 90% covered by a larger CNV. The consensus is the overlapping region.
  - cnv_consensus_seg.gz (WGS samples only - in S3 bucket s3://kf-openaccess-us-east-1-prd-pbta/open-targets/v8/ but not in md5sum.txt file)
- As a result of changing consensus calling criteria and adding new TARGET WXS DNA sample results to cnv-cnvkit.seg.gz and cnv-controlfreec.tsv.gz, the following files were updated:
  - consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz ticket 159 and ticket 160 (only in S3 bucket s3://kf-openaccess-us-east-1-prd-pbta/open-targets/v8/- not included in automatic download)
  - consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz ticket 159 and ticket 160 (only in S3 bucket s3://kf-openaccess-us-east-1-prd-pbta/open-targets/v8/- not included in automatic download)
- Added consensus_wgs_plus_cnvkit_wxs.tsv.gz which is a merge of consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz and consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz per ticket 161
- Updated ensg-hugo-rmtl-mapping.tsv file per ticket 146. The previous release of this file does not contain all gene ENSG IDs and symbols that are present in snv-consensus-plus-hotspots.maf.tsv.gz. This update merged GENCODE V28 and V38 to allow inclusion of more gene ENSG IDs and symbols.
- Futher update ensg-hugo-rmtl-mapping.tsv PR 48 D3b codes to include all gene ENSG ID to symbol mappings in v7 ensg-hugo-rmtl-mapping.tsv.
- Update independent samples files to include TARGET WXS DNA (412 tumor/normal pairs) - ticket 165. Previously, these files were not added to our releases. Starting this release, we will also add independent sample list to our release as well.
- Updated independent samples so that the Kids_First_Biospecimen_ID for allcohorts and eachcohort match if possible: ticket 135
- Updated independent sample module to arrange by Kids_First_Biospecimen_ID before writing out the file: ticket 179
- For now, we will add files that are used by analyses modules in this file and these are the following:
  - independent-specimens.wgswxspanel.primary.eachcohort.tsv
  - independent-specimens.wgswxspanel.relapse.eachcohort.tsv
  - independent-specimens.rnaseq.primary.eachcohort.tsv
  - independent-specimens.rnaseq.relapse.eachcohort.tsv
  - independent-specimens.wgswxspanel.primary.tsv
  - independent-specimens.wgswxspanel.relapse.tsv
  - independent-specimens.rnaseq.primary.tsv
  - independent-specimens.rnaseq.relapse.tsv
- Updated fusion-putative-oncogenic.tsv since at the last step of putative oncogenic fusion filtering, we filter out fusions seen in > 4 broad_histology since they are likely artifacts and with the update of broad_histology, the result will be updated ticket 175
  - fusion-putative-oncogenic.tsv

v8
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
├── WGS.hg38.vardict.100bp_padded.bed
├── cnv-cnvkit.seg.gz
├── cnv-controlfreec.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs.tsv.gz
├── data-files-description.md
├── efo-mondo-map.tsv
├── ensg-hugo-rmtl-mapping.tsv
├── fusion-arriba.tsv.gz
├── fusion-starfusion.tsv.gz
├── fusion-putative-oncogenic.tsv
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── histologies.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.tsv
├── independent-specimens.rnaseq.primary.eachcohort.tsv
├── independent-specimens.rnaseq.relapse.eachcohort.tsv
├── independent-specimens.wgswxspanel.primary.tsv
├── independent-specimens.wgswxspanel.relapse.tsv
├── independent-specimens.rnaseq.primary.tsv
├── independent-specimens.rnaseq.relapse.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── release-notes.md
├── snv-consensus-plus-hotspots.maf.tsv.gz
├── sv-manta.tsv.gz
├── uberon-map-gtex-group.tsv
└── uberon-map-gtex-subgroup.tsv

archived release

release-v7

release date: 2021-07-23
status: available
changes:
- Updated EFO/MONDO mapping file per ticket 88
- Added GTEX UBERON mapping files for subgroup and group per ticket 85
  - Collapsed Cerebellum hemisphere and Cerebellum to Cerebellum since GTEX has the same UBERON code listed for both per ticket 106
  - Renamed Whole Blood to Blood per John Maris’s suggestion to alphabetize and ticket 106.
    - Note: v8 gtex lists “whole blood” subgroup and “whole blood” group as UBERON_0013756, which is mapped to venous blood and “Whole blood” maps to UBERON_0000178.
    - After inquiry at GTEx, we were told they are equivalent terms as seen in this link
- Updated ensg-hugo-rmtl-v1-mapping.tsv with minor updates according to ticket 125 and changed filename to ensg-hugo-rmtl-mapping.tsv
- Histology file updates:
  - Collapsed Cerebellum hemisphere and Cerebellum to Cerebellum since GTEX has the same UBERON code listed for both per ticket 106
  - Renamed Whole Blood to Blood per John Maris’s suggestion to alphabetize and ticket 106.
  - Added inferred strandedness to RNA-Seq samples per ticket 104
  - Added broad_tumor_descriptor to designate grouped Diagnosis and Relapse samples used in SNV, CNV, Fusion tables as well as for grouping on pedcbio per ticket 109
  - Added ploidy information for TARGET AML and NBL WXS samples per ticket 121
  - Collapsed TARGET ids containing suffixes to match the BAM file sample IDs from GDC and match the RDS processed files per comment here
- Added TARGET NBL and AML WXS, PBTA WXS CNV calls to cnv-cnvkit.seg.gz and cnv-controlfreec.tsv.gz per ticket 80
- Added consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz (removed WGS only file consensus_seg_annotated_cn_autosomes.tsv.gz) and consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz (removed WGS only file consensus_seg_annotated_cn_x_and_y.tsv.gz) containing consensus WGS and CNVkit WXS data per ticket 102
- Updated RNA-Seq files to include TARGET RNA (N = 1329) samples:
  - fusion-arriba.tsv.gz
  - fusion-starfusion.tsv.gz
  - fusion-putative-oncogenic.tsv
  - gene-counts-rsem-expected_count-collapsed.rds
  - gene-expression-rsem-tpm-collapsed.rds

archived release

release-v6

release date: 2021-06-29
status: available
changes:
- Within histologies.tsv:
  - Updated cancer_group logic to make updates as per ticket48
  - combine CBTN+PNOC into cohort == PBTA ticket79
  - GMKF tumor ploidy was added ticket46
  - harmonized tumor_descriptor per ticket61
  - updated clinical info for NBL samples which were missing in source files per ticket43
  - updated experimental_strategy for targeted capture samples per ticket62
- Add cnv files with PBTA+GMKF samples per ticket44:
  - cnv-cnvkit.seg.gz
  - cnv-controlfreec.tsv.gz
  - cnv-consensus.seg.gz
  - consensus_seg_annotated_cn_autosomes.tsv.gz
  - consensus_seg_annotated_cn_autosomes_xy.tsv.gz
- Add EFO and MONDO cancer mapping file ticket78:
- Add ENSG to HUGO mapping file with RMTL designation ticket84 and ticket56

archived release

release-v5

release date: 2021-06-17
status: available
changes:
- Removed
  - gtex_target_tcga-gene-expression-rsem-tpm-collapsed.polya.rds
  - gtex_target_tcga-gene-counts-rsem-expected_count-collapsed.rds
- Update RSEM files to include GTEXv8 files
  - gene-expression-rsem-tpm-collapsed.rds
  - gene-counts-rsem-expected_count-collapsed.rds
- Update manifest to include GTEx manifest are now v8, TCGA manifest are from GDC and TARGET manifest from Diskin Lab and @afarrel
  - histologies.tsv
- Added snv PBTA+GMKF maf file
  - snv-consensus-plus-hotspots.maf.tsv.gz
- Released files below

v5
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
├── WGS.hg38.vardict.100bp_padded.bed
├── fusion-arriba.tsv.gz
├── fusion-starfusion.tsv.gz
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-counts-rsem-expected_count.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── gene-expression-rsem-tpm.rds
├── histologies.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── snv-consensus-plus-hotspots.maf.tsv.gz
└── release-notes.md

archived release

release-v4

release date: 2021-06-01
status: available
changes:
- Update rnseq file names to be generic (currently includes PBTA and KFNBL)
  - gene-counts-rsem-expected_count*
  - gene-expression-rsem-tpm*
  - fusion*
- Added mereged gtex_target_tcga expected_count file
  - gtex_target_tcga-gene-counts-rsem-expected_count-collapsed.rds
- Combined PBTA, KFNBL, TARGET, TCGA, GTEX histologies into histologies.tsv
- Released files below

v4
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
├── WGS.hg38.vardict.100bp_padded.bed
├── fusion-arriba.tsv.gz
├── fusion-starfusion.tsv.gz
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-counts-rsem-expected_count.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── gene-expression-rsem-tpm.rds
├── gtex_target_tcga-gene-counts-rsem-expected_count-collapsed.rds
├── histologies.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── kfnbl-snv-lancet.vep.maf.gz
├── kfnbl-snv-mutect2.vep.maf.gz
├── kfnbl-snv-strelka2.vep.maf.gz
├── kfnbl-snv-vardict.vep.maf.gz
└── release-notes.md

archived release

release-v3

release date: 2021-05-21
status: available
changes:
- Update files due to addition of SSF column name
  - kfnbl-snv-vardict.vep.maf.gz
- Added files for downstream analysis output files from collapse-rnaseq
  - kfnbl-gene-counts-rsem-expected_count-collapsed.stranded.rds
- Released files below:

v3
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
├── WGS.hg38.vardict.100bp_padded.bed
├── gtex-gene-expression-rsem-tpm-collapsed.polya.rds
├── gtex-histologies.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── kfnbl-fusion-arriba.tsv.gz
├── kfnbl-fusion-starfusion.tsv.gz
├── kfnbl-gene-counts-rsem-expected_count-collapsed.stranded.rds
├── kfnbl-gene-counts-rsem-expected_count.stranded.rds
├── kfnbl-gene-expression-kallisto.stranded.rds
├── kfnbl-gene-expression-rsem-fpkm-collapsed.stranded.rds
├── kfnbl-gene-expression-rsem-fpkm.stranded.rds
├── kfnbl-gene-expression-rsem-tpm-collapsed.stranded.rds
├── kfnbl-gene-expression-rsem-tpm.stranded.rds
├── kfnbl-histologies.tsv
├── kfnbl-isoform-counts-rsem-expected_count.stranded.rds
├── kfnbl-isoform-expression-rsem-tpm.stranded.rds
├── kfnbl-snv-lancet.vep.maf.gz
├── kfnbl-snv-mutect2.vep.maf.gz
├── kfnbl-snv-strelka2.vep.maf.gz
├── kfnbl-snv-vardict.vep.maf.gz
├── release-notes.md
├── target-gene-expression-rsem-tpm-collapsed.rds
├── target-histologies.tsv
├── tcga-gene-expression-rsem-tpm-collapsed.rds
└── tcga-histologies.tsv

archived release

release-v2

release date: 2021-05-18
status: available

changes:

Updated rnaseq files with addition of BS_ETC8R0TD
- kfnbl-fusion-arriba.tsv.gz
- kfnbl-fusion-starfusion.tsv.gz
- kfnbl-gene-counts-rsem-expected_count.stranded.rds
- kfnbl-gene-expression-kallisto.stranded.rds
- kfnbl-gene-expression-rsem-fpkm.stranded.rds
- kfnbl-gene-expression-rsem-fpkm-collapsed.stranded.rds
- kfnbl-gene-expression-rsem-tpm.stranded.rds
- kfnbl-gene-expression-rsem-tpm-collapsed.stranded.rds
- kfnbl-isoform-counts-rsem-expected_count.stranded.rds
- kfnbl-isoform-expression-rsem-tpm.stranded.rds
- kfnbl-histologies.tsv

Released files below:

open-targets
└── v2
├── gtex-gene-expression-rsem-tpm-collapsed.polya.rds
├── gtex-histologies.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── md5sum.txt
├── kfnbl-fusion-arriba.tsv.gz
├── kfnbl-fusion-starfusion.tsv.gz
├── kfnbl-gene-counts-rsem-expected_count.stranded.rds
├── kfnbl-gene-expression-kallisto.stranded.rds
├── kfnbl-gene-expression-rsem-fpkm.stranded.rds
├── kfnbl-gene-expression-rsem-fpkm-collapsed.stranded.rds
├── kfnbl-gene-expression-rsem-tpm.stranded.rds
├── kfnbl-gene-expression-rsem-tpm-collapsed.stranded.rds
├── kfnbl-isoform-counts-rsem-expected_count.stranded.rds
├── kfnbl-isoform-expression-rsem-tpm.stranded.rds
├── kfnbl-histologies.tsv    
├── kfnbl-snv-lancet.vep.maf.gz
├── kfnbl-snv-mutect2.vep.maf.gz
├── kfnbl-snv-strelka2.vep.maf.gz
├── kfnbl-snv-vardict.vep.maf.gz
├── release-notes.md 
├── target-gene-expression-rsem-tpm-collapsed.rds
├── target-histologies.tsv
├── tcga-gene-expression-rsem-tpm-collapsed.rds
├── tcga-histologies.tsv
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
└── WGS.hg38.vardict.100bp_padded.bed

archived release

release-v1

release date: 2021-04-21
status: available

changes:

Added files below:

open-targets
└── v1
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── md5sum.txt
├── kfnbl-gene-counts-rsem-expected_count.stranded.rds
├── kfnbl-gene-expression-rsem-fpkm.stranded.rds
├── kfnbl-gene-expression-rsem-tpm.stranded.rds
├── kfnbl-histologies.tsv    
├── kfnbl-snv-lancet.vep.maf.gz
├── kfnbl-snv-mutect2.vep.maf.gz
├── kfnbl-snv-strelka2.vep.maf.gz
├── kfnbl-snv-vardict.vep.maf.gz
├── release-notes.md
├── WGS.hg38.lancet.300bp_padded.bed
├── WGS.hg38.lancet.unpadded.bed
├── WGS.hg38.mutect2.vardict.unpadded.bed
├── WGS.hg38.strelka2.unpadded.bed
└── WGS.hg38.vardict.100bp_padded.bed

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