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#ProjectPatients studiedSequenced tumorsTumor IDs in MAFSourceNEW Public URL to MAF (updated GDC to https://portal.gdc.cancer.gov/)ORIGINAL URL to MAF (formerly https://gdc-portal.nci.nih.gov/)Notes
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acc929292gdchttps://portal.gdc.cancer.gov/legacy-archive/files/733bc880-b631-4d7e-8189-80dc20bdd140https://gdc-portal.nci.nih.gov/legacy-archive/files/733bc880-b631-4d7e-8189-80dc20bdd140AWG curators at BCM merged their MAF with Broad's for the publication, but Broad's GSC-generated MAF is selected here since it has fewer false-positives, and includes allele counts.
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blca412413419gdchttps://portal.gdc.cancer.gov/legacy-archive/files/1c0382a7-c3ca-40fd-ba3c-029c4529214fhttps://gdc-portal.nci.nih.gov/legacy-archive/files/1c0382a7-c3ca-40fd-ba3c-029c4529214f1 patient has samples from both primary tumor and metastasis, which share some of the same mutations. And some tumors have multiple aliquot IDs in column 16, so variants/samples may need deduplication.
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brca1,0811,0881,092gdchttps://portal.gdc.cancer.gov/legacy-archive/files/87ac6b5b-806e-4de0-b8d8-ae6888759667https://gdc-portal.nci.nih.gov/legacy-archive/files/87ac6b5b-806e-4de0-b8d8-ae6888759667AWG curators at WU inadvertently filtered out important AKT1/PTEN hotspots using a dbSNP-based filter. So Broad's GSC-generated MAF is selected here. 7 patients have samples from the primary tumor and metastasis, which share some of the same mutations. And some tumors have multiple aliquot IDs in column 16, so variants may need deduplication.
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cesc305307307gdchttps://portal.gdc.cancer.gov/legacy-archive/files/a707c566-b0d3-4025-b921-752fe92ed5e7https://gdc-portal.nci.nih.gov/legacy-archive/files/a707c566-b0d3-4025-b921-752fe92ed5e72 patients have samples from both primary tumor and metastasis, which share some of the same mutations. So variants/samples may need deduplication.
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chol353535gdchttps://portal.gdc.cancer.gov/legacy-archive/files/a8532d87-1eae-4289-8aea-3255d7b313cfhttps://gdc-portal.nci.nih.gov/legacy-archive/files/a8532d87-1eae-4289-8aea-3255d7b313cfAWG curators at HGSC merged calls made by 4 centers. And did a decent job at removing known false-positives.
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coadread577580580gdchttps://portal.gdc.cancer.gov/legacy-archive/files/3437ecf9-355d-4d35-afb4-ffe1a705c206 https://portal.gdc.cancer.gov/legacy-archive/files/7c3e8456-c39f-4292-8cc2-374b14c75446https://gdc-portal.nci.nih.gov/legacy-archive/files/3437ecf9-355d-4d35-afb4-ffe1a705c206 https://gdc-portal.nci.nih.gov/legacy-archive/files/7c3e8456-c39f-4292-8cc2-374b14c75446Listed a MAF each for COAD and READ, that need to be concatenated. Broad's GSC-generated MAFs are selected here, with fewer false positives and more subclonal events than the AWG-curated MAFs from BCM. 1 patient has samples from both primary and met, and 2 other patients have samples for both primary and recurrence. So variants/samples may need deduplication.
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dlbc484848gdchttps://portal.gdc.cancer.gov/legacy-archive/files/9e9d181f-582a-45d4-8189-ae0f9b71eed4https://gdc-portal.nci.nih.gov/legacy-archive/files/9e9d181f-582a-45d4-8189-ae0f9b71eed4It's unclear who the AWG curator is. Only Broad and BCM provided GSC-generated MAFs, and Broad's MAF is selected here. Nearly half the SNPs in BCM's MAF are either germline calls or artifacts per ExAC. Around 34% of Broad's indels have the same problem, but we have to choose the best of what's available.
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esca184185185gdchttps://portal.gdc.cancer.gov/legacy-archive/files/226b7c4e-240b-4d33-94e6-5a2546c5d9e2https://gdc-portal.nci.nih.gov/legacy-archive/files/226b7c4e-240b-4d33-94e6-5a2546c5d9e21 patient has samples from the primary tumor and metastasis, which share some of the same mutations. And some tumors have multiple aliquot IDs in column 16. So variants/samples may need deduplication.
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gbm396408498gdchttps://portal.gdc.cancer.gov/legacy-archive/files/7abdba45-acfd-4e8d-a297-3f4af85362adhttps://gdc-portal.nci.nih.gov/legacy-archive/files/7abdba45-acfd-4e8d-a297-3f4af85362ad12 patients have samples from both primary and recurrence. So variants/samples may need deduplication.
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hnsc508509509dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/hnsc/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_HNSC.IlluminaGA_DNASeq_automated.Level_2.1.4.0/PR_TCGA_HNSC_PAIR_Capture_All_Pairs_QCPASS_v4.aggregated.capture.tcga.uuid.automated.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/hnsc/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_HNSC.IlluminaGA_DNASeq_automated.Level_2.1.4.0/PR_TCGA_HNSC_PAIR_Capture_All_Pairs_QCPASS_v4.aggregated.capture.tcga.uuid.automated.somatic.mafThis is a GSC-generated MAF. Latest AWG curated MAF has ~200 fewer samples. 1 patient has a primary and metastasis in the cohort, which share some mutations.
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kich666666dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/kich/gsc/hgsc.bcm.edu/mixed_dnaseq_curated/mutations/hgsc.bcm.edu_KICH.Mixed_DNASeq_curated.Level_2.1.1.0/hgsc.bcm.edu_KICH.IlluminaGA_DNASeq.1.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/kich/gsc/hgsc.bcm.edu/mixed_dnaseq_curated/mutations/hgsc.bcm.edu_KICH.Mixed_DNASeq_curated.Level_2.1.1.0/hgsc.bcm.edu_KICH.IlluminaGA_DNASeq.1.somatic.mafAWG also uploaded a separate MAF containing a few extra mutation calls from mitochondria. If you want that too, it's down the same path as the main MAF.
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kirc451451548dcc,gdachttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/kirc/gsc/hgsc.bcm.edu/mixed_dnaseq/mutations/hgsc.bcm.edu_KIRC.Mixed_DNASeq.Level_2.1.2.0/hgsc.bcm.edu_KIRC.Mixed_DNASeq.1.somatic.maf http://gdac.broadinstitute.org/runs/tmp/rawMAFs/PR_TCGA_KIRC_PAIR_Capture_All_Pairs_QCPASS_v3.hugo_entrez_remapped.aggregated.capture.tcga.uuid.automated.somatic.maf.txthttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/kirc/gsc/hgsc.bcm.edu/mixed_dnaseq/mutations/hgsc.bcm.edu_KIRC.Mixed_DNASeq.Level_2.1.2.0/hgsc.bcm.edu_KIRC.Mixed_DNASeq.1.somatic.maf http://gdac.broadinstitute.org/runs/tmp/rawMAFs/PR_TCGA_KIRC_PAIR_Capture_All_Pairs_QCPASS_v3.hugo_entrez_remapped.aggregated.capture.tcga.uuid.automated.somatic.maf.txtAWG did some re-capture for gap filling, resulting in multiple aliquot IDs in column 16 of the same tumors, so variants may need deduplication. Also Broad sequenced more samples, that need to be merged in.
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kirp161161161dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/kirp/gsc/hgsc.bcm.edu/mixed_dnaseq_curated/mutations/hgsc.bcm.edu_KIRP.Mixed_DNASeq_curated.Level_2.1.3.0/hgsc.bcm.edu_KIRP.IlluminaGA_DNASeq.1.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/kirp/gsc/hgsc.bcm.edu/mixed_dnaseq_curated/mutations/hgsc.bcm.edu_KIRP.Mixed_DNASeq_curated.Level_2.1.3.0/hgsc.bcm.edu_KIRP.IlluminaGA_DNASeq.1.somatic.maf
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laml200200197dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/laml/gsc/genome.wustl.edu/illuminaga_dnaseq/mutations/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.16.0/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.13.0.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/laml/gsc/genome.wustl.edu/illuminaga_dnaseq/mutations/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.16.0/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.13.0.somatic.maf3 tumor IDs don't get listed in column 16 because of zero mutations detected in exome-seq. This is not unexpected for LAML, because of generally low mutation rates.
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lgg513527530gdachttp://gdac.broadinstitute.org/runs/tmp/rawMAFs/PR_TCGA_LGG_PAIR_Capture_All_Pairs_QCPASS_v7.hugo_entrez_remapped.aggregated.capture.tcga.uuid.automated.somatic.maf.txthttp://gdac.broadinstitute.org/runs/tmp/rawMAFs/PR_TCGA_LGG_PAIR_Capture_All_Pairs_QCPASS_v7.hugo_entrez_remapped.aggregated.capture.tcga.uuid.automated.somatic.maf.txt
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lihc198198198dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/lihc/gsc/hgsc.bcm.edu/mixed_dnaseq_curated/mutations/hgsc.bcm.edu_LIHC.Mixed_DNASeq_curated.Level_2.1.2.0/hgsc.bcm.edu_LIHC.IlluminaGA_DNASeq.1.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/lihc/gsc/hgsc.bcm.edu/mixed_dnaseq_curated/mutations/hgsc.bcm.edu_LIHC.Mixed_DNASeq_curated.Level_2.1.2.0/hgsc.bcm.edu_LIHC.IlluminaGA_DNASeq.1.somatic.maf
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luad542543561dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/luad/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_LUAD.IlluminaGA_DNASeq_automated.Level_2.1.5.0/PR_TCGA_LUAD_PAIR_Capture_All_Pairs_QCPASS_v4.aggregated.capture.tcga.uuid.automated.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/luad/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_LUAD.IlluminaGA_DNASeq_automated.Level_2.1.5.0/PR_TCGA_LUAD_PAIR_Capture_All_Pairs_QCPASS_v4.aggregated.capture.tcga.uuid.automated.somatic.mafThis is a GSC-generated MAF. Latest AWG curated MAF has ~200 fewer samples. Some tumors have multiple aliquot IDs in column 16, and 1 patient has a primary and recurrence sample in the cohort.
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lusc178178178dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/lusc/gsc/broad.mit.edu/illuminaga_dnaseq/mutations/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.1.5.0/LUSC_Paper_v8.aggregated.tcga.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/lusc/gsc/broad.mit.edu/illuminaga_dnaseq/mutations/broad.mit.edu_LUSC.IlluminaGA_DNASeq.Level_2.1.5.0/LUSC_Paper_v8.aggregated.tcga.somatic.maf
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mesodcc
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ov429429426paperhttp://www.nature.com/ncomms/2014/140122/ncomms4156/extref/ncomms4156-s4.xlsxhttp://www.nature.com/ncomms/2014/140122/ncomms4156/extref/ncomms4156-s4.xlsxA DCC version was unavailable. Latest 429-case MAF obtained from a WashU publication. 3 tumor IDs don't get listed in column 16 because of zero mutations detected in exome-seq.
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paad146146146dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/paad/gsc/broad.mit.edu/illuminaga_dnaseq_curated/mutations/broad.mit.edu_PAAD.IlluminaGA_DNASeq_curated.Level_2.1.3.0/freeze2.aggregated.capture.tcga.uuid.curated.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/paad/gsc/broad.mit.edu/illuminaga_dnaseq_curated/mutations/broad.mit.edu_PAAD.IlluminaGA_DNASeq_curated.Level_2.1.3.0/freeze2.aggregated.capture.tcga.uuid.curated.somatic.maf
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pcpg178183183dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/pcpg/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_PCPG.IlluminaGA_DNASeq_automated.Level_2.1.2.0/PR_TCGA_PCPG_PAIR_Capture_All_Pairs_QCPASS_v1.aggregated.capture.tcga.uuid.automated.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/pcpg/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_PCPG.IlluminaGA_DNASeq_automated.Level_2.1.2.0/PR_TCGA_PCPG_PAIR_Capture_All_Pairs_QCPASS_v1.aggregated.capture.tcga.uuid.automated.somatic.mafThis is a GSC-generated MAF. An AWG curated MAF was unavailable.
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prad425425425dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/prad/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_PRAD.IlluminaGA_DNASeq_automated.Level_2.1.5.0/PR_TCGA_PRAD_PAIR_Capture_All_Pairs_QCPASS_v6.aggregated.capture.tcga.uuid.automated.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/prad/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_PRAD.IlluminaGA_DNASeq_automated.Level_2.1.5.0/PR_TCGA_PRAD_PAIR_Capture_All_Pairs_QCPASS_v6.aggregated.capture.tcga.uuid.automated.somatic.maf
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sarc255259259dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/sarc/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_SARC.IlluminaGA_DNASeq_automated.Level_2.1.0.0/SARC_pairs.aggregated.capture.tcga.uuid.automated.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/sarc/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_SARC.IlluminaGA_DNASeq_automated.Level_2.1.0.0/SARC_pairs.aggregated.capture.tcga.uuid.automated.somatic.maf
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skcm367369369gdachttp://gdac.broadinstitute.org/runs/tmp/rawMAFs/PR_TCGA_SKCM_PAIR_Capture_All_Pairs_QCPASS_v4.hugo_entrez_remapped.aggregated.capture.tcga.uuid.automated.somatic.maf.txthttp://gdac.broadinstitute.org/runs/tmp/rawMAFs/PR_TCGA_SKCM_PAIR_Capture_All_Pairs_QCPASS_v4.hugo_entrez_remapped.aggregated.capture.tcga.uuid.automated.somatic.maf.txt
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stad428428428dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/stad/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_STAD.IlluminaGA_DNASeq_automated.Level_{2.1.5.0/PR_TCGA_STAD_PAIR_Capture_All_Pairs_QCPASS_v5.aggregated.capture.tcga.uuid.automated.somatic.maf,2.1.6.0/An_TCGA_STAD_External_capture_All_Pairs.aggregated.capture.tcga.uuid.automated.somatic.maf}https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/stad/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_STAD.IlluminaGA_DNASeq_automated.Level_{2.1.5.0/PR_TCGA_STAD_PAIR_Capture_All_Pairs_QCPASS_v5.aggregated.capture.tcga.uuid.automated.somatic.maf,2.1.6.0/An_TCGA_STAD_External_capture_All_Pairs.aggregated.capture.tcga.uuid.automated.somatic.maf}These are two MAFs that need concatenation.
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tgct149155155dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/tgct/gsc/hgsc.bcm.edu/mixed_dnaseq_curated/mutations/hgsc.bcm.edu_TGCT.Mixed_DNASeq_curated.Level_2.1.0.0/hgsc.bcm.edu_TGCT.IlluminaGA_DNASeq.1.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/tgct/gsc/hgsc.bcm.edu/mixed_dnaseq_curated/mutations/hgsc.bcm.edu_TGCT.Mixed_DNASeq_curated.Level_2.1.0.0/hgsc.bcm.edu_TGCT.IlluminaGA_DNASeq.1.somatic.maf
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thca402405405dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thca/gsc/broad.mit.edu/illuminaga_dnaseq/mutations/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.1.5.0/AN_TCGA_THCA_PAIR_Capture_ALLQC_14Aug2013_429.aggregated.capture.tcga.uuid.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thca/gsc/broad.mit.edu/illuminaga_dnaseq/mutations/broad.mit.edu_THCA.IlluminaGA_DNASeq.Level_2.1.5.0/AN_TCGA_THCA_PAIR_Capture_ALLQC_14Aug2013_429.aggregated.capture.tcga.uuid.somatic.maf3 patients have samples from the primary tumor and metastasis, which share some of the same mutations.
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thym123123123dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thym/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_THYM.IlluminaGA_DNASeq_automated.Level_2.1.0.0/THYM_pairs.aggregated.capture.tcga.uuid.automated.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thym/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_THYM.IlluminaGA_DNASeq_automated.Level_2.1.0.0/THYM_pairs.aggregated.capture.tcga.uuid.automated.somatic.maf
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ucec248248248dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/ucec/gsc/genome.wustl.edu/illuminaga_dnaseq/mutations/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.7.0/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.7.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/ucec/gsc/genome.wustl.edu/illuminaga_dnaseq/mutations/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.7.0/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.7.somatic.mafThis one is missing AKT1:E17K muts which were inadvertently filtered out by a dbSNP-based filter. Curator will need to recover those from calls made by the other two centers.
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ucs565656dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/ucs/gsc/broad.mit.edu/illuminaga_dnaseq_curated/mutations/broad.mit.edu_UCS.IlluminaGA_DNASeq_curated.Level_2.1.0.0/AN_TCGA_UCS_PAIR_Capture_56.aggregated.capture.tcga.uuid.curated.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/ucs/gsc/broad.mit.edu/illuminaga_dnaseq_curated/mutations/broad.mit.edu_UCS.IlluminaGA_DNASeq_curated.Level_2.1.0.0/AN_TCGA_UCS_PAIR_Capture_56.aggregated.capture.tcga.uuid.curated.somatic.maf
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uvm808080dcchttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/uvm/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_UVM.IlluminaGA_DNASeq_automated.Level_2.1.1.0/PR_TCGA_UVM_PAIR_Capture_All_Pairs_QCPASS_v1.aggregated.capture.tcga.uuid.automated.somatic.mafhttps://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/uvm/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_UVM.IlluminaGA_DNASeq_automated.Level_2.1.1.0/PR_TCGA_UVM_PAIR_Capture_All_Pairs_QCPASS_v1.aggregated.capture.tcga.uuid.automated.somatic.maf