COSMIC数据库详细梳理

作者，Evil Genius

目前COSMIC数据库已经更新到了v100版本

cosmic所有的文件解读

• Cosmic_Breakpoints_Tsv_v100_GRCh37.tar ：All breakpoint data from the current release in a tab separated table.
• Cosmic_CompleteCNA_Tsv_v100_GRCh37.tar：All copy number variants from the current release in a tab separated table.
• Cosmic_CancerGeneCensus_Tsv_v100_GRCh37.tar：All cancer gene census data from the current release in a tab separated table.
• Cosmic_MutantCensus_Tsv_v100_GRCh37.tar：All coding mutations in genes listed in the Cancer Gene Census ( https://cancer.sanger.ac.uk/census ) in a tab separated table.
• Cosmic_Classification_Tsv_v100_GRCh37.tar：COSMIC cancer classification information in a tab separated file.
• Cosmic_ClassificationPaper_Tsv_v100_GRCh37.tar：COSMIC paper cancer classification information in a tab-separated file.
• Cosmic_CompleteDifferentialMethylation_Tsv_v100_GRCh37.tar：TCGA Level 3 methylation data from the ICGC portal for the current release in a tab separated table.
• Cosmic_Fusion_Tsv_v100_GRCh37.tar ：All gene fusion mutation data from the current release in a tab-separated table. This file includes all the tested samples, with and without fusion detected.
• Cosmic_CompleteGeneExpression_Tsv_v100_GRCh37.tar：All gene expression level 3 data from the TCGA portal for the current release in a tab-separated table. Please note: The platform codes currently used to produce the COSMIC gene expression values are: IlluminaGA_RNASeqV2, IlluminaHiSeq_RNASeqV2, AgilentG4502A_07_2, AgilentG4502A_07_3.
• Cosmic_Genes_Fasta_v100_GRCh37.tar：CDS sequence for all the coding genes in COSMIC.
• Cosmic_Genes_Tsv_v100_GRCh37.tar：All the COSMIC gene data from the current release in a tab separated file. Genes are associated with COSMIC unique gene identifier, gene symbol, Ensembl gene identifier, Entrez and HGNC mapping.
• Cosmic_GenomeScreensMutant_Tsv_v100_GRCh37.tar ：A tab-separated table of coding point mutations from genome-wide screens (including whole exome sequencing) from the current release.
• Cosmic_GenomeScreensMutant_Vcf_v100_GRCh37.tar ：VCF file of coding point mutations from genome wide screens (including whole exome sequencing) from the current release.
• Cosmic_GenomeScreensMutant_VcfNormal_v100_GRCh37.tar：VCF file of coding point mutations from genome wide screens (including whole exome sequencing) normalized in the current release.
• Cosmic_CancerGeneCensusHallmarksOfCancer_Tsv_v100_GRCh37.tar：A tab-separated table listing the hallmarks of cancer for a subset of cancer census genes.
• Cosmic_MutationTracking_Tsv_v100_GRCh37.tar：A tab-separated table listing the mapping of all COSMIC's legacy mutations (COSMs or COSNs) to the new genomic identifiers (COSVs). This file also helps to identify the transcripts and the accession numbers on which the current mutation is annotated on, along with the mutation type.
• Cosmic_NonCodingVariants_Tsv_v100_GRCh37.tar：A tab separated table of all non-coding mutations from the current release.
• Cosmic_NonCodingVariants_Vcf_v100_GRCh37.tar：VCF file of all non-coding variants in the current release.
• Cosmic_NonCodingVariants_VcfNormal_v100_GRCh37.tar：VCF file of all coding variants ( normalized ) in the current release. The file has the variants 5' shifted as per the VCF standard, and the info part contains the 3' shifted syntaxes for cds and genome, along with the unshifted variants in the OLD_VARIANT field.
• Cosmic_ResistanceMutations_Tsv_v100_GRCh37.tar：A tab-separated table listing the details of all mutations in COSMIC which are known to confer drug resistance.
• Cosmic_Sample_Tsv_v100_GRCh37.tar：All the COSMIC sample data without the features from the current release in a tab-separated file.
• Cosmic_StructuralVariants_Tsv_v100_GRCh37.tar：All structural variants from the current release in a tab-separated table.
• Cosmic_CompleteTargetedScreensMutant_Tsv_v100_GRCh37.tar：A tab separated table of the complete curated COSMIC dataset (targeted screens) from the current release. It includes all coding point mutations, and the negative data set.
• Cosmic_CompleteTargetedScreensMutant_Vcf_v100_GRCh37.tar：CF file of the complete curated COSMIC dataset (targeted screens) from the current release.
• Cosmic_CompleteTargetedScreensMutant_VcfNormal_v100_GRCh37.tar：VCF file of the complete curated COSMIC dataset (targeted screens) normalized from the current release The file has the variants 5' shifted as per the VCF standard, and the info part contains the 3' shifted syntaxes for cds and genome, along with the unshifted variants in the OLD_VARIANT field.
• Cosmic_Transcripts_Tsv_v100_GRCh37.tar：All transcript data in COSMIC is represented by a unique Ensembl transcript accession from the current release in a tab-separated file. Transcripts are associated with a unique COSMIC gene id, strand, biotype and canonical flag.
• Actionability_AllData_Tsv_v11_GRCh37.tar：临床用药信息。

今天我们的重点就是临床药物信息文件

1、数据来源

2、ACTIONABILITY RANK

3、PATIENT PRE-SCREENING

表明纳入试验的患者是否被证实具有突变备注列中所示的variants/表达蛋白。

4、变异的命名法

5、DEVELOPMENT STATUS

Drug development proceeds via a series of widely-recognised phases.Actionability uses an extended version of the FDA’s phase definitions. Possible values are: Approved FDA, Approved other, Phase 3, Phase 2, Phase 1, Experimental, Orphan/Fast track, Case study, Out of trials human study, Retrospective/Meta-analysis, Phase 4, Unknown.

6、TRIAL STATUS

Trial status indicates the progress of the trial. Not all trials specify status and many trials do not report at every stage. Possible values are: Not yet recruiting, Recruiting, Active, Complete, Terminated, Suspended, Withdrawn, Unknown.

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