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app: update the content of the resource README file, #TASK-5501
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| README | ||
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| In this folder, users should store external files to be used by some OpenCGA analysis. | ||
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| 1) roleInCancer.txt[.gz] | ||
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| This file is used by interpretation clinical analysis, e.g., Tiering and TEAM analysis. | ||
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| It stores those genes which contain mutations that have been casually implicated in cancer. This information can be downloaded | ||
| from the Cancer Gene Census (CGC) at https://cancer.sanger.ac.uk/census | ||
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| The file consists of two tab-separated columns: the first one contains the gene name, and the second, the role in cancer, i.e.: oncogne, | ||
| TSG, fusion. In addition, lines starting with # are considered comments and will be ignored. | ||
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| Sample of a roleInCancer file: | ||
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| #Gene name Role in Cancer | ||
| A1CF oncogene | ||
| ABI1 TSG, fusion | ||
| ABL1 oncogene, fusion | ||
| ABL2 oncogene, fusion | ||
| ACKR3 oncogene, fusion | ||
| ACSL3 fusion | ||
| ... | ||
| ... | ||
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| 2) actionableVariants_xxx.txt[.gz] where xxx = assembly, e.g.: grch37 | ||
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| This file is used by interpretation clinical analysis, e.g., TEAM analysis. | ||
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| It stores variants that were identified as clinically actionable variants. The file consists of the following twelve tab-separated columns: | ||
| - Chromosome | ||
| - Start | ||
| - Stop | ||
| - Reference allele | ||
| - Alternate allele | ||
| - dbSNP ID | ||
| - ClinVar Variant ID | ||
| - HGVS | ||
| - Phenotype list | ||
| - Clinical significance | ||
| - Review status | ||
| - Submitter categories | ||
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| In addition, lines starting with # are considered comments and will be ignored. | ||
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| Sample fo an actionableVariants file: | ||
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| #Chromosome Start Stop ReferenceAllele AlternateAllele dbSNP ID ClinVar Variant ID hgvs PhenotypeList ClinicalSignificance ReviewStatus SubmitterCategories | ||
| 2 47702269 47702269 C T rs28929483 1753 NM_000251.2(MSH2):c.1865C>T (p.Pro622Leu) Hereditary cancer-predisposing syndrome;Hereditary nonpolyposis colon cancer;Lynch syndrome;Lynch syndrome I Pathogenic reviewed by expert panel 3 | ||
| 2 47657020 47657020 C T rs63751108 1755 NM_000251.2(MSH2):c.1216C>T (p.Arg406Ter) Carcinoma of colon;Hereditary cancer-predisposing syndrome;Hereditary nonpolyposis colon cancer;Lynch syndrome;Lynch syndrome I;not provided Pathogenic reviewed by expert panel 3 | ||
| ... | ||
| ... | ||
| This directory is designated for OpenCGA analyses to download the necessary external data. | ||
| For instance, during the first Exomiser analysis, the files '2109_hg38.zip' and '2109_phenotype.zip' will be downloaded | ||
| from the OpenCGA analysis URL and stored in the 'exomiser' folder within this directory. Subsequent Exomiser analyses will | ||
| then access this folder to read these files. |