Table 3 Basic genomic data dictionary
From: Local data commons: the sleeping beauty in the community of data commons
Report type | Data elements |
|---|---|
DNAseq | Â |
Variant Type | SNP, insertion, deletions, copy number variant, rearrangement |
Mutation | Gene name, position, coding sequence effect, protein effect, allele fraction, transcript ID, strand |
Copy Number Variant (CNV) | Copy Number, gene name, involved exons, position, CNV type (e.g., loss, amplification) |
Rearrangement | Gene names, positions, rearrangement types (e.g., fusion, truncation, etc.) |
Microsatellite-instability | Result values, category value (i.e., MSS, MSL, MSH) |
Tumor Mutational Burden | Unit (e.g., Mutations per Million Base), Result values |
RNAseq | Â |
Expression | Gene name, expression unit (i.e., RPM/CPM, RPKM/FPKM, TPM, TMM, etc.), expression level, gene type (e.g., mRNA, lncRNA, circRNA, etc.), transcript ID |
Fusion | Positions, Junction read count, fusion sequence, expression unit |