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Variants can be classified based on different criteria (e.g., ClinVar, CiViC), and different vendors may base their classification on different criteria. Is it possible to include this in the example modeling? Or include some language in the leading text on how best to capture this?
ClinVar is a clinical variant database
Questions:
We we talking about an identifier for a variant itself that is in a public database → GFPVRID?- We talking about criteria related to reportable VARIANT IMPACT CLASSIFICATION; i.e., the criteria related to determining the VARIANT IMPACT CLASSIFICATION result; rows 1 and 6?
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| Rows 1, 6: | Show the variant impact classification, a categorization of the phenotypic or clinical significance of the genomic variation, of the BAP1 and CYP2D6 genes respectively. | | Rows 2, 7: | Show the predicted amino acid change based on sequence analysis of the genomic variation in the BAP1 and CYP2D6 genes respectively. | | Rows 3, 8: | Show the predicted coding sequence change based on sequence analysis of the genomic variation in the BAP1 and CYP2D6 genes respectively. | | Rows 4, 9: | Show the read depth, the total number of times the genes loci were sequenced, for BAP1 and CYP2D6 respectively. | | Rows 5, 10: | Show the variant read depth/read depth, the relative measurement of the variant read depth to total read depth of the BAP1 and CYP2D6 genes loci respectively, as percentages. |
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| Row | STUDYID | DOMAIN | USUBJID | GFSEQ | GFREFID | GFTESTCD | GFTEST | GFTSTDTL | GFORRES | GFORRESU | GFSTRESC | GFSTRESN | GFSTRESU | GFGENREF | GFCHROM | GFSYM | GFSYMTYP | GFGENLOC | GFXFN | GFNAM | GFSPEC | GFMETHOD | VISITNUM | VISIT | VISITDY | GFDTC | GFDY | | 1 | GR123 | GF | 10000 | 1 | TRF001338 | SHRTVAR | Short Variation | VARIANT IMPACT CLASSIFICATION | known |
| known |
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| GRCh37.75 | 3 | BAP1 | GENE WITH PROTEIN PRODUCT | 52438573 | /compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xml | ACME XYZ | DNA | TARGETED GENOME SEQUENCING | 1 | SCREENING | 1 | 2022-01-25 | 2 | | 2 | GR123 | GF | 10000 | 2 | TRF001338 | SHRTVAR | Short Variation | PREDICTED AMINO ACID CHANGE | R383fs*15 |
| R383fs*15 |
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| GRCh37.75 | 3 | BAP1 | GENE WITH PROTEIN PRODUCT | 52438573 | /compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xml | ACME XYZ | DNA | TARGETED GENOME SEQUENCING | 1 | SCREENING | 1 | 2022-01-25 | 2 | | 3 | GR123 | GF | 10000 | 3 | TRF001338 | SHRTVAR | Short Variation | PREDICTED CODING SEQUENCE CHANGE | 1145_1146insG |
| 1145_1146insG |
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| GRCh37.75 | 3 | BAP1 | GENE WITH PROTEIN PRODUCT | 52438573 | /compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xml | ACME XYZ | DNA | TARGETED GENOME SEQUENCING | 1 | SCREENING | 1 | 2022-01-25 | 2 | | 4 | GR123 | GF | 10000 | 4 | TRF001338 | SHRTVAR | Short Variation | READ DEPTH | 262 |
| 262 |
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| GRCh37.75 | 3 | BAP1 | GENE WITH PROTEIN PRODUCT | 52438573 | /compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xml | ACME XYZ | DNA | TARGETED GENOME SEQUENCING | 1 | SCREENING | 1 | 2022-01-25 | 2 | | 5 | GR123 | GF | 10000 | 5 | TRF001338 | SHRTVAR | Short Variation | VARIANT READ DEPTH/READ DEPTH | 20 | % | 20 | 20 | % | GRCh37.75 | 3 | BAP1 | GENE WITH PROTEIN PRODUCT | 52438573 | /compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xml | ACME XYZ | DNA | TARGETED GENOME SEQUENCING | 1 | SCREENING | 1 | 2022-01-25 | 2 | | 6 | GR123 | GF | 10000 | 6 | TRF001338 | SHRTVAR | Short Variation | VARIANT IMPACT CLASSIFICATION | unknown |
| unknown |
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| GRCh37.75 | 22 | CYP2D6 | GENE WITH PROTEIN PRODUCT | 42525085 | /compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xml | ACME XYZ | DNA | TARGETED GENOME SEQUENCING | 1 | SCREENING | 1 | 2022-01-25 | 2 | | 7 | GR123 | GF | 10000 | 7 | TRF001338 | SHRTVAR | Short Variation | PREDICTED AMINO ACID CHANGE | W152fs*2 |
| W152fs*2 |
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| GRCh37.75 | 22 | CYP2D6 | GENE WITH PROTEIN PRODUCT | 42525085 | /compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xml | ACME XYZ | DNA | TARGETED GENOME SEQUENCING | 1 | SCREENING | 1 | 2022-01-25 | 2 | | 8 | GR123 | GF | 10000 | 8 | TRF001338 | SHRTVAR | Short Variation | PREDICTED CODING SEQUENCE CHANGE | 454_454delA |
| 454_454delA |
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| GRCh37.75 | 22 | CYP2D6 | GENE WITH PROTEIN PRODUCT | 42525085 | /compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xml | ACME XYZ | DNA | TARGETED GENOME SEQUENCING | 1 | SCREENING | 1 | 2022-01-25 | 2 | | 9 | GR123 | GF | 10000 | 9 | TRF001338 | SHRTVAR | Short Variation | READ DEPTH | 162 |
| 162 |
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| GRCh37.75 | 22 | CYP2D6 | GENE WITH PROTEIN PRODUCT | 42525085 | /compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xml | ACME XYZ | DNA | TARGETED GENOME SEQUENCING | 1 | SCREENING | 1 | 2022-01-25 | 2 | | 10 | GR123 | GF | 10000 | 10 | TRF001338 | SHRTVAR | Short Variation | VARIANT READ DEPTH/READ DEPTH | 51 | % | 51 | 51 | % | GRCh37.75 | 22 | CYP2D6 | GENE WITH PROTEIN PRODUCT | 42525085 | /compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xml | ACME XYZ | DNA | TARGETED GENOME SEQUENCING | 1 | SCREENING | 1 | 2022-01-25 | 2 |
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