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This example
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This example shows findings from an assessment of of genes of interest from an oncology study with the purpose of determining the variation in short sequences of nucleotides in those genes. Short variations are generally defined as insertions or deletions of 50 fifty base pairs or less when compared to a reference sequence.
Glenn Barnes - This example was from an oncology study.
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Shows the variant impact classification, a categorization of the phenotypic or clinical significance of the genomic variation, of the BAP1 gene. The identifier for the genome reference used to generate the reported result is shown in GFGENREF. The designation (name or number) of the chromosome or contig on which the variant appears is shown in GFCHROM. The published symbol for the gene of interest is shown in GFSYM. The description of the type of genomic entity that is represented by the published symbol in GFSYM is shown in GFSYMTYP as GENE WITH PROTEIN PRODUCT. The location within a sequence for the observed value in GFORRES is shown in GFGENLOC. The filename and/or path to external data not stored in the same format and possibly not the same location as the other data for a study is shown in GFFXN.
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In this example an insertion was found for the BAP1 gene and a deletion was found for the CYP2D6 gene. The identifier for the genome reference used to generate the reported result is shown in GFGENREF. The designation (name or number) of the chromosome or contig on which the variant appears is shown in GFCHROM. The published symbol for the gene of interest is shown in GFSYM.
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The description of the type of genomic entity that is represented by the published symbol in GFSYM is shown in GFSYMTYP as GENE WITH PROTEIN PRODUCT. The location within a sequence for the observed value in GFORRES is shown in GFGENLOC. The filename and/or path to external data not stored in the same format and possibly not the same location as the other data for a study is shown in GFFXN.
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| Row 3: | Shows the predicted coding sequence change based on sequence analysis of the genomic variation in the BAP1 gene . The identifier for the genome reference used to generate the reported result is shown in GFGENREF. The designation (name or number) of the chromosome or contig on which the variant appears is shown in GFCHROM. The published symbol for the gene of interest is shown in GFSYM. The description of the type of genomic entity that is represented by the published symbol in GFSYM is shown in GFSYMTYP as GENE WITH PROTEIN PRODUCT. The location within a sequence for the observed value in GFORRES is shown in GFGENLOC. The filename and/or path to external data not stored in the same format and possibly not the same location as the other data for a study is shown in GFFXN. | Row 4: | Shows the read depth, the total number of times the BAP1 gene locus was sequenced. The identifier for the genome reference used to generate the reported result is shown in GFGENREF. The designation (name or number) of the chromosome or contig on which the variant appears is shown in GFCHROM. The published symbol for the gene of interest is shown in GFSYM. The description of the type of genomic entity that is represented by the published symbol in GFSYM is shown in GFSYMTYP as GENE WITH PROTEIN PRODUCT. The location within a sequence for the observed value in GFORRES is shown in GFGENLOC. The filename and/or path to external data not stored in the same format and possibly not the same location as the other data for a study is shown in GFFXN. | Row 5: | Shows the variant read depth/read depth, the relative measurement of the variant read depth to total read depth of the BAP1 gene locus, as a percentage. The identifier for the genome reference used to generate the reported result is shown in GFGENREF. The designation (name or number) of the chromosome or contig on which the variant appears is shown in GFCHROM. The published symbol for the gene of interest is shown in GFSYM. The description of the type of genomic entity that is represented by the published symbol in GFSYM is shown in GFSYMTYP as GENE WITH PROTEIN PRODUCT. The location within a sequence for the observed value in GFORRES is shown in GFGENLOC. The filename and/or path to external data not stored in the same format and possibly not the same location as the other data for a study is shown in GFFXN. | Row 6: | Shows | the variant impact classification, a categorization of the phenotypic or clinical significance of the genomic variation, of the BAP1 and CYP2D6 |
gene Theidentifier for the genome reference used to generate the reported result is shown in GFGENREF. The designation (name or number) of the chromosome or contig on which the variant appears is shown in GFCHROM. The published symbol for the gene of interest is shown in GFSYM. The description of the type of genomic entity that is represented by the published symbol in GFSYM is shown in GFSYMTYP as GENE WITH PROTEIN PRODUCT. The location within a sequence for the observed value in GFORRES is shown in GFGENLOC. The filename and/or path to external data not stored in the same format and possibly not the same location as the other data for a study is shown in GFFXN. | | Rows 2, 7: | Show the predicted amino acid change based |
Row 7: | Shows the predicted amino acid change based on sequence analysis of the genomic variation in the |
CYP2D6 gene. The identifier for the genome reference used to generate the reported result is shown in GFGENREF. The designation (name or number) of the chromosome or contig on which the variant appears is shown in GFCHROM. The published symbol for the gene of interest is shown in GFSYM. The location within a sequence for the observed value in GFORRES is shown in GFGENLOC. The filename and/or path to external data not stored in the same format and possibly not the same location as the other data for a study is shown in GFFXN.BAP1 and CYP2D6 genes respectively. | | Rows 3, 8: | Show |
Row 8: | Shows | the predicted coding sequence change based on sequence analysis of the genomic variation in the BAP1 and CYP2D6 |
gene The identifier for the genome reference used to generate the reported result is shown in GFGENREF. The designation (name or number) of the chromosome or contig on which the variant appears is shown in GFCHROM. The published symbol for the gene of interest is shown in GFSYM. The description of the type of genomic entity that is represented by the published symbol in GFSYM is shown in GFSYMTYP as GENE WITH PROTEIN PRODUCT. The location within a sequence for the observed value in GFORRES is shown in GFGENLOC. The filename and/or path to external data not stored in the same format and possibly not the same location as the other data for a study is shown in GFFXNRow 9: | Shows the read depth, the total number of times the |
CYP2D6 gene locus was sequenced. The identifier for the genome reference used to generate the reported result is shown in GFGENREF. The designation (name or number) of the chromosome or contig on which the variant appears is shown in GFCHROM. The published symbol for the gene of interest is shown in GFSYM. The description of the type of genomic entity that is represented by the published symbol in GFSYM is shown in GFSYMTYP as GENE WITH PROTEIN PRODUCT. The location within a sequence for the observed value in GFORRES is shown in GFGENLOC. The filename and/or path to external data not stored in the same format and possibly not the same location as the other data for a study is shown in GFFXNRow 10: | genes loci were sequenced, for BAP1 and CYP2D6 respectively. | | Rows 5, 10: | Show |
Shows | the variant read depth/read depth, the relative measurement of the variant read depth to total read depth of the |
CYP2D6 gene locus| BAP1 and CYP2D6 genes loci respectively, as |
a percentage Theidentifier for the genome reference used to generate the reported result is shown in GFGENREF. The designation (name or number) of the chromosome or contig on which the variant appears is shown in GFCHROM. The published symbol for the gene of interest is shown in GFSYM. The description of the type of genomic entity that is represented by the published symbol in GFSYM is shown in GFSYMTYP as GENE WITH PROTEIN PRODUCT. The location within a sequence for the observed value in GFORRES is shown in GFGENLOC. The filename and/or path to external data not stored in the same format and possibly not the same location as the other data for a study is shown in GFFXN |
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| Row | STUDYID | DOMAIN | USUBJID | GFSEQGFGRPID | 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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