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This example shows findings from an assessment 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 fifty base pairs or less when compared to a reference sequence. 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. 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 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 ECC-11 - Jira project doesn't exist or you don't have permission to view it. 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.

gf.xpt

gf.xpt

RowSTUDYIDDOMAINUSUBJIDGFSEQGFREFIDGFTESTCDGFTESTGFTSTDTLGFORRESGFORRESUGFSTRESCGFSTRESNGFSTRESUGFGENREFGFCHROMGFSYMGFSYMTYPGFGENLOCGFXFNGFNAMGFSPECGFMETHODVISITNUMVISITVISITDYGFDTCGFDY
1GR123GF100001TRF001338SHRTVARShort VariationVARIANT IMPACT CLASSIFICATIONknown
known

GRCh37.753BAP1GENE WITH PROTEIN PRODUCT52438573/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
2GR123GF100002TRF001338SHRTVARShort VariationPREDICTED AMINO ACID CHANGER383fs*15
R383fs*15

GRCh37.753BAP1GENE WITH PROTEIN PRODUCT52438573/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
3GR123GF100003TRF001338SHRTVARShort VariationPREDICTED CODING SEQUENCE CHANGE1145_1146insG
1145_1146insG

GRCh37.753BAP1GENE WITH PROTEIN PRODUCT52438573/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
4GR123GF100004TRF001338SHRTVARShort VariationREAD DEPTH262
262

GRCh37.753BAP1GENE WITH PROTEIN PRODUCT52438573/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
5GR123GF100005TRF001338SHRTVARShort VariationVARIANT READ DEPTH/READ DEPTH20%2020%GRCh37.753BAP1GENE WITH PROTEIN PRODUCT52438573/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
6GR123GF100006TRF001338SHRTVARShort VariationVARIANT IMPACT CLASSIFICATIONunknown
unknown

GRCh37.7522CYP2D6GENE WITH PROTEIN PRODUCT42525085/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
7GR123GF100007TRF001338SHRTVARShort VariationPREDICTED AMINO ACID CHANGEW152fs*2
W152fs*2

GRCh37.7522CYP2D6GENE WITH PROTEIN PRODUCT42525085/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
8GR123GF100008TRF001338SHRTVARShort VariationPREDICTED CODING SEQUENCE CHANGE454_454delA
454_454delA

GRCh37.7522CYP2D6GENE WITH PROTEIN PRODUCT42525085/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
9GR123GF100009TRF001338SHRTVARShort VariationREAD DEPTH162
162

GRCh37.7522CYP2D6GENE WITH PROTEIN PRODUCT42525085/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
10GR123GF1000010TRF001338SHRTVARShort VariationVARIANT READ DEPTH/READ DEPTH51%5151%GRCh37.7522CYP2D6GENE WITH PROTEIN PRODUCT42525085/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
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