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This example shows findings from an assessment of a sequence rearrangement with the purpose of determining the characteristics of a fusion event between the BRD4 and MYO10 genes. The identifier for the genome reference used to generate the reported result is shown in GFGENREF. 

Based on the description of this example, it seems that the "predicted in-frame indicator" within row 5 is pointing to BRD4, where GFTSTDTL = 'REARRANGEMENT GENE 1'.

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dataset

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Same comment for GFTSTDTL = 'REARRANGEMENT TYPE' of "truncation".

dataset-wrap
Namegf
Rowcaps
Row 1:

Shows the predicted functional impact

on expression

of the BRD4 and MYO10

genes caused by sequence 

sequence rearrangement.

Row 2:

Shows the first gene, BRD4, involved in the fusion event. 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. 

Row 3:Shows the second gene, MYO10, involved in the fusion event. 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. 
Row 4:

Shows the characterization or classification of the structural changes to the genes as a consequence of the sequence rearrangement BRD4 and MYO10 genes.

Row 5:

Shows the predicted effect of the sequence rearrangement on the original reading

frame

frames of the BRD4

gene.

An indication as to whether the genomic variation product retains the original reading frame, as inferred from the coding sequence.

and MYO10 genes.

Row 6:Shows the read depth, the total number of times the locus of the fusion event was sequenced.
Dataset2
RowSTUDYIDDOMAINUSUBJIDGFSEQGFGRPIDGFREFIDGFTESTCDGFTESTGFTSTDTLGFORRESGFORRESUGFSTRESCGFSTRESNGFSTRESUGFGENREFGFCHROMGFSYMGFSYMTYPGFGENLOCGFXFNGFNAMGFSPECGFMETHODVISITNUMVISITVISITDYGFDTCGFDY
1GR123GF1000011TRF001338SEQREARSequence Rearrangement

REARRANGEMENT IMPACT CLASSIFICATION

likely pathogenic
likely pathogenic

GRCh37.75



/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
2GR123GF1000021TRF001338SEQREARSequence RearrangementREARRANGEMENT GENE 1BRD4
BRD4

GRCh37.7519BRD4GENE WITH PROTEIN PRODUCT15383893-15384049/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
3GR123GF1000031TRF001338SEQREARSequence RearrangementREARRANGEMENT GENE 2MYO10
MYO10

GRCh37.755MYO10GENE WITH PROTEIN PRODUCT16724239-16724557/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
4GR123GF1000041TRF001338SEQREARSequence Rearrangement

REARRANGEMENT TYPE

truncation
truncation

GRCh37.75



/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
5GR123GF1000051TRF001338SEQREARSequence Rearrangement

PREDICTED IN-FRAME INDICATOR

unknown
unknown

GRCh37.75



/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252
6GR123GF1000061TRF001338SEQREARSequence RearrangementREAD DEPTH45
4545
GRCh37.75



/compbio/analysis/120718_SN855_0084_AD13D5ACXX_LCNL-361/sampleAnalysis/sample18.TRF001338.01/TRF001338.01.vars.final.xmlACME XYZDNATARGETED GENOME SEQUENCING1SCREENING12022-01-252