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'.
Would it be possible to indicate within the SDTM dataset that GFTSTDTL = 'PREDICTED IN-FRAME INDICATOR' is pointing to the gene specified in "rearrangement gene 1"? (that "rearrangement gene 1" is almost the anchor gene?)
Same comment for GFTSTDTL = 'REARRANGEMENT TYPE' of "truncation".
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| Row 1: | Shows the predicted functional impact |
on expression genes caused by sequence | | 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 frames of the BRD4 and MYO10 genes. | | Row 6: | Shows the read depth, the total number of times the locus of the fusion event was sequenced. |
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| Row | STUDYID | DOMAIN | USUBJID | GFSEQ | GFGRPID | 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 | 1 | TRF001338 | SEQREAR | Sequence Rearrangement | REARRANGEMENT IMPACT CLASSIFICATION | likely pathogenic |
| likely pathogenic |
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| GRCh37.75 |
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| /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 | 1 | TRF001338 | SEQREAR | Sequence Rearrangement | REARRANGEMENT GENE 1 | BRD4 |
| BRD4 |
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| GRCh37.75 | 19 | BRD4 | GENE WITH PROTEIN PRODUCT | 15383893-15384049 | /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 | 1 | TRF001338 | SEQREAR | Sequence Rearrangement | REARRANGEMENT GENE 2 | MYO10 |
| MYO10 |
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| GRCh37.75 | 5 | MYO10 | GENE WITH PROTEIN PRODUCT | 16724239-16724557 | /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 | 1 | TRF001338 | SEQREAR | Sequence Rearrangement | REARRANGEMENT TYPE | truncation |
| truncation |
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| GRCh37.75 |
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| /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 | 1 | TRF001338 | SEQREAR | Sequence Rearrangement | PREDICTED IN-FRAME INDICATOR | unknown |
| unknown |
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| GRCh37.75 |
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| /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 | 1 | TRF001338 | SEQREAR | Sequence Rearrangement | READ DEPTH | 45 |
| 45 | 45 |
| GRCh37.75 |
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| /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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