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This example shows findings from a cytogenetic assessment of EGFR gene copy number amplification with the purpose of determining the diagnostic status of patients with non-small cell lung cancer. In this example, the findings are generated using fluorescence in situ hybridization (FISH) methodology and semi-quantitative microscopic assessment by a pathologist. Microscopic assessments are then summarized to a diagnostic status using a specific algorithm represented in GFANMTH.
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| Rows 1, 5: | Show the total number of centromere probe signals in the nuclei of the counted cells associated with the location represented in variable GFGENLOC for chromosome 7. | | Rows 2, 6: | Show the total number of EGFR probe signals in the nuclei of the counted cells. | | Rows 3, 7: | Show the calculated ratio of the EGFR probe signals to centromere probe signals. | | Rows 4, 8: | Show the EGFR amplification status of the sample according to the 2009 Colorado Scoring Method for EGFR Gene Amplification Algorithm. |
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Units need to be confirmed. Should we have a value for chromosome. GENSR is this applicable or needed (e.g., for exon) | Rowcaps |
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| Row 1: | Shows | Row 2: | Row 3: | Row 4: | | Dataset2 |
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| | Row | STUDYID | DOMAIN | USUBJID | GFSEQ | GFREFID | GFTESTCD | GFTEST | GFTSTDTL | GFORRES | GFORRESU | GFSTRESC | GFSTRESN | GFSTRESU | GFCHROM | GFSYM | GFSYMTYP |
GFGENSR | GFSTAT | GFREASND| GFGENLOC | GFNAM | GFSPEC | GFMETHOD | GFANMETH | VISITNUM | VISIT | VISITDY | GFDTC | GFDY | | 1 | ABC0023 | GF | AB23-001 | 1 | 45785-01 | CPNUMAMP | Copy Number Amplification | CENTROMERE SIGNALS | 147 | /50 Cells | 147 | 147 | /50 Cells | 7 |
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| 7p11.1-q11.1 | ACME GENOMICS LABS | DNA | FISH |
| -1 | SCREENING | -1 | 2023-06-21 | -2 | | 2 | ABC0023 | GF | AB23-001 | 2 | 45785-01 | CPNUMAMP | Copy Number Amplification | GENOME-SPECIFIC TARGET SIGNALS | 166 | /50 Cells | 166 | 166 | /50 Cells | 7 | EGFR | GENE WITH PROTEIN PRODUCT |
| ACME GENOMICS LABS | DNA | FISH |
| -1 | SCREENING | -1 | 2023-06-21 | -2 | | 3 | ABC0023 | GF | AB23-001 | 3 | 45785-01 | CPNUMAMP | Copy Number Amplification | COPY NUMBER RATIO | 1.1 |
| 1.1 | 1.1 |
| 7 | EGFR | GENE WITH PROTEIN PRODUCT |
| ACME GENOMICS LABS | DNA | FISH |
| -1 | SCREENING | - |
26/21/2023122| 4 | 45785-01 | CPNUMAMP | Copy Number Amplification | DETECTION | NEGATIVE |
| NEGATIVE |
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| 7 | EGFR | GENE WITH PROTEIN PRODUCT |
| ACME GENOMICS LABS | DNA | FISH | COLORADO SCORING METHOD FOR EGFR GENE AMPLIFICATION 2009 ALGORITHM | -1 | SCREENING | -1 | 2023-06-21 | -2 |
| | 5 | ABC0023 | GF | AB23-002 | 1 | 78678-01 | CPNUMAMP | Copy Number Amplification | CENTROMERE SIGNALS | 165 | /50 Cells | 165 | 165 | /50 Cells | 7 |
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| 7p11.1-q11.1 | ACME GENOMICS LABS | DNA | FISH |
| -1 | SCREENING | -1 | 2023-06-28 |
6/21/20233001345785| 78678-01 | CPNUMAMP | Copy Number Amplification |
CENTROMERE SIGNALS | 147 | PLACEHOLDER | 147 | 147 | | GENOME-SPECIFIC TARGET SIGNALS | 208 | /50 Cells | 208 | 208 | /50 Cells | 7 |
PLACEHOLDER | EGFR | GENE WITH PROTEIN PRODUCT |
| ACME GENOMICS LABS | DNA | FISH |
| -1 | SCREENING | - |
26/21/20234001445785| 78678-01 | CPNUMAMP | Copy Number Amplification |
GENOME-SPECIFIC TARGET SIGNALS | 166 | PLACEHOLDER | 166 | 166 | | COPY NUMBER RATIO | 1.3 |
| 1.3 | 1.3 |
| 7 | EGFR | GENE WITH PROTEIN PRODUCT |
| ACME GENOMICS LABS | DNA | FISH |
| -1 | SCREENING | -1 | 2023-06-28 | -1 | | 8 | ABC0023 | GF | AB23-002 | 4 | 78678-01 | CPNUMAMP | Copy Number Amplification | DETECTION | POSITIVE |
| POSITIVE | POSITIVE |
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PLACEHOLDER | EGFR | GENE WITH PROTEIN PRODUCT |
| ACME GENOMICS LABS | DNA | FISH | COLORADO SCORING METHOD FOR EGFR GENE AMPLIFICATION 2009 ALGORITHM | -1 | SCREENING | - |
26/21/2023 |
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