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.
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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gf.xpt
Row
STUDYID
DOMAIN
USUBJID
GFSEQ
GFREFID
GFTESTCD
GFTEST
GFTSTDTL
GFORRES
GFORRESU
GFSTRESC
GFSTRESN
GFSTRESU
GFCHROM
GFSYM
GFSYMTYP
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
7p11.1-q11.1
ACME GENOMICS LABS
DNA
FISH
-1
SCREENING
-2
6/21/2023
-1
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
-2
6/21/2023
-1
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
-2
6/21/2023
-1
4
ABC0023
GF
AB23-001
4
45785-01
CPNUMAMP
Copy Number Amplification
DETECTION
NEGATIVE
NEGATIVE
7
EGFR
GENE WITH PROTEIN PRODUCT
ACME GENOMICS LABS
DNA
FISH
COLORADO SCORING METHOD FOR EGFR GENE AMPLIFICATION 2009 ALGORITHM