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.
gf.xpt
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
-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
-1
2023-06-21
-2
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
-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
7p11.1-q11.1
ACME GENOMICS LABS
DNA
FISH
-1
SCREENING
-1
2023-06-28
-1
6
ABC0023
GF
AB23-002
2
78678-01
CPNUMAMP
Copy Number Amplification
GENOME-SPECIFIC TARGET SIGNALS
208
/50 Cells
208
208
/50 Cells
7
EGFR
GENE WITH PROTEIN PRODUCT
ACME GENOMICS LABS
DNA
FISH
-1
SCREENING
-1
2023-06-28
-1
7
ABC0023
GF
AB23-002
3
78678-01
CPNUMAMP
Copy Number Amplification
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
7
EGFR
GENE WITH PROTEIN PRODUCT
ACME GENOMICS LABS
DNA
FISH
COLORADO SCORING METHOD FOR EGFR GENE AMPLIFICATION 2009 ALGORITHM