Units need to be confirmed. Should we have a value for chromosome. GENSR is this applicable or needed for CEP-7? Should EGFR and symbol types populated in row 1? Add chromosome?
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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Show variation at a particular allele for the single nucleotide variation identified in GFPVRID. An arbitrary identifier for the allele is represented in GFCOPYID.
Row 1:
Shows the number of centromere probe signals in the nuclei of the counted cells.
Row 2:
Shows the number of EGFR probe signals in the nuclei of the counted cells.
Row 3:
Row 4:
gf.xpt
gf.xpt
Row
STUDYID
DOMAIN
USUBJID
GFSEQ
GFREFID
GFTESTCD
GFTEST
GFTSTDTL
GFORRES
GFORRESU
GFSTRESC
GFSTRESN
GFSTRESU
GFCHROM
GFSYM
GFSYMTYP
GFGENSR
GFSTAT
GFREASND
GFNAM
GFSPEC
GFMETHOD
GFANMETH
VISITNUM
VISIT
VISITDY
GFDTC
GFDY
1
ABC0023
GF
AB23-001
1
45785-01
CPNUMAMP
Copy Number Amplification
CENTROMERE SIGNALS
147
PLACEHOLDER
147
147
PLACEHOLDER
EGFR
GENE WITH PROTEIN PRODUCT
CEP-7?
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
PLACEHOLDER
166
166
PLACEHOLDER
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
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
EGFR
GENE WITH PROTEIN PRODUCT
ACME GENOMICS LABS
DNA
FISH
COLORADO SCORING METHOD FOR EGFR GENE AMPLIFICATION 2009 ALGORITHM