Cytogenetic Assessment of Copy Number Amplification

Tags: FISH, EGFR, Cytogenetic, cytogenetics

This example is currently in draft.

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.

Units need to be confirmed. Should we have a value for chromosome. GENSR is this applicable or needed (e.g., for exon)

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gf.xpt

Row	STUDYID	DOMAIN	USUBJID	GFSEQ	GFREFID	GFTESTCD	GFTEST	GFTSTDTL	GFORRES	GFORRESU	GFSTRESC	GFSTRESN	GFSTRESU	GFSYM	GFSYMTYP	GFNAM	GFSPEC	GFMETHOD	GFANMETH	VISITNUM	VISIT	VISITDY	GFDTC	GFDY
1	ABC0023	GF	AB23-001	1	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
2	ABC0023	GF	AB23-001	2	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	-1	SCREENING	-2	6/21/2023	-1
3	ABC0023	GF	AB23-001	3	45785-01	CPNUMAMP	Copy Number Amplification	CENTROMERE SIGNALS	147	PLACEHOLDER	147	147	PLACEHOLDER	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	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

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Cytogenetic Assessment of Copy Number Amplification