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.

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.
Row 2, 6:	Show the total number of EGFR probe signals in the nuclei of the counted cells.
Row 3, 7:	Show the calculated ratio of the EGFR probe signals to centromere probe signals.
Row 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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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	-1	SCREENING	-2	6/21/2023	-1
							Copy Number Amplification	CENTROMERE SIGNALS	165
							Copy Number Amplification	GENOME-SPECIFIC TARGET SIGNALS	208
							Copy Number Amplification	COPY NUMBER RATIO	1.3
							Copy Number Amplification	DETECTION	POSITIVE

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Cytogenetic Assessment of Copy Number Amplification