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.
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

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	2023-06-21	-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	2023-06-21	-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	2023-06-21	-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	2023-06-21	-1
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	-2	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	-2	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	-2	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	-1	SCREENING	-2	2023-06-28	-1

$warningHtml

Dataset Wrapper Debug Message

Please add a row column to your dataset.

Page tree

Cytogenetic Assessment of Copy Number Amplification