Re-curate arm-level CNA as discrete generic assay data

[jjgao]

Currently, the arm-level CNA data in TCGA PanCancer Atlas studies are curated as clinical attributes (Figure 1). It would be good to re-curate them into generic assay format, for example:

ENTITY_STABLE_ID	NAME	DESCRIPTION	TCGA-xx-xxx1	TCGA-xx-xxx2	TCGA-xx-xxx3
1p	1p	Copy number status of 1p	gained	diploid	lost
1q	1q	Copy number status of 1q	lost	diploid	lost
2p	2p	Copy number status of 2p	diploid	gained	NA
2q	2q	Copy number status of 2q	NA	gained	gained

The current values (Figure 2) can be mapped:

• Gained -> gained
• Lost -> lost
• Not Called -> diploid

Figure 1

Figure 2

[jjgao]

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