Hi,
I was looking at OmicsAbsoluteCNGene values (24Q4) for the gene DCC on chromosome 18q, in relation to the segment value in OmicsAbsoluteCNSegmentsProfile (also 24Q4). For cell line ACH‑000679 (profile ID PR-pjbPYg), I am finding that the OmicsAbsoluteCNGene = 1, but if you map the gene coordinates for DCC into the segments file, OmicsAbsoluteCNSegmentsProfile would predict that the segment to which DCC maps onto has a SegmentAbsoluteCN of 2 and an LoHStatus of being copy-neutral LOH.
The genomic coordinates for DCC are chr18:52340197-53535899 (hg38) or chr18:49866567-51062269 (hg19). I’m not sure what mapping was used to generate the OmicsAbsoluteCNGene values, but both the hg19 and hg38 coordinates map to a region of SegmentAbsoluteCN = 2 in the segment file. My first thought was that the discrepancy was just due to me using different genomic coordinates than what was used in the original pipeline. However, I’m not sure the exact genomic coordinates that were used in the original pipeline are available as a source file (please direct me there if that is available!).
Any help on understanding how the OmicsAbsoluteCNGene calls were made would be helpful. For context, for my research project it would be very important to distinguish between copy-neutral LOH and copy-deletion LOH.
