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13 months ago
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I have run Absolute on tumour SNP data and I have not found an explanation of what the headers of the output files exactly mean. I would very much appreciate help to interpret the meaning of columns copy_ratio, modal_cn, subclonal and hz.

Input segmented values I have given as input to run ABSOLUTE:

Sample Chromosome Start End Num_Probes Segment_Mean

Sample1 1 82154 1222895 316 0.0342

Output from absolute: sample Chromosome Start.bp End.bp n_probes length seg_sigma W copy_ratio modal_cn expected_cn subclonal cancer_cell_frac ccf_ci95_low ccf_ci95_high hz

34_T_SF 1 82154 1222895 316 1140741 0.00703 0.00039 0.51199 2 2.00000 0 1 1 1 0

To get copy ratio, we calculate 2^Segment_Mean, which for the probe with Segment_Mean -0.133 should be 1.0234, but ABSOLUTE computed it as 0.5 * 2 ^ Segment_Mean.

The modal_cn column represents the absolute copy number of a particular genomic location? If so, I am not sure how to interpret absolute copy number values in the context of ploidy of a cell. In case of a diploid genome, I was doing the bellow interpretation for modal_cn values:

0-homozygous deletion

1- heterozygous deletion

2- wt allele

3-heterozygous amplification

4-homozygous amplification

But then, assuming the above interpretation is correct, how would a 5 in absolute copy number value be interpreted as? Would it be the case for aneuploid cases that have had genome doubling events, and thus have another copy of that allele?

snp sequence R genome • 412 views