Has anyone reproduced the result of the ABSOLUTE?
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7.3 years ago
chocls ▴ 10

Hello,

I have tried reproducing the result of the ABSOLUTE. I failed to run SNPFileCreator and HAPSEG with TCGA GBM Affy SNP6.0 dataset. So I tried APT with HAPSEG 1.1.1 and ABSOLUTE 1.0.6 but tumor purity is significantly different from the supplementary table. Any comments are highly appreciated.

absolute hapseg • 2.2k views
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Which publication do you mean?

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It means Absolute quantification of somatic DNA alterations in human cancer, doi: 10.1038/nbt.2203

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6.3 years ago
shlee ▴ 60

The GenePattern site has example data for use in the original HAPSEG-ABSOLUTE workflow. Perhaps you can start with this.

ABSOLUTE.summarize and ABSOLUTE.review are an integral part of the ABSOLUTE workflow. It should be clarified that ABSOLUTE provides a number of mathematically computed models of purity and ploidy that it ranks for you based on the combined likelihoods stemming from copy ratios data, mutation data (if provided), and matched reference karyotype. Researchers are expected to manually review the provided solutions and select the most reasonable one, which isn't necessarily the top ranked solution provided by ABSOLUTE. For example, if a sample is from a solid tumor versus metastasized tumor, you probably have an idea of the expected tumor fraction of the sample, e.g. higher for the solid tumor sample than the metastasized sample, that then you would keep in mind when weighing the provided solutions. You modify ABSOLUTE.summarize's calls file to override the top ranked solution with your choice of solution and provide this to ABSOLUTE.review for finalized results.

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It has been a long time so I might be wrong. The pipeline in GenePattern did not support allele specific option for SNP 6.0. I have no idea whether the pipeline has been updated or not.

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