challenging sample due to subclonal scnas – prefer 1 st solution
TRANSCRIPT
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Challenging sample due to subclonal SCNAs –Prefer 1st solution
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Extensive subclonal SCNAs – but 1st solution looks correct.
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Possible genome doubling? Unlikely, because of SSNV data – no or few SSNVs at multiplicity=1 in doubled solution (below) – this would imply that no SSNVs occurred between doubling and sampling (unlikely)
Prefer 1st solution
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Prefer 2nd solution – genome doubling does not help explain the SCNAs.Also – 1st solution SSNV multiplicity peak at 1.4 – bad fit.
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A challenging sample due to a small # of subclonal populations having extensive SNCAs – tendency to over-fit with high-ploidy solution.
Notice that solution #1 has allelic balance of 0.17 at CN=3 – this is very unlikely to be real (only expect balance at powers of 2).
Prefer much simpler solution #6 (below)
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OOPS – ABSOLUTE did not find the correct mode – this happens rarely – will be fixed in future releases – for now leave these uncalled.
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Challenging sample – likely a ‘bad’ SNP hybridizationPrefer 2nd solution – lower complexity. Also – excellent multiplicity peaks.
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A challenging sample – extensive apparent subclonal SCNAs / SSNVsPrefer 2nd solution (low ploidy) – due to lower complexity
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A challenging sample: low purity + subclones
Prefer 2nd solution due to LOH peak
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Calling with no SCNAs: SSNVs only
You need to override the ‘non-aneuploid’ status in the calls file (change to ‘1’ in this case). This will be fixed in future version (when SSNVs are present).
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A strange call by ABSOLUTE (oops) – no apparent reason to prefer 1st solution – override to 2nd simpler solution.
Hopefully fixed in future version.
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Some unusual Karyotypes –
Near haploid genomes (a,b). Uncommon, but found in lung adeno, GBM, stomach cancer, and assorted other cancers.
Hyperploid (>6n) (c)
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Genome doubling or not? Tough call – even with SSNVs.