Question

Detecting aneuploidy in sequencing data or copy number profile?

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4.7 years ago

vctrm67 ▴ 90

Is there a package/way to detect per-chromosome aneuploidy for NGS data or copy number profiles?

ngs • 1.0k views

ADD COMMENT • link updated 4.7 years ago by igor 13k • written 4.7 years ago by vctrm67 ▴ 90

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get the average depth for the whole genome and compare with the depth per chromosome ?

ADD REPLY • link 4.7 years ago by Pierre Lindenbaum 166k

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But let's say I had a whole genome duplication and then one of the chromosomes was subsequently deleted (so 4 copies of each chromosome). By read depth only, everything would still have the same read depth except that one chromosome. Wouldn't it be difficult to distinguish this case from simply aneuploidy of the chromosome without a whole genome duplication because the relative read counts in either case would be the same?

ADD REPLY • link 4.7 years ago by vctrm67 ▴ 90

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Also for whole genome duplication.

ADD REPLY • link 4.7 years ago by vctrm67 ▴ 90

score 0 · Answer 1 · 2020-09-03

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4.7 years ago

igor 13k

A lot of the copy number packages will use BAFs to try to estimate ploidy. The Sequenza paper has a nice figure illustrating how this is possible:

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ADD COMMENT • link 4.7 years ago by igor 13k