Question

Amount of mappable circulating DNA

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9.9 years ago

Phil S. ▴ 700

Hi guys,

Does any one of you have an Idea / a link to a reference how much of circulating DNA should be mappable to the human reference genome (at the moment I don't care which version of it).

Thanks, in advance!

Best,
Phil

mapping human DNA • 2.0k views

ADD COMMENT • link updated 2.4 years ago by Ram 43k • written 9.9 years ago by Phil S. ▴ 700

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If the dna source is human, it will map like any other. If the dna source is non-human, that will probably vary a lot on a case-by-case basis.

ADD REPLY • link 9.9 years ago by karl.stamm 4.1k

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so basically you mean that you are able to map like 95% of reads coming from human CNAPS to the human reference genome?

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 9.9 years ago by Phil S. ▴ 700

Ram · Answer 1 · 2014-07-27

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9.7 years ago

mikhail.shugay 3.5k

Hello!

I believe the answer to your question has a strong dependence on sample quality and source (serum/plasma) and library preparation procedure.

The literature contains some info on your question. See e.g. this paper, especially Table 2 with around 10% unaligned and 20% ambiguously mapped sequences

ADD COMMENT • link updated 2.4 years ago by Ram 43k • written 9.7 years ago by mikhail.shugay 3.5k