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Is there a way to identify mixed samples based on SNPs?

Example input (table of genotypes for multiple samples):

|      | sample1 | sample2 | sample3 |
|------|---------|---------|---------|
| rs1  | AA      | BB      | AB      |
| rs2  | AA      | BB      | AB      |
| rs3  | AA      | BB      | AB      |
| rs4  | AA      | BB      | AB      |

Desired output: Sample relationships/distances. In this example, sample1 and sample2 are distinct, but sample3 is likely a mix of two (biological or technical).

Based on this simple example, the calculation seems doable, but maybe it's impossible in more complex realistic scenarios.

There is a nice tool peddy that does something conceptually similar, but it expects pedigree information as well as genotype frequencies for both the input samples and population.

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  • $\begingroup$ I updated the question. I didn't initially realize it was not clear. $\endgroup$
    – burger
    Sep 15, 2018 at 1:48
  • $\begingroup$ Thanks, but this still remains a question that is mostly without context. What is the specific problem that you are trying to solve? As presented here, those samples could be individuals and the problem is a phasing problem, rather than mixed groups. What platform is being used to carry out the genotyping? How far away from each other are the variants? $\endgroup$
    – gringer ♦
    Sep 15, 2018 at 5:19

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Yes. The general term for identifying subsets from a mixed group is deconvolution.

This is easier to do when there is haplotype-level information available (e.g. sequenced reads that span multiple SNPs), but it is possible to get some indication of sample mixes from unlinked SNPs alone.

Deconvolution is helped a lot by having proportional data in the input (e.g. frequencies of genotypes, rather than a single genotype). Most SNPchip platforms have multiple probes per variant, and can provide some indication of variant proportion when digging down into the raw data. Deconvolution is also a lot easier with some knowledge about the component mixes. It's much easier to simulate mixes than to guess at possible mixes.

Here's a paper about the application of deconvolution in forensics.

Here's a paper about a program called CIBERSORT which carries out a deconvolution of immune populations based on gene counts:

Here's another paper which discusses the idea in more general terms.

You might find more information on one of these Biostars posts:

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  • $\begingroup$ I am familiar with the expression-based deconvolution, but that's a different problem. And you can have the same mix of cell populations regardless of how many individuals are mixed in a single library. Do you have any suggestions for SNP-based deconvolution? $\endgroup$
    – burger
    Sep 14, 2018 at 19:29
  • $\begingroup$ Could you please clarify this in your question. It's not clear how much research you've done on this already, and whether or not you have haplotype-level information available. $\endgroup$
    – gringer ♦
    Sep 14, 2018 at 23:12

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