Why Are Monomorphic Loci Excluded From Analysis?

Question

[714]

As the title suggest, I was wondering why it is a good idea to exclude monomorphic loci from SNP analysis. How would including them affect a PCA plot for example?

Answer 1

[Fabio Marroni]

In my understanding, monomorphic means something that appears in just one state (or form), in contrast to polymorphic that means something that appears in more than one form. SNPs are by definition polymorphic. A monomorphic site is one site in which all the individuals have the same form (genotype). It is a good idea to exclude it from analysis because it gives no information. Please, note that you implicitly always exclude from analysis the majority of the 3 billion positions of the human genome for which you find no variation.

[714]

Would there be any harm in keeping monomorphic loci in the dataset given that they do not seem to contribute to any of the variation that we might see?

[Fabio Marroni]

As Josh already said, it does no harm in terms of results (they are uninformative), but it wastes computer time.

Answer 2

[Josh Herr]

You would inflate your SNP numbers and misrepresent your data.

How would you differentiate between a sequencing error, one-off single mutation or transcription error, and a bona-fide SNP? SNPs are found across individuals in a population -- monomorphic loci represent one individual's nucleotide state and may be the result of errors across numerous levels. When you see a SNP in multiple individuals you can infer it is not from sequencing error or a mutation found in a single individual.

[714]

That makes some sense, howeforver I'm afraid I don't quite understand all of it. For example, if 100 individuals were gentyped at loci A-D and all were homozygous C/C at locus A, then why would one exclude locus A from the dataset and subsequently, analysis?

[Josh Herr]

In your example, locus A would be not informative and it would be pointless to leave that nucleotide alignment position in the analysis -- it would provide you with no information and would also waste compute time (meh, probably negligible). You would want to remove uninformative characters -- this would include non-variable sites as well as monomorphic sites (one "mutation" and not a SNP) or highly variable sites.

Answer 3

[blacktomato27]

Hi, How to consider heterozygous allelic state of parents in polymorphism analysis, for example SNP1 SNP2 SNP3 p1 AA AT AA p2 AA AA TT here i want to see polymorphism between p1 and p2, This is my expected results SNP1 SNP2 SNP3 p1 mono ? poly p2
Thanks in advance

[Josh Herr]

I don't quite understand your question? (This isn't an answer by the way, so it should be placed as an additional question in a new thread). Are you asking how to differentiate between heterozygosity and SNP polymorphisms?