Apicomplexa (Plasmodium spp.) SNP analysis - ploidy

[mstagliamonte]

Dear All,

I am learning SNP analysis to be carried out on Plasmodium parasites. These parasites have a diploid state in the mosquito, but are then haploid in the human host. This makes me think I should use diploid settings when analysing samples from human blood (as I should still have both alleles that were in the mosquito). Also, there may be multiclonal infections in the human host --> more than one variant could be in the blood.
I read a few articles on Plasmodium SNP analysis, but I am not sure which settings were used.

Has anyone of you already worked with similar organims? Can I ask for a free advice?

Thanks for your help and attention
Max

[Embunnik]

Hi Max,

I have never done SNP analysis in Plasmodium myself, but I know that Micah Manary at UCSD (Winzeler lab) has been working on this. I'm sure he'll be willing to help you out.

Evelien

[mstagliamonte]

Hey,

Thanks for your suggestion.

Regards,
Max