sequencing microsatellites

koen de gelas · 07-27-2011, 11:28 PM

Dear all,

I was wondering if any of you have information on sequencing microsatellite repeats (amplicons) on a 454 platform.

Essentially, I would like to get some information on the accuracy when sequencing microsatellite amplicons. Do you get the two alleles (e.g. heterozygotes) in equal proportions or do you get a distribution of several repeat lengths due to pcr-errors? If so, what kind of coverage (50x, 100x) do you need to estimate the "correct" alleles?
And is there any difference between di-, tri, tetra or penta-repeats as you would expect?

I would be gratefull if any of you could point me to some papers on this topic or share your experience.
Thanks!

Note: I do not ask for info on how to use 454 seq to develop new microsats. There are plenty of papers on that.

njbayonav · 08-29-2012, 03:50 PM

Hi Koen,

I am wondering the same thing. Please if you have any information of some labs that have already tried this methodology please let me know. In our lab we are thinking of a pilot project using Illumina for amplicon sequencing. But I would like to know if there is some body that have tryied and pros and cons of the technique, actually for me is strange that no-body has published about this issue.

Thanks for you post and looking forward for any help

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07-27-2011, 11:28 PM	#1
koen de gelas Junior Member Location: leuven Join Date: Jun 2010 Posts: 1	sequencing microsatellites Dear all, I was wondering if any of you have information on sequencing microsatellite repeats (amplicons) on a 454 platform. Essentially, I would like to get some information on the accuracy when sequencing microsatellite amplicons. Do you get the two alleles (e.g. heterozygotes) in equal proportions or do you get a distribution of several repeat lengths due to pcr-errors? If so, what kind of coverage (50x, 100x) do you need to estimate the "correct" alleles? And is there any difference between di-, tri, tetra or penta-repeats as you would expect? I would be gratefull if any of you could point me to some papers on this topic or share your experience. Thanks! Note: I do not ask for info on how to use 454 seq to develop new microsats. There are plenty of papers on that. Last edited by koen de gelas; 07-27-2011 at 11:43 PM.

08-29-2012, 03:50 PM	#2
njbayonav Junior Member Location: Mexico City Join Date: Aug 2012 Posts: 4	Hi Koen, I am wondering the same thing. Please if you have any information of some labs that have already tried this methodology please let me know. In our lab we are thinking of a pilot project using Illumina for amplicon sequencing. But I would like to know if there is some body that have tryied and pros and cons of the technique, actually for me is strange that no-body has published about this issue. Thanks for you post and looking forward for any help