missing alleles?

Robert Whittier rfwhittier at hotmail.com
Thu Nov 14 21:17:51 EST 2002


Well, I've no idea whether bad paternity should account for 12%
discrepancies, (do you see this with other SNP diagnostics or
SNP loci?) and I have never used the SnuPe kit, but another
possibility is that your amplification method prior to SNP
diagnosis might be biased. For example, if you are amplifying by
PCR, either or both amplification primers might themselves lie on
top of SNP sequences. This could result in a false diagnosis of
SNP homozygosity, when in fact a parent is heterozygous.

Bob

>>Has any of you ever encountered such a problem: We typed a big series of 
>>families for a SNP somewhere in genome using MegaBace's SnuPe Kit 
>>(minisequencing). About 12 % of families turned to be somehow problematic. 
>>It looked like that the child wouldn't belong to the family, because the 
>>genotypes of parents and child didn't match. For example a child of CC 
>>father and TT mother might have been CC or TT or the child of CC father 
>>and CT mother might have been TT. The samples haven't been mixed and the 
>>findings were repetead with sequencing with 2 different sequencers.
>
>
>12%? a little low maybe but within the bounds of children sired by men not 
>assumed to be their fathers. How many of your anomalous results have 
>alleles not present in the mother? or are they all alleles not present in 
>the father?
>







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