Genotyping: Help with calling tetranucleotide repeat peaks

Dr N.I.Leaves nleaves at hgmp.mrc.ac.uk
Mon Mar 18 05:55:50 EST 2002


Hi Al'

What do the genotypes look like in other individuals? this doesnt look
like a nuclear family to me, if it was you could determine some of the
genotypes from a haplotype. Why are your genotype bins so much wider for
some alleles rather than others? As always... if in doubt they should the
classed as unknown. Bad genotypes are squillion times worse than missing
ones.

Dont forget... repeats are mutable and as such might not appear truely
Mendelian... at some point they have to change and will appear as bad
inheritance. Also, I have seen  genotypes which are compounded by a rare
ins/del polymorphism which give very strange but correctly inherited
and very rare alleles.

Hope some of this helps...

Best wishes

nick


 On 15 Mar 2002, Alison Brown wrote:

> I'm having problems calling several of the allele peaks of a
> tetranucleotide repeat.  I have pasted a picture of several examples of
> it onto a web site in the hope that someone can help me with it.  Sorry
> about the quality of the picture - it was the best I could do.
>  http://dnaseq.bwh.harvard.edu/problem-tetra.html
>
> The allele in question is 162 - if you can't read the labels that's the
> second peak of the first lane.
>
> Lane 1 - looks good to me for both alleles ( peak sizes 150.08 and 162.00)
> Lane 2 - 2nd peak looks good at 166.93, but what should the peak at
> 163.88 be called as?
> Lane 3 - Main peak is at 161.98 and 2nd at 162.97
> Lane 4 -  Peak is at 162.91
>
> So is this +A addition?  Does this happen to tetra's, I thought it
> happened only to dinucleotide repeats.  Reverse primer has 7 base tail
> to force +A addition.
>
> Any help is great!
> Thanks,
> Alison
>
> --
> Alison Brown
> Laboratory Manager and Technical Director
> Harvard Partners Center for Genetics and Genomics
> High Throughput Genotyping Facility
> Brigham and Women's Hospital
> 221 Longwood Avenue, LM114
> Boston, MA 02115.
>
> Lab Tel: 617 732 5949
> Office Tel: 617 732 5561
> Fax: 617 264 5135
>
>
> ---
>
>

end
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Dr N I Leaves
Mouse Sequencing
MRC HGMP Resource Centre
Hinxton
Cambridge CB10 1SB
tel: 01223 494557 (office) or 01223 494541 (lab)
email: nleaves at hgmp.mrc.ac.uk
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