Hi,
We do find tetranucleotide repeats having alleles with 1 or 2 base
pair difference . So it's not always a +A addition. In the 3rd lane
of your example the peak is wider than in the 1st lane; small peak at
161 and high ones at 162 and 163. If you look in the 1st lane there
is a small peak at 161 and a high one at 162. In lane 1 I would
consider 162 as being the +A of 161;(so homozygote 162). In the 3rd
lane though trere's an extra peak and I would say this is a
heterozygote 162/163. You often see an extra peak 4 bp smalleer than
the "real" peak. You can see this in the 4th lane and in the 3rd lane
you can clearly see 2 small peaks (at 158 and 159), supporting this
being a heterozygote.
Because of the bad quality of the picture and the small number of
samples I wouldn't rely on it. Typing more samples and also taking
along CEPH controll samples gives more certainty.
Another thing is that you also have an allele at 164; so this makes
162, 163 and 164. I definitely would check your internal lanestandard
because this can ruin your sizecalling.
Good luck,
Alfons
>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
>**************************************************
>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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