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Sizing STRp alleles.

Robyn Wallace rwallace at mad.adelaide.edu.au
Mon Apr 17 18:40:30 EST 1995

John Maris wrote:

>I am planning on haplotyping a few families at one chromosomal location
>with a panel of tetranucleotide repeat polymorphisms.  It is not clear to
>me what to use as a DNA size marker.  I would like to accurately size the
>alleles to look for the frequency of rare alleles.
>Any suggestions?  Thanks.

The best marker to use is a sequencing reaction.  A known sequence run
against your STRs on a denaturing polyacrylamide gel will give you the
exact length of your alleles.  You only need to do this once, then prepare
an allelic ladder by mixing samples with different length alleles.  This
should provide you with an accurate marker containing all the expected
length alleles.  Rare alleles such as very large, very small and those
whose lengths vary by more or less than 4bp can be easily detected.

If you have access to an ABI automated sequencer (and plenty of money)
genotyping can be carried out using the GeneScan software.  This
automatically determines the lengths of alleles by comparing them to a
known standard.

Robyn Wallace
Department of Cytogenetics and Molecular Genetics         /\_/\
Womens and Childrens Hospital                            ( o o )           
North Adelaide, South Australia  5006                     > - <
Ph  61 08 204 6442
Fax 61 08 204 7342
Email  rwallace at mad.adelaide.edu.au

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