How to standardize microsatellite allele sizes?
vaysseix at genethon.fr
Mon Mar 15 17:36:14 EST 1993
In article <1993Mar11.121736.1 at kean.ucs.mun.ca> tlyoung at kean.ucs.mun.ca writes:
> The practice of genotyping a member of the CEPH collection of families,
>especially when using a microsatellite marker (ie. dinucleotide repeat),
>is a good way to standardize the "sizes" of alleles reported by various
> [...] Weissenbach et al., Nature 359, 794 (1992)
>uses person 134702 (the paper doesn't include the alleles from person
>134702 but they are available by anonymous FTP from Genethon).
> It would be NICE if everyone was using the same reference DNA as a
>standard. Are efforts being made in this direction? If not, what would it
>take to get people to use the same reference DNA?
Reply from Jean Weissenbach (jsbach at genethon.fr) :
> I have read your letter on a uniform standard. It is indeed unfortunate
> that different standards are being used. Let me just give a brief
> Our mapping project started about 3 years ago, when no standard
> existed. One of the first steps was to produce DNA shotgun libraries.
> At that time we realized that we should take a CEPH individual for
> reasons mentionned in your letter. I decided to choose 134702 because
> CEPH had very large amounts of this DNA. We sequenced at least one and
> sometimes both alleles from that individual in our M13 library when we
> developed new microsatellite markers. We therefore know the exact size
> of one or both alleles from that individual. As an additional control
> we run a PCR product of the sequenced M13 clone to compare its size
> with the source DNA. We feel this gives us the most accurate size
> determination and therefore use this individual as a standard. In our
> lab, allele sizes from 133101 and 133102 are only obtained by
> comparison with 134702 and are thus more indirect, I therefore hesitate
> to use these DNAS as standards for our markers.
> The 134702 cell line is available from Camden as item GM10859. Sizes
> from our genotyped individuals including 133101 and 133102 are
> available in version 6 of the CEPH database.
> Yours sincerely Jean Weissenbach
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