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Archiver > GENEALOGY-DNA > 2003-11 > 1068442709


From: "Nancy Custer" <>
Subject: RE: [DNA] Measurement of fragment lengths
Date: Sun, 9 Nov 2003 21:38:29 -0800
In-Reply-To: <002101c3a724$272037f0$a3f18690@pc>


I don't know if Malcolm's example was from an actual report or a
hypothetical example. I think it is rare to have a non-integer result.
Butler, et al in NOVEL MULTIPLEX FOR SIMULTANEOUS AMPLIFICATION OF 20 Y
CHROMOSOME STR MARKERS Sept 10, 2002 issue of Forensic Science
International, pp. 10-24 report only three such instances out of 1036
markers from 74 individuals.
http://www.cstl.nist.gov/biotech/strbase/y20plex_files/REPRINT.pdfm

It could be the result of a variant allele. A variant allele is an STR
allele with an incomplete repeat. For example a 9.3 would mean 9
repeats of a four nucleotide "motif" plus 3 nucleotides of a tenth
repeat where one nucleotide has been lost by deletion (a kind of
mutation.) I don't know what an 11.46 or 11.44 would represent.

I think that non-integer results could also be the result of "stutter"
in the PCR reaction but that type of error should be corrected during
primer design so that it wouldn't be a problem in practical application.

I'm not really clear about the circumstances of the results that Malcolm
is reporting nor how frequently he has found it. I do not think it is a
serious concern for project administrators but maybe Max or Bennett or
Alastair can elaborate.

Nancy

-----Original Message-----
From: Fred Vines [mailto:]
Sent: Sunday, November 09, 2003 4:47 PM
To:
Subject: Re: [DNA] Measurement of fragment lengths

Malcolm I wish I hadn't read this, you have now made me doubt my
simplistic understanding of what this DNA for
genealogy is all about. Even re-reading Nancy Custers excellent Contexo
website is starting to convince me that I
need a little more than the uneducated grey matter I'm stuck with. I
have been cruising along thinking that the
test results are integer numbers of the replicates at each marker
position. If the tests determine a number to 2
decimals what is this measuring? How do fragment lengths become involved
in counting the number of replicates? Why
would FTDNA feel the need to round off such results if it causes us to
then see a mutation, for a difference of
0.02? Nancy, HELP!
Fred Vines


----- Original Message -----
From: "Malcolm Dodd" <>
To: <>
Sent: Sunday, November 09, 2003 11:53 PM
Subject: [DNA] Measurement of fragment lengths


> Others with more technical expertise will be able to comment on a
perceived
> problem.
> When two cousins have DNA STR markers which are measured at say
> Male A 11.46
> Male B 11.44
> the group administrator would be unaware of this information as it
would
> probably be reported as
> Male A 11.46 = 11.5 = 12
> Male B 11.44 = 11.4 = 11
> a one-step difference.
> Non-experts such as myself tend to treat the results from the
laboratories
> as "gospel truth" but it is not necessarily that simple and we may
well make
> assumptions about the genetic distance and MRCA on a false assumption.
> Malcolm
>
> ______________________________



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