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From:
Subject: Re: [DNA] FTDNA read the wrong strand on an HVR2 mtDNA test [not the case]
Date: Mon, 3 May 2004 17:37:54 EDT


In a message dated 05/02/04 11:44:10 PM Pacific Daylight Time,
writes:

> But then I noticed that for HVR2, most of Betty's values were the opposite
> of mine. For example, mine is 73G and hers is 73A. I should also mention that
> the DNA molecule is two strands and when they machine read the sequence,
> they are reading off only one strand. The other strand will have different, but
> predictable readings. For example, wherever one strand has a G, the other
> will have an A. Similarly, where one has a T, the other will have a C. I noticed
> that for most of the values, your Betty's had the complimentary value to
> mine. So I suspect that perhaps FTDNA read the wrong strand. If so, then your
> Betty and I are very similar. We are not certain matches only on three values.
> But since the first two (309.1 and 315.1) of these are insertion mutations
> instead of point mutations, the fact that FTDNA might have been reading the
> wrong strand might have thrown the computer off enough that it did not recognize
> it was on an insertion and perhaps the nucleotides it did read in !
> that region tricked the computer into "thinking" that some standard value
> was there. If 309.1 is off, then 315.1 might also be off. So might the point
> mutation of 489 be off.


Not to worry -- FTDNA and all the other labs read the mtDNA molecule in a
standardized way. They use primers which amplify only one strand. Actually, the
complementary pairs are A-T and G-C.


> And then I checked the big mtDNA concordance. So far (i.e. 1998), not a
> single person in the world has been discovered to by 73G or 150C. When I saw
> that, I knew they read the wrong strand.

The Concordance only lists differences from the Cambridge Reference Sequence,
which is 73A and 150C. Thus the Concordance will have entries for anything
which is not the same, e.g. 73G and 150T. Theoretically, A could change to G or
T or C, but in practice, the vast majority of A's change to G. This is because
A and G most closely resemble each other in size. As you can see on Nancy
Custer's website, A and G both have three "ring structures," while C and T have
two.

http://www.contexo.info/DNA_Basics/Nucleic_Acids_(DNA).htm

When the bases are pairing with each other on the complementary strands,
every "rung" of the ladder pairs a big molecule and a little molecule, so the
width of the rungs are constant.

As far as insertions are concerned, they would throw the sequence out of
alignment for a very large number of positions. There's probably a computer
program to realign the sequence once it sees that happening, although I used to see
technical papers saying that sequences were manually aligned.

Ann Turner - GENEALOGY-DNA List Administrator
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