Archiver > GENEALOGY-DNA > 2002-03 > 1015863118

Subject: Re: [DNA] basic concept help needed
Date: Mon, 11 Mar 2002 11:12:00 EST

In a message dated 03/07/02 10:56:59 AM Pacific Standard Time,

> 2) Y-chromosome research, I understand, does not test individual base
> pairs, but rather tests regions on the Y-chromosome (between 12-24) and
> how many times each region (called haplotypes?) repeats its base
> sequence. Although there is no standard, eventually they will have
> enough sequences to possibly create a standard? Also, do I understand
> correctly, that Y-chromosome testing isn't as specific and does not
> theoretically trace as far back in time as the mtDNA sample because they
> don't check for individual base pairs yet (as they do for mtDNA)? This
> must be because they don't know as much about the Y-chromosome as they
> do about the mtDNA yet?

Haplotype in this context means the results on a set of markers (10-23
markers are currently offered by commercial DNA testing companies). Each
marker has a name, e.g. DYS390, DYS392, and each marker is known to have a
range of values for the number of repeats (alleles). Often times you will see
a haplotype written out as 14-12-23-11-13. One thing which is confusing is
that different companies and research articles use different STRs, and even
if they use the same STRs, they don't always print them out in the same
order. So if you want to share your results with someone, it's always
important to label the STR names.

I rather doubt there will ever be a Y chromosome reference sequence
comparable to the Cambridge Reference Sequence for mitochondrial DNA. mtDNA
only has 16,569 bases (with a trivial amount of variation in length) while
the Y chromosome has ~59 million bases, with much variability in length due
to insertions and deletions. When I went to NCBI (National Center for
Biotechnology Information) to check what the length was, I was surprised to
see how little of the Y chromosome (less than half) has been sequenced. I
thought the human genome project was "complete!";

BTW, there's nothing special about the Cambridge Reference Sequence -- it's
just the sample which happened to be used the first time they succeeded in
determining the whole sequence. There's even some controversy about whether
it is the sequence from one or several persons, but from what I understand,
it is in fact one person, for the hypervariable region at least (the part
used by genealogical testing companies).

As far as being "specific" -- mtDNA sequences may stay the same for longer
periods of time, hundreds or even thousands of years, whereas you are likely
to find a change in at least one of the 10-23 Y STRs tested within a
genealogical time frame. This is actually helpful in defining branches of a
family, so in that sense, the Y chromosome tests are more specific. However,
mtDNA tests typically cover 400 bases, each of which has the potential for a
point mutation, so there's quite a bit of diversity in mtDNA haplotypes.

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