Archiver > GENEALOGY-DNA > 2009-05 > 1242683902

Subject: Re: [DNA] DNA Test Panel Options
Date: Mon, 18 May 2009 14:58:22 -0700
References: <COL109-W37D678E90721F40C80E06CDE5A0@phx.gbl>
In-Reply-To: <COL109-W37D678E90721F40C80E06CDE5A0@phx.gbl>

There are currently around 900 Y-SNPs (counting duplicate names) whose positions are known on the Y-DNA phylogenetic tree. This is only a small fraction of the thousands known on the Y-chromosome. The problem (in my opinion) is that we don't where all these "other" SNPs should be placed on the tree. The true hierarchial structure of these "other" SNPs requires extensive testing of individuals. Some geneticists estimate that, on average over the entire human genome, there's one SNP for every 500 nucleotide pairs. With the Y-chromosome having about 57.7 million nucleotide pairs, that means there must be a huge number of Y-SNPs yet to be analyzed.

There seems to be no correlation between the position of a SNP on the Y-chromosome and the position of other SNPs that would add an additional twig to the Y-tree. So, for example in a "Walk on the Y", it's not possible to select a segment of the Y-chromosome that will give a higher probability than other segments for finding SNPs to further subdivide a subclade (say of the I or R haplogroup). To me, it seems similar to throwing darts at a stock market page to select stocks. The odds of success with a walk on the Y may not be too good, but with current technology, it may be best way to proceed.

From: George Chandler<mailto:>
To: <mailto:>
Sent: Monday, May 18, 2009 2:11 PM
Subject: [DNA] DNA Test Panel Options

Richard wrote:

"It's not a problem of number crunching. It's doing the lab procedures using special reagents and expensive equipment. E.g, the first step Marligen gives is to extract DNA from a buccal sample. The next step is amplification by PCR, followed by other steps. To do just these first two steps would require using certain reagents to do the extraction. To do PCR, you would at least need a thermal cycler. Later steps require even more expensive equipment."

Ok I think I understand what you're saying..and I have to admit I'm not expert on the exact "extraction" process in this case. Companies such as "23andMe", "Marligen" etc contract out to them (Illumina)for their desired bead chip testing. This being stated though..these companies are only looking for "known" SNP mutations which have already been found..correct? Let's say that there are 4 mutations thought to be located downstream of L21 - then these companies may test for that through Illumina. What I'm looking for is the mutations (if any) located downstream of my specific L21 mutation which have not been found.

Let me know if I'm off base here..over even in the right ball park.

George Chandler

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