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Subject: [DNA] whole genome scans
Date: Fri, 16 Nov 2007 16:11:48 EST


Clearly we're going to need to study the Illumina set of SNPs (Single
Nucleotide Polymorphisms) in more detail, but here are some pointers just for general
background:

A whole genome SCAN is not the same thing as a whole genome SEQUENCE (which
currently costs about a million dollars and has only been done for Watson and
Venter). It's analogous to the haplogroup H subclade test at FTDNA. You can
order a test for 19 specific SNPs to "scan" the coding region at the locations
that are of special interest (for defining haplogroups in this case) -- or you
can request a complete sequence that gives you the 15,000 some coding region
bases in order. The SNPs in the subclade test are selected because they occur
with some frequency in the general population (often enough to define a
subclade). The complete sequence will pick up "private" mutations as well.

The million SNPs in the Illumina chip are spaced out over the whole genome,
that is, they cover all the chromosomes. They are targeting specific locations
that have already been demonstrated to show variations in some population --
the P in SNP is for polymorphism (poly = many, morph = form).

I contacted the support team at deCODEme this morning. You will receive the
raw data along with reference numbers for the SNPs. Old timers will remember
how we studied some of the SNPs from DNAPrint's Ancestry by DNA test. Here is a
sample listing from dbSNP for one of those. DNAPrint selected it because it
occurred in varying frequencies in different populations (scroll down to see
sample data)

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&;
rs=rs1800498

The SNPs on the Illumina chip are presumably selected for a variety of
reasons, not just population frequencies, but they are pre-selected precisely
because they've been proven to show *some* variation. That makes them more
interesting than the 99.whatever percent of bases that are identical in all human
beings tested to date.

I'm just guessing that deCODEme purchases chips from Illumina in large
quantities for its research, so the general consumer is benefiting from considerable
economies of scale here. There's some interesting background in this article
from Forbes:

http://www.forbes.com/free_forbes/2007/0618/052_4.html?boxes=custom

Ann Turner






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