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From: "Ian Logan" <>
Subject: [DNA] Are these SNP's tested by deCodeMe ?
Date: Sun, 6 Jan 2008 11:24:28 -0000


List

A few list members have been genetic pioneers and had many
hundreds of thousands SNPs tested by deCodeMe. And I 'salute them'.

But what do they make of their results ? And are they looking for things
to do with their results ?

So for these pioneers here is something they might like to check.

Chr1:554327..560167 corresponds to the "Herrnstadt" NUMT
and there are 32 SNP's; see the list below.
The reference for Herrnstadt's original paper is:
Herrnstadt C, et.al.
A Novel Mitochondrial DNA-like Sequence in the Human Nuclear Genome.
Genomics. 1999 Aug 15;60(1):67-77.

I haven't looked to see if any of the SNPs are included in the set of SNPs
tested by deCodeMe - but no doubt someone will be able to tell me
if they are.

Of the SNPs, rs11497407 chr1:558390 A/G, looks the most
relevant to genealogy as it appears to discriminate 'Europeans'
- and a full study of this SNP might therefore prove to be useful.

If any list wants to follow up on these SNPs, this URL
gives additional data. Search on the region 'chr1:554327..560167'
http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/

Data on individual SNPs can also be found by using the NCBI site at
http://www.ncbi.nlm.nih.gov/sites/entrez
and selecting 'SNP' in the Search box, entering for example 'rs11497407'
in the For box, and pressing Go.

As a point of interest, rs4988647 is also a SNP from another NUMT
and might be useful for African genealogy.
Is this on the deCodeMe list ? And does anyone have this SNP ?

There are possibly several hundreds of SNPs that occur in NUMTs
and I wonder if it would be useful to make up a proper list.

After tomorrow I am going to be off-line for a couple of weeks, but I should
see any quick responses beforehand - if there are any !

Ian

www.ianlogan.co.uk

....................
The 32 "Herrnstadt" NUMT SNPs

Base order:
rs6650104 chr1:554340 A/G
rs11240781 chr1:554395 A/G
rs6594028 chr1:554461 A/G
rs10458597 chr1:554484 C/T
rs9701661 chr1:555134 A/G
rs9701055 chr1:555296 C/T
rs7349153 chr1:555353 C/T
rs7417504 chr1:555800 C/T
rs7340022 chr1:555955 C/T
rs7340122 chr1:556364 A/G

rs2185539 chr1:556738 C/T
rs2185540 chr1:556823 C/T
rs9651229 chr1:557530 C/T
rs1972379 chr1:557560 A/G
rs9699555 chr1:557572 A/G
rs4098613 chr1:558224 C/T
rs8179287 chr1:558258 A/G
rs3905037 chr1:558282 C/T
rs11490925 chr1:558021 A/G
rs4098611 chr1:558064 C/T

rs10159005 chr1:558151 C/G
rs9699599 chr1:558185 A/G
rs11497407 chr1:558390 A/G
rs9326624 chr1:558615 C/T
rs11510104 chr1:559259 C/T
rs9645429 chr1:559467 A/G
rs6594035 chr1:559487 C/T
rs2096045 chr1:559666 A/G
rs9700408 chr1:559712 A/G
rs2096047 chr1:559846 A/G

rs10449773 chr1:560059 C/T
rs9326626 chr1:560041 A/G
............
Repeated in Numerical order:
rs1972379 chr1:557560 A/G
rs2096045 chr1:559666 A/G
rs2096047 chr1:559846 A/G
rs2185539 chr1:556738 C/T
rs2185540 chr1:556823 C/T
rs3905037 chr1:558282 C/T
rs4098611 chr1:558064 C/T
rs4098613 chr1:558224 C/T
rs6594028 chr1:554461 A/G
rs6650104 chr1:554340 A/G

rs6594035 chr1:559487 C/T
rs7340022 chr1:555955 C/T
rs7340122 chr1:556364 A/G
rs7349153 chr1:555353 C/T
rs7417504 chr1:555800 C/T
rs8179287 chr1:558258 A/G
rs9326624 chr1:558615 C/T
rs9326626 chr1:560041 A/G
rs9645429 chr1:559467 A/G
rs9651229 chr1:557530 C/T

rs9699555 chr1:557572 A/G
rs9699599 chr1:558185 A/G
rs9700408 chr1:559712 A/G
rs9701055 chr1:555296 C/T
rs9701661 chr1:555134 A/G
rs10159005 chr1:558151 C/G
rs10449773 chr1:560059 C/T
rs10458597 chr1:554484 C/T
rs11240781 chr1:554395 A/G
rs11490925 chr1:558021 A/G

rs11497407 chr1:558390 A/G
rs11510104 chr1:559259 C/T
............

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