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Archiver > GENEALOGY-DNA > 2010-03 > 1269324655


From: "Nick n Dale" <>
Subject: Re: [DNA] Re : Usefulness of SNP tests
Date: Tue, 23 Mar 2010 17:10:55 +1100
References: <63040.73363.qm@web25904.mail.ukl.yahoo.com>


Thanks Didier, I did take a look at Relative Finder and also Family Finder
and comments in this list's archives. At $249 FTDNA is very competitive on
price compared with 23andMe's $449 for Complete (>1 person) although with
only half the results. I've already got a Y chromosome 43 marker test from
DNAHeritage and Y & Mito results from smgf but no SNPs. I wonder if FF does
Y & mito as does RF? It seems that some people have done tests with both RF
& FF. How did the raw data compare SNP for SNP? If I do go with 23&Me I hope
they won't upgrade so that early tests won't be able to be compared with
those later on. I hear others describing their chip as the 'old Illumina
550'.
Sorry for being slow to reply. Last weekend I had another look at the
Mendels on 23&Me as a dry run to try to work out what else might come out of
testing. Being smallish I chose chromosome 17 and put their downloaded
results into a spread sheet. From a total of 15,310 SNPs approx 10,500 were
homozygous, 4,800 hetero and 40ish discarded. I then went on to create a
fictional child made up from the parents SNPs and found that 1842 sites were
double heterozygous ie unresolvably ambiguous. Meaning that it was possible
to correctly assign almost 88% of the alleles to each chromosome of the
child. With that in mind, I'm also thinking that by comparing my 2 sons
results it should be possible to assign specific SNP sequences to both my
own and wife's chromosomes based on regions of correspondence between them.
Does this make sense? And does 23&Me or FTDNA do this for you anyway given
only 2 generations?

As I said earlier I'm not hopeful of too much coming out of the medical
SNPs. If I'm wrong please let me know. (OT: 23&Me say they can provide
information on psoriasis susceptibility. But when you look at the Raw
Results for the Mendels 2 of the major suspect genes PSORS1 on Chr 6 &
PSORS2 on Chr 17 have no SNPs listed because the genes can't be positioned
they say. I do hope we will get *all* the raw data in future). Those gripes
aside I commend them for making the raw data available to the public so that
we can play around. I am somewhat more sanguine about the genealogical
prospects and genetic info (phasing) as above.and will probably go ahead and
put in an order. And hopefully get some of my more distant cousins with
questionable parentage to come on board.

Nick
PS does it usually take 23and Me 7 days to answer an email?
----- Original Message -----
From: "vernade didier" <>
To: <>
Sent: Tuesday, March 16, 2010 4:26 PM
Subject: [DNA] Re : Usefulness of SNP tests


> Until now the best results from 23andME are the Y SNPs and those SNPs used
> by Relative Finder . You also get SNP testing on mtDNA .
>
> Didier
>
>> I am trying to convince myself of the
>> value of massive SNP tests like that offered by 23andMe.
>> Their Complete test covers both genealogy and health areas.
>> Am I wrong in thinking that detecting latent defective
>> genes (ie as a carrier) is a very hit & miss affair? I
>> opened a free account and browsed the chromosomes of the
>> "Mendel" family and found that the number of SNPs offered
>> for a particular gene is a long way short of the constituent
>> nucleotide pairs (possible mutations). A lot were in
>> introns, not that that necessarily rules out an effect on
>> protein functionality. I know that some mutations are
>> concentrated on one locus (eg Cystic Fibrosis CFTR-~70% in
>> Caucasians), but what about the other 30%, not to mention
>> the other genes where mutations are spread more evenly.
>> Surely sequencing is the way to go to get complete coverage?
>> I did have to do a lot of manual searching elsewhere like
>> the NCBI databases to find out what each SNP was about--is
>> the information more accessible at 23andMe once you've paid
>> your money and get the results back?
>>
>> Sorry about that first bit. I realise it's a bit off topic
>> in a genealogy list. But in order to be able to browse raw
>> results one has to get the Complete test not just the
>> Ancestry part. Also I am wondering about the usefulness of
>> getting Complete tests for my wife and 2 sons. Would it be
>> possible to piece together chunks of the genome and sort out
>> all our chromosomes?
>>
>> Nick
>>
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