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23andme v3 genechip GMAFs

v3 genechip 23andme gmaf

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#1 mag1

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Posted 08 May 2016 - 07:52 PM


Everyone, due to overwhelming popular demand I have run the 23andme v3 genechip SNPs through the dbsnp server.

Attached is the first installment of GMAFs for the first 25,000 partition. 

 

Further exciting updates will be provided, if we can all be nice.

 

{The more observant will notice that for some unexplained reason there are about 100 stray SNPs included with the file.

  Have no idea what might have caused this.}

Attached Files



#2 mag1

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Posted 18 May 2016 - 04:09 AM

Chromosome 7 SNPs on 23andme v3.

2508 vcf for most of Chromosome 7.

PMS2 vcf. 

Attached Files


Edited by mag1, 18 May 2016 - 04:23 AM.


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#3 niner

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Posted 18 May 2016 - 05:00 PM

mag, could you tell us what information the gzips contain?  What is a GMAF?  How would we use this information?



#4 genereader

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Posted 19 May 2016 - 06:10 AM

I'm not the OP, but GMAF shows how rare (or common) an allele is.      https://www.snpedia.com/index.php/GMAF



#5 mag1

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Posted 19 May 2016 - 11:58 PM

Thanks genereader.

That's the one.

 

GMAF is the global minor allele frequency.

Minor allele frequencies vary across populations, so dbsnp gives you an average.

I think another helpful statistic they could include would be the frequencies in different populations.

There is some effort in this direction on dbsnp, though with some SNPs they only include small numbers in different populaitons.

 

With some rare SNPs, say 1 in a thousand, I would be much less worried about them if a population somewhere in the world had

a MAF of 10%. Given the current state of genetic technology one would expect that a SNP with a MAF of 10% in any large population

would be known to be either benign or damaging.

 

The GMAF was the main interest I had when making these files. I later realized that dbsnp also provided the identity of the minor allele, though

this was in another of its many file formats. Knowing which SNPs in a file are rare seems to be very useful information. I have used this as a sorting filter for 

my exome scan. I tried to upload a spreadsheet version of my results which would unlock much of the helpful informaiton in my files without the need

for programming skills though the uploader did not like the file format.

 

For the 23andme file I thought that the GMAFs would be helpful in finding DNA relatives. If anyone on the forum could help me think this through it would

be greatly appreciated. My thinking is that if there is a DNA relative with a 5 cM match then if this relative also had shared a rare heterozygous match

then it would be likely that this match were true. Typically a 5 cM is considered to likely not be a true match. However, let's say that I have a heterozygous

SNP on the shared segment with a GMAF of 0.0001 (23andme does have such rare SNPs.) If I were to ask the possible match what their genotype is for this 

SNP and they also reported it as heterozygous, wouldn't this suggest that the 5 cM match were real? Anyone?

 

If this makes sense then it would allow me to find more of the true matches with low cMs.

 

 

 


Edited by mag1, 20 May 2016 - 12:02 AM.


#6 ymc

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Posted 24 May 2016 - 12:52 AM

To find DNA relatives, identity by descent with SNP data is the more well established method.



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#7 mag1

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Posted 24 May 2016 - 01:10 AM

Thank you ymc, for posting!

 

Yes, I realize that IBD is more established, though does what I have suggested make sense?

 

If two relatives on a 5 cM stretch share a heterozygous genotype on a SNP with a MAF of 0.0001, I really do not see

how this would not confirm the segment. It is very unclear to me why 23andme would not use such information in their

calculations. Throwing out the MAFs and only looking at stretches of genotypically compatible runs (i.e. those that

are not homozygous for different alleles at a locus) does not make a great deal of sense to me.


Edited by mag1, 24 May 2016 - 01:11 AM.






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