Different Maf, 1000 genomes versus Hapmap

Question

[avari]

Hello,

I wondered if someone can shed light on why the MAF for a SNP within a population might be discordant between the HapMap and 1000 genome project on dbSNP.

For example: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs5980432

Thanks!

[Denise CS]

Are the populations and samples within those populations exactly the same between HapMap and 1000Genomes? Perhaps 1000Genomes sequenced some individuals from YRI, whereas HapMap genotyped different samples within YRI? It may be easier seeing the Population genetics data for rs5980432 in the 1000Genomes browser. It seems the allele counts are different for YRI for example.

[avari]

Thanks, good point. I'll check that!

Answer 1

[Emily]

There are more people and more populations in 1000 Genomes.

[avari]

Thanks, both answers seem eminently reasonable, however it does seem like quite a difference in scale. The 1000genome project MAF for this SNV is European is about 0.24 while the MAF from HapMap for European is about 0.009!

Answer 2

[Giovanni M Dall'Olio]

Probably due to different technologies being used in Hapmap and 1000Genomes.

Hapmap genotypes were mostly obtained through Affymetrix chips, if I am not wrong.

1000Genomes SNPs were called through NGS, mostly Illumina sequencing.

[avari]

Thanks, just wondered if you could elaborate on that ?