December 16, 2011

1000 Genomes at 2,100+ and counting

The latest working data on 1000 Genomes data include 2,123 individuals. I had already included some Khmer Vietnamese (KHV) from the previous working data for use with my K12a calculator. The list of populations in the datafile currently include:

GBR FIN CHS PUR CDX CLM IBS PEL KHV ACB CEU CHD YRI CHB JPT LWK ASW MXL TSI GIH MKK

I will probably take the time to extract anew the population data from the newest file, as well as split some (such as IBS) for which I have some more regional information. By my last count, I now have about ~10,600 individuals to work with (some are duplicates, e.g., between the HapMap and 1000 Genomes Project).

In other news, I see some 23/11/2011 data on Y-chromosome SNPs. I haven't worked on those myself, but I know that many hobbyists are interested in the Y-chromosome aspect of the project, so those might be useful.

Finally, there are slides from the ICHG seminar on the 1000 Genomes Project, which should be interesting reading.

7 comments:

truth said...

Please, can you till which regions of Spain are the IBS sample ? Thanks,

Dienekes said...

Check here:
http://ccr.coriell.org/Sections/Search/Panel_Detail.aspx?Ref=MGP00010&PgId=202

truth said...

Thanks. It is confirmed what I suspeceted, that there are Canarian individuals, I knew when I saw the portraits of the V3, the last 4 or 5 are not normal. Canarians should not be included, they are not ethnic Iberians, and this sample is about Iberians, that's an error for their part.

Onur said...

Thanks. It is confirmed what I suspeceted, that there are Canarian individuals, I knew when I saw the portraits of the V3, the last 4 or 5 are not normal. Canarians should not be included, they are not ethnic Iberians, and this sample is about Iberians, that's an error for their part.

truth, there are only 2 Canarian individuals in the part of the IBS dataset for which there is regional information. That is a pretty small number and does not affect the genetic average results of the IBS dataset in any noticeable way.

Onur said...

BTW, the Canarians are not genetically much different from the non-Basque Iberian mainlanders. A little elevated "Northwest African" and "East African" components do not make a big difference. With these genotypes, they must be phenotypically indistinguishable from non-Basque Iberian mainlanders.

anthrospain said...

@Onur

This is not true. In fact there have been studies with canarians, and they are quite different. Not only from a maternal point of view (they have more than 40% of mtDNA U6, while in Iberia it doesn't even reach 1%) but also from an autosomal point of view, they showed around 18% of Berber admixture, and on PCA plots they don't cluster with Iberians.
As for the phenotype, many Canarians have a different look, that you don't find in Iberia. This is obvious for spaniards when they go to the Canaries, or when canarians go to mainland Spain.

Onur said...

anthrospain, I am referring to the IBS samples who are known to be Canarians. They are indeed genetically not much different from the non-Basque Iberian mainlander samples. But there are only two IBS samples who are known to be Canarians, so they may not be representative of Canarians as a whole. Thus the case is open to interpretation and there is no definitive answer yet on the genetics of Canarians as a whole.