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.
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7 comments:
Please, can you till which regions of Spain are the IBS sample ? Thanks,
Check here:
http://ccr.coriell.org/Sections/Search/Panel_Detail.aspx?Ref=MGP00010&PgId=202
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.
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.
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.
@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.
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.
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