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Archiver > GENEALOGY-DNA > 2010-02 > 1266459558


From: argiedude <>
Subject: Re: [DNA] Complete Khoisan and Bantu genomes from southernAfrica reported in Nature this week
Date: Thu, 18 Feb 2010 00:19:18 -0200
References: <COL123-DS17BEB6ACFA1E64140E49C5C8480@phx.gbl>
In-Reply-To: <COL123-DS17BEB6ACFA1E64140E49C5C8480@phx.gbl>


> From:
> To:
> Date: Wed, 17 Feb 2010 12:20:11 -0800
> Subject: [DNA] Complete Khoisan and Bantu genomes from southern Africareported in Nature this week
>
> The genomes of two South Africans representing very early lineages have been sequenced, as reported in the following article from the latest issue of Nature, dated 17 Feb 2010. The title of the article is:
>
> Complete Khoisan and Bantu genomes from southern Africa
>
> The authors' summary is:
>
> The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is
>
> important for understanding human diversity. Studies based on mitochondrial and small sets of nuclear markers have shown that
>
> these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans. However, until now,
>
> fully sequenced human genomes have been limited to recently diverged populations. Here we present the complete genome
>
> sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding
>
> regions from an additional three hunter-gatherers from disparate regions of the Kalahari. Wecharacterize the extent of whole-genome
>
> and exome diversity among the fivemen, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid
>

So we knew previously of 10 million SNPs, and now there are 1.3 million more, is that it? And 23andme regularly scans for 0,650 million of these 10 million already known SNPs, correct?

I'd presume that the discovery of these 1.3 million novel SNPs in Khoisan doesn't mean they have 1.3 million SNPs that the rest of the world doesn't have, but rather that given the extremely few genomes fully sequenced, these 1.3 million hadn't yet been detected simply due to luck. And that they probably exist everywhere in the world, as has been the case with the SNPs scanned in the HGDP samples; virtually none of them was absent from the 3 main population blocs of Africa, West and East Eurasia, but for a significant minority of them what was different was the frequency at which they were found in each continent, resulting in the FST distances of about 0.12 between the major continental blocs.

How many genomes have been sequenced so far? I would presume that with each new sequenced genome we would get progressively less novel SNPs, for example, 4 million with the first, then 4 million again, then 2, 1, 0.5, 0.25, etc. How many novel SNPs were found in the Korean genome sequenced last year?



> variants. In terms of nucleotide substitutions, the Bushmen seem to be, on average, more different from each other than, for example, a
>
> European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations
>
> to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in
>
> medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.
>
>
> Richard R. Kenyon ("Dick")
>


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