August 12, 2014

168 South Asian Genomes

PLoS ONE 9(8): e102645. doi:10.1371/journal.pone.0102645

The South Asian Genome

John C. Chambers et al.

The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.

Link

6 comments:

andrew said...

The study really underscores the fact that South Asians are far more West Eurasian than East Eurasian, and reaffirms the conclusion that the Ancestral South Asian component of South Asian population genetics is the source of most distinctively South Asian genetic variation. It also suggests that lots of the scatter in variation of South Asian population genetics in PCA charts is due to noise associated with lower coverage percentages rather than genuine genetic diversity.

aniasi said...

Dienekes,

First thank you for this article. It is great to see more research being done on the subcontinent's population genetics.

Second, do you think this will tell us more about the history of its population? Besides the general North Indian closer to West Eurasian etc, do you think this might be able to go further in terms of history and anthropology?

SB said...

It appears the authors have completely misunderstood the concept of ASI-ASI vis a vis current Indian populations. But otherwise, this database is great!

terryt said...

"The study really underscores the fact that South Asians are far more West Eurasian than East Eurasian, and reaffirms the conclusion that the Ancestral South Asian component of South Asian population genetics is the source of most distinctively South Asian genetic variation".

Indicating it is far easier to enter or exit South Asia from the west than from the east. That tends to make the great southern migration theory very unlikely.

bmdriver said...

''North Indian closer to West Eurasian''

The other way round.

V.R. said...

@ Andrew,

I glean from reading such posts that most S Asians have more W than E Eurasian ancestry,
but I'm not sure what you mean by 'far more'. Are you assuming that all S Asians
(exclusive of Tibeto-Burman speakers, NE Indians)
have insignificant E Eurasian ancestry in comparison to W Eurasian ancestry?
Relative amounts of East Eurasian Ancestry in S Asians (and in particular Indians)
will vary as per geography and caste. It is important to note that the sample of
S Asian genomes is rather strongly skewed toward Punjabis and those from the west
(ie Gujaratis, Konkan/Kerala Christians, Muslims(?) from Pakistan),and these population
groups tend to have lesser amounts of ASI as compared to most Indian/ Sri Lankan populations.
The sample is not representative of S Asians in S Asia, but is rather,
as the authors state, representative of S Asians in the UK. I would also assume
(though caste affiliation was not recorded)
that the lower castes were under-represented, as individuals from these population
groups would have been less likely to emigrate from India/ Pakistan to England in the first place.
Davidski calculated a Paniya individual as having well over 40% ENA ancestry (and possibly even over 50%)
in his analysis of "ANE admixture across Asia". Assuming this calculation
to be an accurate approximation,then can one
generalize all S Asians as having small E:W Eurasian ratios?
Feel free to correct me if this seems completely off base.