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Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.

Ilyas M, Kim JS, Cooper J, Shin YA, Kim HM, Cho YS, Hwang S, Kim H, Moon J, Chung O, Jun J, Rastogi A, Song S, Ko J, Manica A, Rahman Z, Husnain T, Bhak J - BMC Genomics (2015)

Bottom Line: Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes.Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.It is a useful resource to understand genetic variation and human migration across the whole Asian continent.

View Article: PubMed Central - PubMed

Affiliation: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. milyaskh@hotmail.com.

ABSTRACT

Background: Pakistan covers a key geographic area in human history, being both part of the Indus River region that acted as one of the cradles of civilization and as a link between Western Eurasia and Eastern Asia. This region is inhabited by a number of distinct ethnic groups, the largest being the Punjabi, Pathan (Pakhtuns), Sindhi, and Baloch.

Results: We analyzed the first ethnic male Pathan genome by sequencing it to 29.7-fold coverage using the Illumina HiSeq2000 platform. A total of 3.8 million single nucleotide variations (SNVs) and 0.5 million small indels were identified by comparing with the human reference genome. Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes. SNVs were annotated for health consequences and high risk diseases, as well as possible influences on drug efficacy. We confirmed that the Pathan genome presented here is representative of this ethnic group by comparing it to a panel of Central Asians from the HGDP-CEPH panels typed for ~650 k SNPs. The mtDNA (H2) and Y haplogroup (L1) of this individual were also typical of his geographic region of origin. Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.

Conclusions: We present a whole-genome sequence and analyses of an ethnic Pathan from the north-west province of Pakistan. It is a useful resource to understand genetic variation and human migration across the whole Asian continent.

Show MeSH
Inferred historical population sizes by Pairwise Sequential Markovian Coalescent analysis. PSMC (Pairwise Sequentially Markovian Coalescent) analysis was performed to reconstruct the demographic population history of Pathans, compared with a set of 11 HGDP genomes from around the world (Africa: Dinka, Yoruba, Mandenka, Mbuti, San; Asia: Dai, Han; Europe: French, Sardinian; Oceania: Papuan; Americas: Karitiana).
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Fig3: Inferred historical population sizes by Pairwise Sequential Markovian Coalescent analysis. PSMC (Pairwise Sequentially Markovian Coalescent) analysis was performed to reconstruct the demographic population history of Pathans, compared with a set of 11 HGDP genomes from around the world (Africa: Dinka, Yoruba, Mandenka, Mbuti, San; Asia: Dai, Han; Europe: French, Sardinian; Oceania: Papuan; Americas: Karitiana).

Mentions: We inferred the demographic history of the Pathan using the pairwise sequentially Markovian coalescent (PSMC) model [51] (Figure 3), and compared it to a panel of worldwide populations based on a number of HGDP genomes [52]. As previously reported, all populations share a similar demographic history between 1 million to 200kyr ago. From 200kyr ago to 20kyr ago, the Pathan follow a similar trajectory to other Asian and European populations, with an inferred effective population size smaller than African populations, reflecting the out of Africa bottleneck. Over the last 20 k years, the Pathan shows an explosion in effective population size, contemporaneous to other Eurasian populations but much greater in magnitude. The very large effective population size likely reflects admixture between European and Asian lineages giving rise to modern Pathans (as also suggested by the analysis of mtDNA and Y-chromosome), rather than an actual increase in census sizes.Figure 3


Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.

Ilyas M, Kim JS, Cooper J, Shin YA, Kim HM, Cho YS, Hwang S, Kim H, Moon J, Chung O, Jun J, Rastogi A, Song S, Ko J, Manica A, Rahman Z, Husnain T, Bhak J - BMC Genomics (2015)

Inferred historical population sizes by Pairwise Sequential Markovian Coalescent analysis. PSMC (Pairwise Sequentially Markovian Coalescent) analysis was performed to reconstruct the demographic population history of Pathans, compared with a set of 11 HGDP genomes from around the world (Africa: Dinka, Yoruba, Mandenka, Mbuti, San; Asia: Dai, Han; Europe: French, Sardinian; Oceania: Papuan; Americas: Karitiana).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4362645&req=5

Fig3: Inferred historical population sizes by Pairwise Sequential Markovian Coalescent analysis. PSMC (Pairwise Sequentially Markovian Coalescent) analysis was performed to reconstruct the demographic population history of Pathans, compared with a set of 11 HGDP genomes from around the world (Africa: Dinka, Yoruba, Mandenka, Mbuti, San; Asia: Dai, Han; Europe: French, Sardinian; Oceania: Papuan; Americas: Karitiana).
Mentions: We inferred the demographic history of the Pathan using the pairwise sequentially Markovian coalescent (PSMC) model [51] (Figure 3), and compared it to a panel of worldwide populations based on a number of HGDP genomes [52]. As previously reported, all populations share a similar demographic history between 1 million to 200kyr ago. From 200kyr ago to 20kyr ago, the Pathan follow a similar trajectory to other Asian and European populations, with an inferred effective population size smaller than African populations, reflecting the out of Africa bottleneck. Over the last 20 k years, the Pathan shows an explosion in effective population size, contemporaneous to other Eurasian populations but much greater in magnitude. The very large effective population size likely reflects admixture between European and Asian lineages giving rise to modern Pathans (as also suggested by the analysis of mtDNA and Y-chromosome), rather than an actual increase in census sizes.Figure 3

Bottom Line: Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes.Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.It is a useful resource to understand genetic variation and human migration across the whole Asian continent.

View Article: PubMed Central - PubMed

Affiliation: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. milyaskh@hotmail.com.

ABSTRACT

Background: Pakistan covers a key geographic area in human history, being both part of the Indus River region that acted as one of the cradles of civilization and as a link between Western Eurasia and Eastern Asia. This region is inhabited by a number of distinct ethnic groups, the largest being the Punjabi, Pathan (Pakhtuns), Sindhi, and Baloch.

Results: We analyzed the first ethnic male Pathan genome by sequencing it to 29.7-fold coverage using the Illumina HiSeq2000 platform. A total of 3.8 million single nucleotide variations (SNVs) and 0.5 million small indels were identified by comparing with the human reference genome. Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes. SNVs were annotated for health consequences and high risk diseases, as well as possible influences on drug efficacy. We confirmed that the Pathan genome presented here is representative of this ethnic group by comparing it to a panel of Central Asians from the HGDP-CEPH panels typed for ~650 k SNPs. The mtDNA (H2) and Y haplogroup (L1) of this individual were also typical of his geographic region of origin. Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.

Conclusions: We present a whole-genome sequence and analyses of an ethnic Pathan from the north-west province of Pakistan. It is a useful resource to understand genetic variation and human migration across the whole Asian continent.

Show MeSH