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BMC Genomics

, 16:172

First Online: 12 March 2015Received: 12 February 2014Accepted: 29 January 2015DOI: 10.1186-s12864-015-1290-1

Cite this article as: Ilyas, M., Kim, JS., Cooper, J. et al. BMC Genomics 2015 16: 172. doi:10.1186-s12864-015-1290-1

Abstract

BackgroundPakistan 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.

ResultsWe 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.

ConclusionsWe 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.

AbbreviationsPTNPathan

SNVSingle nucleotide variation

indelsInsertions and deletions

CDSCoding DNA sequence

UTRUntranslated regions

nsSNVNonsynonymous SNV

CNVRCopy number variation region

MDSMultidimensional scaling

SAIFSouth Asian Indian Female

SJKSeong-Jin Kim First Korean Genome

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-1290-1 contains supplementary material, which is available to authorized users.

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Autor: Muhammad Ilyas - Jong-Soo Kim - Jesse Cooper - Young-Ah Shin - Hak-Min Kim - Yun Sung Cho - Seungwoo Hwang - Hyunho Kim -

Fuente: https://link.springer.com/



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