ArticleBMC genomics2015
Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection.iScience · 2024Article
- Cancer incidence in Khyber Pakhtunkhwa, Pakistan, 2020.BMC public health · 2023Article
- Whole genome sequencing data of multiple individuals of Pakistani descent.Scientific data · 2020Article
- Mitochondrial DNA diversity in the Khattak and Kheshgi of the Peshawar Valley, Pakistan.Genetica · 2020Article
- Beyond sequencing: re-visiting annotations for PJL as a test case.BMC research notes · 2019Article
- Genetic structure of Kho population from north-western Pakistan based on mtDNA control region sequences.Genetica · 2019Article
- A new self-learning computational method for footprints of early human migration processes.Molecular genetics and genomics : MGG · 2018Article
- Whole genome sequencing data for two individuals of Pakistani descent.Scientific data · 2018Article
- A comprehensive Y-STR portrait of Yousafzai's population.International journal of legal medicine · 2017Article
- HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing.Nucleic acids research · 2016Article
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Authors and funding
18 authors.
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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.
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