title: Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.
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.
authors.affiliation: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. milyaskh@hotmail.com.|Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. milyaskh@hotmail.com.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Ilyas
authors.affiliation: Theragen Bio Institute, TheragenEtex, Suwon, Republic of Korea. jongsoo.kim@therabio.kr.
authors.forename: Jong-Soo
authors.initials: JS
authors.lastname: Kim
authors.affiliation: Theragen Bio Institute, TheragenEtex, Suwon, Republic of Korea. jessejcooper@gmail.com.
authors.forename: Jesse
authors.initials: J
authors.lastname: Cooper
authors.affiliation: Theragen Bio Institute, TheragenEtex, Suwon, Republic of Korea. thymos41@gmail.com.
authors.forename: Young-Ah
authors.initials: YA
authors.lastname: Shin
authors.affiliation: Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. howmany2@gmail.com.|The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. howmany2@gmail.com.
authors.forename: Hak-Min
authors.initials: HM
authors.lastname: Kim
authors.affiliation: Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. joys0406@gmail.com.|The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. joys0406@gmail.com.
authors.forename: Yun Sung
authors.initials: YS
authors.lastname: Cho
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea. swhwang@kribb.re.kr.
authors.forename: Seungwoo
authors.initials: S
authors.lastname: Hwang
authors.affiliation: The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. pgi.kimhh@gmail.com.
authors.forename: Hyunho
authors.initials: H
authors.lastname: Kim
authors.affiliation: Theragen Bio Institute, TheragenEtex, Suwon, Republic of Korea. jaewoo.moon@therabio.kr.
authors.forename: Jaewoo
authors.initials: J
authors.lastname: Moon
authors.affiliation: Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. okokookk219@gmail.com.
authors.forename: Oksung
authors.initials: O
authors.lastname: Chung
authors.affiliation: Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. junjh0701@gmail.com.
authors.forename: JeHoon
authors.initials: J
authors.lastname: Jun
authors.affiliation: Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. achal13rastogi@gmail.com.
authors.forename: Achal
authors.initials: A
authors.lastname: Rastogi
authors.affiliation: Theragen Bio Institute, TheragenEtex, Suwon, Republic of Korea. sanghoon.song@therabio.kr.
authors.forename: Sanghoon
authors.initials: S
authors.lastname: Song
authors.affiliation: Theragen Bio Institute, TheragenEtex, Suwon, Republic of Korea. junsu.ko@therabio.kr.
authors.forename: Junsu
authors.initials: J
authors.lastname: Ko
authors.affiliation: Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK. am315@cam.ac.uk.
authors.forename: Andrea
authors.initials: A
authors.lastname: Manica
authors.affiliation: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. zia.cemb@pu.edu.pk.
authors.forename: Ziaur
authors.initials: Z
authors.lastname: Rahman
authors.affiliation: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. tayyabhusnain@yahoo.com.
authors.forename: Tayyab
authors.initials: T
authors.lastname: Husnain
authors.affiliation: Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. jongbhak@genomics.org.|Theragen Bio Institute, TheragenEtex, Suwon, Republic of Korea. jongbhak@genomics.org.|The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. jongbhak@genomics.org.
authors.forename: Jong
authors.initials: J
authors.lastname: Bhak
mesh_terms: D041322:Chromosomes, Human, Y; D004272:DNA, Mitochondrial / Q000737:chemistry; D003710:Demography; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D008297:Male; D010154:Pakistan / Q000208:ethnology; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial