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Altitude adaptation in Tibet caused by introgression of Denisovan-like DNA

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      Most cited references 43

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      An integrated map of genetic variation from 1,092 human genomes

      Summary Through characterising the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help understand the genetic contribution to disease. We describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methodologies to integrate information across multiple algorithms and diverse data sources we provide a validated haplotype map of 38 million SNPs, 1.4 million indels and over 14 thousand larger deletions. We show that individuals from different populations carry different profiles of rare and common variants and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways and that each individual harbours hundreds of rare non-coding variants at conserved sites, such as transcription-factor-motif disrupting changes. This resource, which captures up to 98% of accessible SNPs at a frequency of 1% in populations of medical genetics focus, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations.
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        SOAP: short oligonucleotide alignment program.

        We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets.
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          Generating samples under a Wright-Fisher neutral model of genetic variation.

           R Hudson (2002)
          A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model. The program assumes an infinite-sites model of mutation, and allows recombination, gene conversion, symmetric migration among subpopulations, and a variety of demographic histories. The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models.

            Author and article information

            [1 ]BGI-Shenzhen, Shenzhen, 518083, China
            [2 ]Department of Integrative Biology, University of California, Berkeley, CA
            [3 ]School of Natural Sciences, University of California, Merced, CA
            [4 ]School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
            [5 ]Binhai Institute of Gene Technology, BGI-Tianjin, Tianjin, 300308, China
            [6 ]Tianjin Medical Genomics Engineering Center, BGI-Tianjin, Tianjin, 300308, China
            [7 ]The People’s Hospital of Lhasa, Lhasa, 850000, China
            [8 ]Bioinformatics and Computational Biology Program, Iowa State University
            [9 ]Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
            [10 ]The No.2 people’s hospital of Tibet Autonomous Region, 850000, China
            [11 ]The hospital of XiShuangBanNa Dai Nationalities, Autonomous Jinghong 666100, Yunnan, China
            [12 ]The Guangdong Enterprise Key Laboratory of Human Disease Genomics, BGI-Shenzhen, Shenzhen, China
            [13 ]Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen, China
            [14 ]Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia
            [15 ]James D. Watson Institute of Genome Science, Hangzhou, China
            [16 ]Department of Biology, University of Copenhagen, Ole MaaløesVej 5, 2200 Copenhagen, Denmark
            [17 ]Macau University of Science and Technology, AvenidaWai long, Taipa, Macau 999078, China
            [18 ]Department of Medicine, University of Hong Kong, Hong Kong
            [19 ]Department of Statistics, University of California, Berkeley, CA
            [20 ]Department of Biology, University of Copenhagen, Copenhagen, Denmark
            Author notes

            These authors contributed equally to this work.

            6 June 2014
            02 July 2014
            14 August 2014
            14 February 2015
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