Sequencing of 50 human exomes reveals adaptation to high altitude.

PubWeight™: 11.27‹?› | Rank: Top 0.1%

🔗 View Article (PMC 3711608)

Published in Science on July 02, 2010

Authors

Xin Yi1, Yu Liang, Emilia Huerta-Sanchez, Xin Jin, Zha Xi Ping Cuo, John E Pool, Xun Xu, Hui Jiang, Nicolas Vinckenbosch, Thorfinn Sand Korneliussen, Hancheng Zheng, Tao Liu, Weiming He, Kui Li, Ruibang Luo, Xifang Nie, Honglong Wu, Meiru Zhao, Hongzhi Cao, Jing Zou, Ying Shan, Shuzheng Li, Qi Yang, Asan, Peixiang Ni, Geng Tian, Junming Xu, Xiao Liu, Tao Jiang, Renhua Wu, Guangyu Zhou, Meifang Tang, Junjie Qin, Tong Wang, Shuijian Feng, Guohong Li, Huasang, Jiangbai Luosang, Wei Wang, Fang Chen, Yading Wang, Xiaoguang Zheng, Zhuo Li, Zhuoma Bianba, Ge Yang, Xinping Wang, Shuhui Tang, Guoyi Gao, Yong Chen, Zhen Luo, Lamu Gusang, Zheng Cao, Qinghui Zhang, Weihan Ouyang, Xiaoli Ren, Huiqing Liang, Huisong Zheng, Yebo Huang, Jingxiang Li, Lars Bolund, Karsten Kristiansen, Yingrui Li, Yong Zhang, Xiuqing Zhang, Ruiqiang Li, Songgang Li, Huanming Yang, Rasmus Nielsen, Jun Wang, Jian Wang

Author Affiliations

1: BGI-Shenzhen, Shenzhen 518083, China.

Articles citing this

(truncated to the top 100)

A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet (2011) 59.36

Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science (2012) 17.12

A global reference for human genetic variation. Nature (2015) 12.85

Initial impact of the sequencing of the human genome. Nature (2011) 9.18

Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet (2011) 8.34

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics (2011) 8.19

Hypoxia-inducible factors in physiology and medicine. Cell (2012) 8.16

Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A (2011) 7.36

Hypoxia-inducible factors and the response to hypoxic stress. Mol Cell (2010) 7.20

A major genome region underlying artemisinin resistance in malaria. Science (2012) 6.25

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol (2010) 6.07

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84

Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet (2012) 3.74

Exome sequencing: the sweet spot before whole genomes. Hum Mol Genet (2010) 3.50

Genetic heterogeneity of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A (2013) 3.25

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature (2014) 3.24

A genomic history of Aboriginal Australia. Nature (2016) 3.24

The genetic landscape of mutations in Burkitt lymphoma. Nat Genet (2012) 3.03

High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq. Blood (2011) 3.00

Increased blood-oxygen binding affinity in Tibetan and Han Chinese residents at 4200 m. Exp Physiol (2014) 2.70

Identifying recent adaptations in large-scale genomic data. Cell (2013) 2.57

Robust demographic inference from genomic and SNP data. PLoS Genet (2013) 2.48

SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One (2012) 2.37

Giant sucking sound: can physiology fill the intellectual void left by the reductionists? J Appl Physiol (1985) (2011) 2.31

Adaptive and maladaptive cardiorespiratory responses to continuous and intermittent hypoxia mediated by hypoxia-inducible factors 1 and 2. Physiol Rev (2012) 2.24

The genetics of monarch butterfly migration and warning colouration. Nature (2014) 2.16

Unlocking the vault: next-generation museum population genomics. Mol Ecol (2013) 1.77

EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda. Proc Natl Acad Sci U S A (2010) 1.74

Exome sequencing generates high quality data in non-target regions. BMC Genomics (2012) 1.72

Evidence of widespread selection on standing variation in Europe at height-associated SNPs. Nat Genet (2012) 1.71

Tibetans living at sea level have a hyporesponsive hypoxia-inducible factor system and blunted physiological responses to hypoxia. J Appl Physiol (1985) (2013) 1.64

Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci U S A (2011) 1.60

An oxygen-regulated switch in the protein synthesis machinery. Nature (2012) 1.56

Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools. PLoS Genet (2015) 1.55

Phenotypic plasticity and genetic adaptation to high-altitude hypoxia in vertebrates. J Exp Biol (2010) 1.55

Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia. Am J Hum Genet (2016) 1.53

Genetic adaptation to high altitude in the Ethiopian highlands. Genome Biol (2012) 1.48

The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science (2016) 1.47

Regulation of erythropoiesis by hypoxia-inducible factors. Blood Rev (2013) 1.47

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics (2013) 1.46

Low haemoglobin concentration in Tibetan males is associated with greater high-altitude exercise capacity. J Physiol (2015) 1.43

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nat Genet (2012) 1.43

Hypoxia inducible factor 3α plays a critical role in alveolarization and distal epithelial cell differentiation during mouse lung development. PLoS One (2013) 1.42

Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia. Genome Res (2014) 1.42

A time transect of exomes from a Native American population before and after European contact. Nat Commun (2016) 1.41

Quantifying population genetic differentiation from next-generation sequencing data. Genetics (2013) 1.41

On the origin of Tibetans and their genetic basis in adapting high-altitude environments. PLoS One (2011) 1.40

Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele. PLoS Genet (2015) 1.40

The genetic architecture of adaptations to high altitude in Ethiopia. PLoS Genet (2012) 1.38

Finding the lost treasures in exome sequencing data. Trends Genet (2013) 1.36

Ten questions about systems biology. J Physiol (2011) 1.36

Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection. Am J Hum Genet (2011) 1.35

A genetic mechanism for Tibetan high-altitude adaptation. Nat Genet (2014) 1.35

Genetic signatures reveal high-altitude adaptation in a set of ethiopian populations. Mol Biol Evol (2013) 1.33

Admixture facilitates genetic adaptations to high altitude in Tibet. Nat Commun (2014) 1.32

Three-stage quality control strategies for DNA re-sequencing data. Brief Bioinform (2013) 1.30

vipR: variant identification in pooled DNA using R. Bioinformatics (2011) 1.29

A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster. PLoS Genet (2013) 1.29

Erythropoietin. Cold Spring Harb Perspect Med (2013) 1.28

Evidence for archaic adaptive introgression in humans. Nat Rev Genet (2015) 1.28

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics (2012) 1.28

Genetic evidence for natural selection in humans in the contemporary United States. Proc Natl Acad Sci U S A (2016) 1.27

On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol Biol Evol (2014) 1.25

Draft genome sequence of the Tibetan antelope. Nat Commun (2013) 1.22

Exome sequencing identifies SLCO2A1 mutations as a cause of primary hypertrophic osteoarthropathy. Am J Hum Genet (2011) 1.22

Robust identification of local adaptation from allele frequencies. Genetics (2013) 1.21

Mitochondrial DNA variant associated with Leber hereditary optic neuropathy and high-altitude Tibetans. Proc Natl Acad Sci U S A (2012) 1.21

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data. BMC Bioinformatics (2011) 1.21

Genetic determinants of Tibetan high-altitude adaptation. Hum Genet (2011) 1.21

Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases. Philos Trans R Soc Lond B Biol Sci (2013) 1.19

Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer. Gigascience (2012) 1.18

Recent human adaptation: genomic approaches, interpretation and insights. Nat Rev Genet (2013) 1.15

The role of nitrogen oxides in human adaptation to hypoxia. Sci Rep (2011) 1.14

The promise and limitations of population exomics for human evolution studies. Genome Biol (2011) 1.13

Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder. Mol Psychiatry (2014) 1.11

Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. Mol Biol Evol (2013) 1.10

Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinformatics (2013) 1.10

Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics (2013) 1.10

Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection. PLoS Genet (2013) 1.09

Joint genotyping on the fly: identifying variation among a sequenced panel of inbred lines. Genome Res (2012) 1.09

Human high-altitude adaptation: forward genetics meets the HIF pathway. Genes Dev (2014) 1.09

The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood (2014) 1.08

The chromosome 2p21 region harbors a complex genetic architecture for association with risk for renal cell carcinoma. Hum Mol Genet (2011) 1.08

Exome sequencing identifies PDE4D mutations in acrodysostosis. Am J Hum Genet (2012) 1.07

Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data. BMC Genomics (2014) 1.07

Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Am J Hum Genet (2013) 1.06

Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. Proc Natl Acad Sci U S A (2015) 1.06

Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude. Genome Biol (2013) 1.06

Evolution. Genes for high altitudes. Science (2010) 1.05

Genomic insights into adaptation to high-altitude environments. Heredity (Edinb) (2011) 1.05

A beginners guide to SNP calling from high-throughput DNA-sequencing data. Hum Genet (2012) 1.05

The Kalash genetic isolate: ancient divergence, drift, and selection. Am J Hum Genet (2015) 1.04

Porcine colonization of the Americas: a 60k SNP story. Heredity (Edinb) (2012) 1.04

Genomics and genetics in the biology of adaptation to exercise. Compr Physiol (2011) 1.02

Deletion of iron regulatory protein 1 causes polycythemia and pulmonary hypertension in mice through translational derepression of HIF2α. Cell Metab (2013) 1.02

Genome-wide analysis of cold adaptation in indigenous Siberian populations. PLoS One (2014) 1.02

Population Genomics of Human Adaptation. Annu Rev Ecol Evol Syst (2013) 1.01

Targeted capture in evolutionary and ecological genomics. Mol Ecol (2015) 1.01

Genetic variants in EPAS1 contribute to adaptation to high-altitude hypoxia in Sherpas. PLoS One (2012) 1.00

Articles cited by this

SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47

Direct selection of human genomic loci by microarray hybridization. Nat Methods (2007) 17.73

Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet (2009) 9.16

Differential roles of hypoxia-inducible factor 1alpha (HIF-1alpha) and HIF-2alpha in hypoxic gene regulation. Mol Cell Biol (2003) 8.12

Balancing acts: molecular control of mammalian iron metabolism. Cell (2004) 7.82

A gain-of-function mutation in the HIF2A gene in familial erythrocytosis. N Engl J Med (2008) 5.11

The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Hum Genomics (2004) 3.53

The origins of lactase persistence in Europe. PLoS Comput Biol (2009) 3.34

Expression of ARNT, ARNT2, HIF1 alpha, HIF2 alpha and Ah receptor mRNAs in the developing mouse. Mech Dev (1998) 3.04

Two routes to functional adaptation: Tibetan and Andean high-altitude natives. Proc Natl Acad Sci U S A (2007) 2.78

Disrupted in schizophrenia 1 (DISC1): association with schizophrenia, schizoaffective disorder, and bipolar disorder. Am J Hum Genet (2004) 2.71

Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin. Proc Natl Acad Sci U S A (2009) 2.32

Human genetic adaptation to high altitude. High Alt Med Biol (2001) 2.27

Identifying positive selection candidate loci for high-altitude adaptation in Andean populations. Hum Genomics (2009) 2.18

Arterial oxygen saturation in Tibetan and Han infants born in Lhasa, Tibet. N Engl J Med (1995) 2.13

Structural and functional effects of hereditary hemolytic anemia-associated point mutations in the alpha spectrin tetramer site. Blood (2008) 2.12

Epilepsy and brain abnormalities in mice lacking the Otx1 gene. Nat Genet (1996) 1.63

Hemoglobin levels in Qinghai-Tibet: different effects of gender for Tibetans vs. Han. J Appl Physiol (1985) (2004) 1.59

Suppression of hypoxia-inducible factor 1alpha (HIF-1alpha) transcriptional activity by the HIF prolyl hydroxylase EGLN1. J Biol Chem (2005) 1.54

Smaller alveolar-arterial O2 gradients in Tibetan than Han residents of Lhasa (3658 m). Respir Physiol (1996) 1.45

Hypoxia-reoxygenation induces premature senescence in FA bone marrow hematopoietic cells. Blood (2005) 1.44

Identical point mutations of the R-type pyruvate kinase (PK) cDNA found in unrelated PK variants associated with hereditary hemolytic anemia. Blood (1992) 1.39

A genetic association study of chromosome 11q22-24 in two different samples implicates the FXYD6 gene, encoding phosphohippolin, in susceptibility to schizophrenia. Am J Hum Genet (2007) 1.33

The EPAS1 gene influences the aerobic-anaerobic contribution in elite endurance athletes. Hum Genet (2005) 1.29

Articles by these authors

A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39

SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13

Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49

The diploid genome sequence of an Asian individual. Nature (2008) 46.29

De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91

A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63

A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78

SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41

Enterotypes of the human gut microbiome. Nature (2011) 24.36

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89

Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48

The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27

Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21

SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96

The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76

WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06

Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55

Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet (2008) 12.51

A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25

A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68

piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature (2009) 11.27

Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol (2005) 11.26

Natural selection on protein-coding genes in the human genome. Nature (2005) 10.84

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59

Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science (2003) 9.20

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One (2007) 9.17

Regulating intracellular antiviral defense and permissiveness to hepatitis C virus RNA replication through a cellular RNA helicase, RIG-I. J Virol (2005) 9.11

Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet (2008) 8.92

TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38

The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23

The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19

A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell (2004) 8.06

An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94

Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model (2006) 7.93

Regulation of interferon regulatory factor-3 by the hepatitis C virus serine protease. Science (2003) 7.91

Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics (2004) 7.79

Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77

The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol (2009) 7.59

Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51

A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res (2008) 7.45

Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism. Cell (2012) 7.36

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol (2002) 7.21

Acute renal failure and sepsis. N Engl J Med (2004) 7.18

The evolution of gene expression levels in mammalian organs. Nature (2011) 7.16

Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med (2011) 7.11

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08

Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia. Nat Genet (2010) 7.08

Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93

High-performance neuroprosthetic control by an individual with tetraplegia. Lancet (2012) 6.66

TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63

Ascertainment bias in studies of human genome-wide polymorphism. Genome Res (2005) 6.63

A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62

Proportionally more deleterious genetic variation in European than in African populations. Nature (2008) 6.61

Aberrant excitatory neuronal activity and compensatory remodeling of inhibitory hippocampal circuits in mouse models of Alzheimer's disease. Neuron (2007) 6.60

Clinical features of the initial cases of 2009 pandemic influenza A (H1N1) virus infection in China. N Engl J Med (2009) 6.45

Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Natl Acad Sci U S A (2005) 5.94

The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84

Selectable subgenomic and genome-length dicistronic RNAs derived from an infectious molecular clone of the HCV-N strain of hepatitis C virus replicate efficiently in cultured Huh7 cells. J Virol (2002) 5.81

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73

Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A (2007) 5.64

Control of antiviral defenses through hepatitis C virus disruption of retinoic acid-inducible gene-I signaling. Proc Natl Acad Sci U S A (2005) 5.64

Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62

New loci associated with kidney function and chronic kidney disease. Nat Genet (2010) 5.58

Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58

Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med (2008) 5.54

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54