Der Sarkissian C, Allentoft ME, Avila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernandez R, da Fonseca R, Ginolhac A, et al. Ancient genomics. Philos Trans R Soc Lond Ser B Biol Sci. 2015;370(1660):20130387.
Article
Google Scholar
Kelso J, Prüfer K. Ancient humans and the origin of modern humans. Curr Opin Genet Dev. 2014;29:133–8.
CAS
Article
PubMed
Google Scholar
Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014;505(7481):43–9.
Article
PubMed
Google Scholar
Sankararaman S, Mallick S, Dannemann M, Prufer K, Kelso J, Paabo S, Patterson N, Reich D. The genomic landscape of Neanderthal ancestry in present-day humans. Nature. 2014;507(7492):354–7.
CAS
Article
PubMed
PubMed Central
Google Scholar
Vernot B, Akey JM. Resurrecting surviving Neandertal lineages from modern human genomes. Science. 2014;343(6174):1017–21.
CAS
Article
PubMed
Google Scholar
Harris K, Nielsen R. The genetic cost of Neanderthal introgression. Genetics. 2016;203(2):881–91.
CAS
Article
PubMed
PubMed Central
Google Scholar
Juric I, Aeschbacher S, Coop G. The Strength of Selection Against Neanderthal Introgression. PLoS Genetics. 2016;12(11):e1006340.
Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, et al. The Simons genome diversity project: 300 genomes from 142 diverse populations. Nature. 2016;538(7624):201–6.
CAS
Article
PubMed
PubMed Central
Google Scholar
Dannemann M, Andres AM, Kelso J. Introgression of Neandertal- and Denisovan-like haplotypes contributes to adaptive variation in human toll-like receptors. Am J Hum Genet. 2016;98(1):22–33.
CAS
Article
PubMed
PubMed Central
Google Scholar
Deschamps M, Laval G, Fagny M, Itan Y, Abel L, Casanova JL, Patin E, Quintana-Murci L. Genomic signatures of selective pressures and introgression from archaic Hominins at human innate immunity genes. Am J Hum Genet. 2016;98(1):5–21.
CAS
Article
PubMed
PubMed Central
Google Scholar
Mendez FL, Watkins JC, Hammer MF. A haplotype at STAT2 Introgressed from neanderthals and serves as a candidate of positive selection in Papua New Guinea. Am J Hum Genet. 2012;91(2):265–74.
CAS
Article
PubMed
PubMed Central
Google Scholar
Gittelman RM, Schraiber JG, Vernot B, Mikacenic C, Wurfel MM, Akey JM. Archaic Hominin admixture facilitated adaptation to out-of-Africa environments. Curr Biol. 2016;26(24):3375–82.
CAS
Article
PubMed
Google Scholar
Racimo F, Gokhman D, Fumagalli M, Ko A, Hansen T, Moltke I, Albrechtsen A, Carmel L, Huerta-Sanchez E, Nielsen R. Archaic adaptive introgression in TBX15/WARS2. Mol Biol Evol. 2017;34(3):509–24.
PubMed
Google Scholar
Lin Y-L, Pavlidis P, Karakoc E, Ajay J, Gokcumen O. The evolution and functional impact of human deletion variants shared with archaic Hominin genomes. Mol Biol Evol. 2015;32(4):1008–19.
CAS
Article
PubMed
PubMed Central
Google Scholar
Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, et al. The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res. 2013;23(5):749–61.
CAS
Article
PubMed
PubMed Central
Google Scholar
Hasan MS, Wu X, Zhang L. Performance evaluation of indel calling tools using real short-read data. Hum Genomics. 2015;9:20.
Article
PubMed
PubMed Central
Google Scholar
Mullaney JM, Mills RE, Pittard WS, Devine SE. Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet. 2010;19(R2):R131–6.
CAS
Article
PubMed
PubMed Central
Google Scholar
Neuman JA, Isakov O, Shomron N. Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Brief Bioinform. 2013;14(1):46–55.
Article
PubMed
Google Scholar
Kvikstad EM, Duret L. Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome. Mol Biol Evol. 2014;31(1):23–36.
CAS
Article
PubMed
Google Scholar
Belinky F, Cohen O, Huchon D. Large-scale parsimony analysis of metazoan indels in protein-coding genes. Mol Biol Evol. 2010;27(2):441–51.
CAS
Article
PubMed
Google Scholar
Sjödin P, Bataillon T, Schierup MH. Insertion and deletion processes in recent human history. PLoS One. 2010;5(1):e8650.
Article
PubMed
PubMed Central
Google Scholar
Huang S, Li J, Xu A, Huang G, You L. Small insertions are more deleterious than small deletions in human genomes. Hum Mutat. 2013;34(12):1642–9.
CAS
Article
PubMed
Google Scholar
1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. 2015;526(7571):68–74.
Fan Y, Wang W, Ma G, Liang L, Shi Q, Tao S. Patterns of insertion and deletion in mammalian genomes. Curr Genomics. 2007;8(6):370–8.
CAS
Article
PubMed
PubMed Central
Google Scholar
Matthee CA, Eick G, Willows-Munro S, Montgelard C, Pardini AT, Robinson TJ. Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics. Mol Phylogenet Evol. 2007;42(3):827–37.
CAS
Article
PubMed
Google Scholar
Ophir R, Graur D. Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene. 1997;205(1–2):191–202.
CAS
Article
PubMed
Google Scholar
McDonald JH, Kreitman M. Adaptive protein evolution at the Adh locus in drosophila. Nature. 1991;351(6328):652–4.
CAS
Article
PubMed
Google Scholar
Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. Recent and ongoing selection in the human genome. Nat Rev Genet. 2007;8(11):857–68.
CAS
Article
PubMed
PubMed Central
Google Scholar
Fay JC, Wyckoff GJ, Wu CI. Positive and negative selection on the human genome. Genetics. 2001;158(3):1227–34.
CAS
PubMed
PubMed Central
Google Scholar
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics. 2010;26(16):2069–70.
CAS
Article
PubMed
PubMed Central
Google Scholar
Kondrashov AS, Rogozin IB. Context of deletions and insertions in human coding sequences. Hum Mutat. 2004;23(2):177–85.
CAS
Article
PubMed
Google Scholar
Kvikstad EM, Chiaromonte F, Makova KD. Ride the wavelet: a multiscale analysis of genomic contexts flanking small insertions and deletions. Genome Res. 2009;19(7):1153–64.
CAS
Article
PubMed
PubMed Central
Google Scholar
Kvikstad EM, Tyekucheva S, Chiaromonte F, Makova KD. A macaque's-eye view of human insertions and deletions: differences in mechanisms. PLoS Comput Biol. 2007;3(9):1772–82.
CAS
Article
PubMed
Google Scholar
Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature. 2014;513(7518):409–13.
CAS
Article
PubMed
PubMed Central
Google Scholar
Sankararaman S, Patterson N, Li H, Paabo S, Reich D. The date of interbreeding between Neandertals and modern humans. PLoS Genet. 2012;8(10):e1002947.
CAS
Article
PubMed
PubMed Central
Google Scholar
Elks CE, Perry JR, Sulem P, Chasman DI, Franceschini N, He C, Lunetta KL, Visser JA, Byrne EM, Cousminer DL, et al. Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. Nat Genet. 2010;42(12):1077–85.
CAS
Article
PubMed
PubMed Central
Google Scholar
Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, Palmer CD, Chen GK, Wang K, Buxbaum SG, Akylbekova EL, et al. The landscape of recombination in African Americans. Nature. 2011;476(7359):170–5.
CAS
Article
PubMed
PubMed Central
Google Scholar
Huerta-Sanchez E, Jin X, Asan, Bianba Z, Peter BM, Vinckenbosch N, Liang Y, Yi X, He M, Somel M, et al. altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature. 2014;512(7513):194–7.
CAS
Article
PubMed
PubMed Central
Google Scholar
Mills RE, Pittard WS, Mullaney JM, Farooq U, Creasy TH, Mahurkar AA, Kemeza DM, Strassler DS, Ponting CP, Webber C, et al. Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res. 2011;21(6):830–9.
CAS
Article
PubMed
PubMed Central
Google Scholar
Fan J, Akabane H, Zheng X, Zhou X, Zhang L, Liu Q, Zhang YL, Yang J, Zhu GZ. Male germ cell-specific expression of a novel patched-domain containing gene Ptchd3. Biochem Biophys Res Commun. 2007;363(3):757–61.
CAS
Article
PubMed
Google Scholar
White MJ, Risse-Adams O, Goddard P, Contreras MG, Adams J, Hu D, Eng C, Oh SS, Davis A, Meade K, et al. Novel genetic risk factors for asthma in African American children: precision medicine and the SAGE II study. Immunogenetics. 2016;68(6–7):391–400.
CAS
Article
PubMed
PubMed Central
Google Scholar
Ghahramani Seno MM, Kwan BY, Lee-Ng KK, Moessner R, Lionel AC, Marshall CR, Scherer SW. Human PTCHD3 nulls: rare copy number and sequence variants suggest a non-essential gene. BMC Med Genet. 2011;12:45.
Article
PubMed
PubMed Central
Google Scholar
Ramirez Rozzi FV, Bermudez de Castro JM. surprisingly rapid growth in Neanderthals. Nature. 2004;428(6986):936–9.
CAS
Article
PubMed
Google Scholar
Smith TM, Tafforeau P, Reid DJ, Pouech J, Lazzari V, Zermeno JP, Guatelli-Steinberg D, Olejniczak AJ, Hoffman A, Radovcic J, et al. Dental evidence for ontogenetic differences between modern humans and Neanderthals. Proc Natl Acad Sci U S A. 2010;107(49):20923–8.
CAS
Article
PubMed
PubMed Central
Google Scholar
The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005;437(7055):69–87.
Article
Google Scholar
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, et al. Insights into hominid evolution from the gorilla genome sequence. Nature. 2012;483(7388):169–75.
CAS
Article
PubMed
PubMed Central
Google Scholar
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 2011;469(7331):529–33.
CAS
Article
PubMed
PubMed Central
Google Scholar
Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, et al. Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014;513(7517):195–201.
CAS
Article
PubMed
PubMed Central
Google Scholar
Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007;316(5822):222–34.
CAS
Article
PubMed
Google Scholar
The Marmorset Sequencing and Analysis Consortium. The common marmoset genome provides insight into primate biology and evolution. Nat Genet. 2014;46(8):850–7.
Article
Google Scholar
Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, et al. The UCSC Genome Browser database: 2016 update. Nucleic Acids Res. 2016;44(D1):D717–25.
Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, et al. The bonobo genome compared with the chimpanzee and human genomes. Nature. 2012;486(7404):527–31.
PubMed
PubMed Central
Google Scholar
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004;14(4):708–15.
CAS
Article
PubMed
PubMed Central
Google Scholar
The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. 2015;526(7571):68–74.
R Core Team: R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing; 2017.
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46(3):310–5.
CAS
Article
PubMed
PubMed Central
Google Scholar
Li MJ, Wang P, Liu X, Lim EL, Wang Z, Yeager M, Wong MP, Sham PC, Chanock SJ, Wang J. GWASdb: a database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res. 2012;40(Database issue):D1047–54.
CAS
Article
PubMed
Google Scholar
Prüfer K, Muetzel B, Do HH, Weiss G, Khaitovich P, Rahm E, Paabo S, Lachmann M, Enard W. FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics. 2007;8:41.
Article
PubMed
PubMed Central
Google Scholar
Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, et al. Ensembl 2015. Nucleic Acids Res. 2015;43(D1):D662–9.
CAS
Article
PubMed
Google Scholar
Fritsche LG, Chen W, Schu M, Yaspan BL, Yu Y, Thorleifsson G, Zack DJ, Arakawa S, Cipriani V, Ripke S, et al. Seven new loci associated with age-related macular degeneration. Nat Genet. 2013;45(4):433–9. 439e431-432
CAS
Article
PubMed
Google Scholar
Beaty TH, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB, Liang KY, Wu T, Murray T, Fallin MD, et al. A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet. 2010;42(6):525–9.
CAS
Article
PubMed
PubMed Central
Google Scholar
de Boer RA, Verweij N, van Veldhuisen DJ, Westra HJ, Bakker SJ, Gansevoort RT, Muller Kobold AC, van Gilst WH, Franke L, Mateo Leach I, et al. A genome-wide association study of circulating galectin-3. PLoS One. 2012;7(10):e47385.
Article
PubMed
PubMed Central
Google Scholar
Cho YS, Chen CH, Hu C, Long J, Ong RT, Sim X, Takeuchi F, Wu Y, Go MJ, Yamauchi T, et al. Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians. Nat Genet. 2011;44(1):67–72.
Article
PubMed
PubMed Central
Google Scholar
Perlis RH, Huang J, Purcell S, Fava M, Rush AJ, Sullivan PF, Hamilton SP, McMahon FJ, Schulze TG, Potash JB, et al. Genome-wide association study of suicide attempts in mood disorder patients. Am J Psychiatry. 2010;167(12):1499–507.
Article
PubMed
PubMed Central
Google Scholar
Chen G, Bentley A, Adeyemo A, Shriner D, Zhou J, Doumatey A, Huang H, Ramos E, Erdos M, Gerry N, et al. Genome-wide association study identifies novel loci association with fasting insulin and insulin resistance in African Americans. Hum Mol Genet. 2012;21(20):4530–6.
CAS
Article
PubMed
PubMed Central
Google Scholar