Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data

Human Genetics

Volumn 131, Issue 5, 2012, Pages 665-674

  Hu, Min ^a   Ayub, Qasim ^a   Guerra Assunção, José Afonso ^a   Long, Quan ^a,b   Ning, Zemin ^a   Huang, Ni ^a   Romero, Irene Gallego ^a   Mamanova, Lira ^a   Akan, Pelin ^a,c   Liu, Xin ^a   Coffey, Alison J ^a   Turner, Daniel J ^a,d   Swerdlow, Harold ^a   Burton, John ^a   Quail, Michael A ^a   Conrad, Donald F ^a,e   Enright, Anton J ^a   Tyler Smith, Chris ^a   Xue, Yali ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b GREGOR MENDEL INSTITUTE OF MOLECULAR PLANT BIOLOGY   (Austria)

^c ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^d Oxford Nanopore Technologies Ltd   (United Kingdom)

^e WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; CHROMOSOME 10; CHROMOSOME 4; CONTROLLED STUDY; GENE; GENE CONTROL; GENE FREQUENCY; GENE LOCUS; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC SELECTION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HAPLOTYPE MAP; HUMAN; HUMAN GENOME; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; SPERM PROTEIN GENE SPAG6; BIOLOGICAL MODEL; DNA SEQUENCE; GENETIC POLYMORPHISM; HAPLOTYPE;

GENOME, HUMAN; GENOTYPE; HAPLOTYPES; HAPMAP PROJECT; HUMANS; MODELS, BIOLOGICAL; POLYMORPHISM, GENETIC; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84862260324     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-011-1111-9     Document Type: Article

References (51)

1. Akey JM (2009) Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res 19:711-722
2. Bustamante CD et al (2005) Natural selection on protein-coding genes in the human genome. Nature 437:1153-1157
3. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The history and geography of human genes. Princeton University Press, Princeton
4. Coop G, Bullaughey K, Luca F, Przeworski M (2008) The timing of selection at the human FOXP2 gene. Mol Biol Evol 25:1257-1259
5. Enard W et al (2002) Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418:869-872
6. Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413
7. Fisher RA (1954) Statistical methods for research workers. Oliver and Boyd, Edinburgh
8. Fujimoto A et al (2008) A scan for genetic determinants of human hair morphology: EDAR is associated with Asian hair thickness. Hum Mol Genet 17:835-843
9. Ginjala V et al (2011) BMI1 is recruited to DNA breaks and contributes to DNA damage induced H2A ubiquitination and repair. Mol Cell Biol 31:1972-1982
10. Graf J, Hodgson R, van Daal A (2005) Single nucleotide polymorphisms in the MATP gene are associated with normal human pigmentation variation. Hum Mutat 25:278-284
11. Grossman SR et al (2010) A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327:883-886
12. Guerra-Assunção JA, Enright AJ (2010) MapMi: automated mapping of microRNA loci. BMC Bioinformatics 11:133
13. Hamblin MT, Thompson EE, Di Rienzo A (2002) Complex signatures of natural selection at the Duffy blood group locus. Am J Hum Genet 70:369-383
14. Heintzman ND et al (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459:108-112
15. Hernandez RD et al (2011) Classic selective sweeps were rare in recent human evolution. Science 331:920-924
16. Hofacker IL et al (1994) Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie 125:167-188
17. Jobling MA, Hurles ME, Tyler-Smith C (2004) Human evolutionary genetics. Garland Science, New York and Abingdon
18. Kimura R et al (2009) A common variation in EDAR is a genetic determinant of shovel-shaped incisors. Am J Hum Genet 85:528-535
19. King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188:107-116
20. Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851-1858
21. Li H et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079
22. Maine GN, Burstein E (2007) COMMD proteins: Comming to the scene. Cell Mol Life Sci 64:1997-2005
23. Neilson LI et al (1999) cDNA cloning and characterization of a human sperm antigen (SPAG6) with homology to the product of the Chlamydomonas PF16 locus. Genomics 60:272-280
24. Nielsen R et al (2005) Genomic scans for selective sweeps using SNP data. Genome Res 15:1566-1575
25. Ning Z, Cox AJ, Mullikin JC (2001) SSAHA: a fast search method for large DNA databases. Genome Res 11:1725-1729
26. Pickrell JK et al (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Res 19:826-837
27. Piriyapongsa J, Jordan IK (2007) A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS One 2:e203
28. Ptak S et al (2009) Linkage disequilibrium extends across putative selected sites in FOXP2. Mol Biol Evol 26:2181-2184
29. Quach H et al (2009) Signatures of purifying and local positive selection in human miRNAs. Am J Hum Genet 84:316-327
30. Quail MA et al (2008) A large genome center's improvements to the Illumina sequencing system. Nat Methods 5:1005-1010
31. Sabeti PC et al (2006) Positive natural selection in the human lineage. Science 312:1614-1620
32. Sabeti PC et al (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449:913-918
33. Saleh M et al (2004) Differential modulation of endotoxin responsiveness by human caspase-12.1 polymorphisms. Nature 429:75-79
34. Sapiro R et al (2002) Male infertility, impaired sperm motility, and hydrocephalus in mice deficient in sperm-associated antigen 6. Mol Cell Biol 22:6298-6305
35. Schaffner SF et al (2005) Calibrating a coalescent simulation of human genome sequence variation. Genome Res 15:1576-1583
36. Schuringa JJ, Vellenga E (2010) Role of the polycomb group gene BMI1 in normal and leukemic hematopoietic stem and progenitor cells. Curr Opin Hematol 17:294-299
37. Shakhova O, Leung C, Marino S (2005) Bmi1 in development and tumorigenesis of the central nervous system. J Mol Med 83:596-600
38. Stephens M, Donnelly P (2003) A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73:1162-1169
39. Suzuki Y et al (2008) Gain-of-function haplotype in the epithelial calcium channel TRPV6 is a risk factor for renal calcium stone formation. Hum Mol Genet 17:1613-1618
40. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595
41. Teshima KM, Coop G, Przeworski M (2006) How reliable are empirical genomic scans for selective sweeps? Genome Res 16:702-712
42. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061-1073
43. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437:1299-1320
44. Thornton KR, Jensen JD (2007) Controlling the false-positive rate in multilocus genome scans for selection. Genetics 175:737-750
45. van der Lugt NM et al (1994) Posterior transformation, neurological abnormalities, and severe hematopoietic defects in mice with a targeted deletion of the bmi-1 proto-oncogene. Genes Dev 8:757-769
46. Veyrieras JB et al (2008) High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 4:e1000214
47. Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4:e72
48. Xue Y et al (2006) Spread of an inactive form of caspase-12.1 in humans is due to recent positive selection. Am J Hum Genet 78:659-670
49. Xue Y et al (2009) Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation. Genetics 183:1065-1077
50. Yngvadottir B, MacArthur DG, Jin H, Tyler-Smith C (2009) The promise and reality of personal genomics. Genome Biol 10:237
51. Zhang J, Sarge KD (2009) Identification of a polymorphism in the RING finger of human Bmi-1 that causes its degradation by the ubiquitin-proteasome system. FEBS Lett 583:960-964