Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Choudhury, Ananyo ^a,b   Hazelhurst, Scott ^a   Meintjes, Ayton ^c   Achinike Oduaran, Ovokeraye ^a,b   Aron, Shaun ^a   Gamieldien, Junaid ^d   Jalali Sefid Dashti, Mahjoubeh ^d   Mulder, Nicola ^c   Tiffin, Nicki ^d   Ramsay, Michèle ^a,b  

^a UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^b UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^c UNIVERSITY OF CAPE TOWN   (South Africa)

^d UNIVERSITY OF THE WESTERN CAPE   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN;

AFRICA; AFRICAN; ARTICLE; CHINESE; CLUSTER ANALYSIS; DEMOGRAPHY; ETHNIC GROUP; FUNCTIONAL ASSESSMENT; FUNCTIONAL GENOMICS; GENETIC ASSOCIATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN GENOME; HUMAN GENOME PROJECT; JAPANESE (PEOPLE); MOLECULAR EVOLUTION; NERVE CELL DIFFERENTIATION; POPULATION GENETICS; POPULATION RESEARCH; SAMPLE SIZE; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; ALLELE; ANCESTRY GROUP; BIOLOGY; GENETIC SELECTION; GENETICS; HUMAN; NUCLEIC ACID DATABASE;

SUGARCANE STREAK VIRUS;

ALLELES; COMPUTATIONAL BIOLOGY; CONTINENTAL POPULATION GROUPS; DATABASES, NUCLEIC ACID; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC; SELECTION, GENETIC;

EID: 84903894586     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-437     Document Type: Article

References (103)

1. Barbujani G, Colonna V. Human genome diversity: frequently asked questions. Trends Genet 2010, 26:285-295.
2. Henn BM, Cavalli-Sforza LL, Feldman MW. The great human expansion. Proc Natl Acad Sci 2012, 109:17758-17764.
3. Balaresque PL, Ballereau SJ, Jobling MA. Challenges in human genetic diversity: demographic history and adaptation. Hum Mol Genet 2007, 16:R134-R139.
4. Scheinfeldt LB, Tishkoff SA. Recent human adaptation: genomic approaches, interpretation and insights. Nat Rev Genet 2013, 14:692-702.
5. Hancock AM, Witonsky DB, Alkorta-Aranburu G, Beall CM, Gebremedhin A, Sukernik R, Utermann G, Pritchard JK, Coop G, Di Rienzo A. Adaptations to climate-mediated selective pressures in humans. PLoS Genet 2010, 7:e1001375.
6. The International HapMap Consortium A haplotype map of the human genome. Nature 2005, 437:1299-1320. The International HapMap Consortium.
7. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. Genetic structure of human populations. Science (80- ) 2002, 298:2381-2385.
8. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM. Worldwide human relationships inferred from genome-wide patterns of variation. Science (80- ) 2008, 319:1100-1104.
9. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR. Whole-genome patterns of common DNA variation in three human populations. Science (80- ) 2005, 307:1072-1079.
10. Nelson MR, Bryc K, King KS, Indap A, Boyko AR, Novembre J, Briley LP, Maruyama Y, Waterworth DM, Waeber G, Vollenweider P, Oksenberg JR, Hauser SL, Stirnadel HA, Kooner JS, Chambers JC, Jones B, Mooser V, Bustamante CD, Roses AD, Burns DK, Ehm MG, Lai EH. The population reference sample, POPRES: a resource for population, disease, and pharmacological genetics research. Am J Hum Genet 2008, 83:347-358.
11. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung H-C, Szpiech ZA, Degnan JH, Wang K, Guerreiro R, Bras JM, Schymick JC, Hernandez DG, Traynor BJ, Simon-Sanchez J, Matarin M, Britton A, van de Leemput J, Rafferty I, Bucan M, Cann HM, Hardy JA, Rosenberg NA, Singleton AB. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 2008, 451:998-1003.
12. Novembre J, Ramachandran S. Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet 2011, 12:245-274.
13. Theunert C, Tang K, Lachmann M, Hu S, Stoneking M. Inferring the history of population size change from genome-wide SNP data. Mol Biol Evol 2012, 29:3653-3667.
14. Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, Atzmon G, Burns E, Ostrer H, Price AL, Reich D. The history of African gene flow into Southern Europeans, Levantines, and Jews. PLoS Genet 2011, 7:e1001373.
15. Albrechtsen A, Nielsen FC, Nielsen R. Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol 2010, 27:2534-2547.
16. Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, Grarup N, Guo Y, Hellman I, Jin X, Li Q, Liu J, Liu X, Sparso T, Tang M, Wu H, Wu R, Yu C, Zheng H, Astrup A, Bolund L, Holmkvist J, Jorgensen T, Kristiansen K, Schmitz O, Schwartz TW, et al. Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet 2010, 42:969-972.
17. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073.
18. The 1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes. Nature 2012, 491:56-65. The 1000 Genomes Project Consortium.
19. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM, Broad GO, Seattle GO, . on behalf of the NESP Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science (80- ) 2012, 337:64-69. on behalf of the NESP.
20. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH-Y, Hansen NF, Durand EY, Malaspinas A-S, Jensen JD, Marques-Bonet T, Alkan C, Prã1-Aprfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Hã¶ber B, Hã¶ffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, et al. A draft sequence of the neandertal genome. Science (80- ) 2010, 328:710-722.
21. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PLF, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin J-J, Kelso J, Slatkin M, Paabo S. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 2010, 468:1053-1060.
22. Alves I, Sramkova Hanulova A, Foll M, Excoffier L. Genomic data reveal a complex making of humans. PLoS Genet 2012, 8:e1002837.
23. Hammer MF, Woerner AE, Mendez FL, Watkins JC, Wall JD. Genetic evidence for archaic admixture in Africa. Proc Natl Acad Sci 2011, 108:15123-15128.
24. Lachance J, Vernot B, Elbers CC, Ferwerda B, Froment A, Bodo J-M, Lema G, Fu W, Nyambo TB, Rebbeck TR, Zhang K, Akey JM, Tishkoff SA. Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. Cell 2012, 150:457-469.
25. Slatkin M. Allele age and a test for selection on rare alleles. Philos Trans R Soc London Ser B Biol Sci 2000, 355:1663-1668.
26. Gibson G. Rare and common variants: twenty arguments. Nat Rev Genet 2012, 13:135-145.
27. Kryukov GV, Pennacchio LA, Sunyaev SR. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet 2007, 80:727-739.
28. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW, Goddard ME, Visscher PM. Common SNPs explain a large proportion of the heritability for human height. Nat Genet 2010, 42:565-569.
29. Hartford CM, Duan S, Delaney SM, Mi S, Kistner EO, Lamba JK, Huang RS, Dolan ME. Population-specific genetic variants important in susceptibility to cytarabine arabinoside cytotoxicity. Blood 2009, 113:2145-2153.
30. Prescott NJ, Dominy KM, Kubo M, Lewis CM, Fisher SA, Redon R, Huang N, Stranger BE, Blaszczyk K, Hudspith B, Parkes G, Hosono N, Yamazaki K, Onnie CM, Forbes A, Dermitzakis ET, Nakamura Y, Mansfield JC, Sanderson J, Hurles ME, Roberts RG, Mathew CG. Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease. Hum Mol Genet 2010, 19:1828-1839.
31. Parra EJ, Marcini A, Akey J, Martinson J, Batzer MA, Cooper R, Forrester T, Allison DB, Deka R, Ferrell RE, Shriver MD. Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet 1998, 63:1839-1851.
32. Lohmueller KE, Bustamante CD, Clark AG. The effect of recent admixture on inference of ancient human population history. Genetics 2010, 185:611-622.
33. The International HapMap Consortium The international HapMap project. Nature 2003, 426:789-796. The International HapMap Consortium.
34. The International HapMap Consortium A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449:851-861. The International HapMap Consortium.
35. Baye TM, Wilke RA, Olivier M. Genomic and geographic distribution of private SNPs and pathways in human populations. Per Med 2009, 6:623-641.
36. Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, Project NES, Akey JM. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 2013, 493:216-220.
37. Chen J, Zheng H, Bei J-X, Sun L, Jia W, Li T, Zhang F, Seielstad M, Zeng Y-X, Zhang X, Liu J. Genetic structure of the Han Chinese population revealed by genome-wide SNP variation. Am J Hum Genet 2009, 85:775-785.
38. Qin P, Li Z, Jin W, Lu D, Lou H, Shen J, Jin L, Shi Y, Xu S. A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese. Eur J Hum Genet 2013, 22:248-253.
39. Xu S, Yin X, Li S, Jin W, Lou H, Yang L, Gong X, Wang H, Shen Y, Pan X, He Y, Yang Y, Wang Y, Fu W, An Y, Wang J, Tan J, Qian J, Chen X, Zhang X, Sun Y, Zhang X, Wu B, Jin L. Genomic dissection of population substructure of Han Chinese and its implication in association studies. Am J Hum Genet 2009, 85:762-774.
40. Murray T, Beaty TH, Mathias RA, Rafaels N, Grant AV, Faruque MU, Watson HR, Ruczinski I, Dunston GM, Barnes KC. African and non-African admixture components in African Americans and an African Caribbean population. Genet Epidemiol 2010, 34:561-568.
41. Campbell MC, Tishkoff SA. The evolution of human genetic and phenotypic variation in Africa. Curr Biol 2010, 20:R166-R173.
42. Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, Froment A, Hirbo JB, Awomoyi AA, Bodo J-M, Doumbo O, Ibrahim M, Juma AT, Kotze MJ, Lema G, Moore JH, Mortensen H, Nyambo TB, Omar SA, Powell K, Pretorius GS, Smith MW, Thera MA, Wambebe C, Weber JL, Williams SM. The genetic structure and history of Africans and African Americans. Science (80-) 2009, 324:1035-1044.
43. De Filippo C, Bostoen K, Stoneking M, Pakendorf B. Bringing together linguistic and genetic evidence to test the Bantu expansion. Proc R Soc B Biol Sci 2012, 279:3256-3263.
44. Joubert BR, North KE, Wang Y, Mwapasa V, Franceschini N, Meshnick SR, Lange EM. Comparison of genome-wide variation between Malawians and African ancestry HapMap populations. J Hum Genet 2010, 55:366-374.
45. Nakaoka H, Mitsunaga S, Hosomichi K, Shyh-Yuh L, Sawamoto T, Fujiwara T, Tsutsui N, Suematsu K, Shinagawa A, Inoko H, Inoue I. Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population. PLoS One 2013, 8:e60793.
46. Hanihara K. Dual structure model for the population history of the Japanese. Japan Rev 1991, 2:1-33.
47. Yamaguchi-Kabata Y, Tsunoda T, Kumasaka N, Takahashi A, Hosono N, Kubo M, Nakamura Y, Kamatani N. Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes. J Hum Genet 2012, 57:326-334.
48. Ralph P, Coop G. The geography of recent genetic ancestry across Europe. PLoS Biol 2013, 11:e1001555.
49. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD. Genes mirror geography within Europe. Nature 2008, 456:98-101.
50. Palo JU, Ulmanen I, Lukka M, Ellonen P, Sajantila A. Genetic markers and population history: Finland revisited. Eur J Hum Genet 2009, 17:1336-1346.
51. Salmela E, Lappalainen T, Fransson I, Andersen PM, Dahlman-Wright K, Fiebig A, Sistonen P, Savontaus M-L, Schreiber S, Kere J, Lahermo P. Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe. PLoS One 2008, 3:e3519.
52. Chuang JH, Li H. Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome. PLoS Biol 2004, 2:e29.
53. Lindblad-Toh K, Winchester E, Daly MJ, Wang DG, Hirschhorn JN, Laviolette J-P, Ardlie K, Reich DE, Robinson E, Sklar P, Shah N, Thomas D, Fan J-B, Gingeras T, Warrington J, Patil N, Hudson TJ, Lander ES. Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nat Genet 2000, 24:381-386.
54. Tenaillon MI, Austerlitz F, Tenaillon O. Apparent mutational hotspots and long distance linkage disequilibrium resulting from a bottleneck. J Evol Biol 2008, 21:541-550.
55. Sainudiin R, Clark A, Durrett R. Simple models of genomic variation in human SNP density. BMC Genomics 2007, 8:146.
56. McDonald MJ, Wang W-C, Huang H-D, Leu J-Y. Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. PLoS Biol 2011, 9:e1000622.
57. Amos W. Even small SNP clusters are non-randomly distributed: is this evidence of mutational non-independence?. Proc R Soc B Biol Sci 2010, 277:1443-1449.
58. Hofer T, Foll M, Excoffier L. Evolutionary forces shaping genomic islands of population differentiation in humans. BMC Genomics 2012, 13:107.
59. Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res 2005, 15:1553-1565.
60. Weir BS, Cardon LR, Anderson AD, Nielsen DM, Hill WG. Measures of human population structure show heterogeneity among genomic regions. Genome Res 2005, 15:1468-1476.
61. Schmid K, Yang Z. The trouble with sliding windows and the selective pressure in BRCA1. PLoS One 2008, 3:e3746.
62. Pasanen MK, Neuvonen PJ, Niemi M. Global analysis of genetic variation in SLCO1B1. Pharmacogenomics 2007, 9:19-33.
63. Mwinyi J, Köpke K, Schaefer M, Roots I, Gerloff T. Comparison of SLCO1B1 sequence variability among German, Turkish, and African populations. Eur J Clin Pharmacol 2008, 64:257-266.
64. Turner TL, Hahn MW. Locus- and population-specific selection and differentiation between incipient species of anopheles gambiae. Mol Biol Evol 2007, 24:2132-2138.
65. Harr B. Genomic islands of differentiation between house mouse subspecies. Genome Res 2006, 16:730-737.
66. Myles S, Tang K, Somel M, Green RE, Kelso J, Stoneking M. Identification and analysis of genomic regions with large between-population differentiation in humans. Ann Hum Genet 2008, 72:99-110.
67. Hofer T, Ray N, Wegmann D, Excoffier L. Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection. Ann Hum Genet 2009, 73:95-108.
68. Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. Recent and ongoing selection in the human genome. Nat Rev Genet 2007, 8:857-868.
69. Feder JL, Nosil P. The efficacy of divergence hitchhiking in generating genomic islands during ecological speciation. Evolution (N Y) 2010, 64:1729-1747.
70. Voight BF, Kudaravalli S, Wen X, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol 2006, 4:e72.
71. Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZXP, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, Zheng H, Liu T, He W, Li K, Luo R, Nie X, Wu H, Zhao M, Cao H, Zou J, Shan Y, Li S, Yang Q, Asan, Ni P, Tian G, Xu J, Liu X, Jiang T, Wu R, et al. Sequencing of 50 human exomes reveals adaptation to high altitude. Science (80- ) 2010, 329(Pool JE, Xu X):75-78.
72. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES. Genome-wide detection and characterization of positive selection in human populations. Nature 2007, 449:913-918.
73. Chen H, Patterson N, Reich D. Population differentiation as a test for selective sweeps. Genome Res 2010, 20:393-402.
74. Duret L, Arndt PF. The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet 2008, 4:e1000071.
75. Hellmann I, Prüfer K, Ji H, Zody MC, Pääbo S, Ptak SE. Why do human diversity levels vary at a megabase scale?. Genome Res 2005, 15:1222-1231.
76. Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A, Jonasdottir A, Walters GB, Jonasdottir A, Gylfason A, Kristinsson KT, Gudjonsson SA, Frigge ML, Helgason A, Thorsteinsdottir U, Stefansson K. Fine-scale recombination rate differences between sexes, populations and individuals. Nature 2010, 467:1099-1103.
77. Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, Palmer CD, Chen GK, Wang K, Buxbaum SG, Akylbekova EL, Aldrich MC, Ambrosone CB, Amos C, Bandera EV, Berndt SI, Bernstein L, Blot WJ, Bock CH, Boerwinkle E, Cai Q, Caporaso N, Casey G, Adrienne Cupples L, Deming SL, Ryan Diver W, Divers J, Fornage M, Gillanders EM, Glessner J, Harris CC, et al. The landscape of recombination in African Americans. Nature 2011, 476:170-175.
78. Laayouni H, Montanucci L, Sikora M, Melé M, Dall'Olio GM, Lorente-Galdos B, McGee KM, Graffelman J, Awadalla P, Bosch E, Comas D, Navarro A, Calafell F, Casals F, Bertranpetit J. Similarity in recombination rate estimates highly correlates with genetic differentiation in humans. PLoS One 2011, 6:e17913.
79. Adzhubei I, Schmidt S, Peshkin L, Ramensky V, Gerasimova A, Bork P, Kondrashov A, Sunyaev S. A method and server for predicting damaging missense mutations. Nat Methods 2010, 7:248-249.
80. Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res 2001, 11(5):863-874.
81. Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Meth 2010, 7:575-576.
82. Chun S, Fay JC. Identification of deleterious mutations within three human genomes. Genome Res 2009, 19(9):1553-1561.
83. Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 2012, 22:1790-1797.
84. Ingenuity Pathway analysis Ingenuity® systems. http://www.ingenuity.com, Ingenuity Pathway analysis.
85. Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009, 37:1-13.
86. Amato R, Pinelli M, Monticelli A, Marino D, Miele G, Cocozza S. Genome-wide scan for signatures of human population differentiation and their relationship with natural selection, functional pathways and diseases. PLoS One 2009, 4:e7927.
87. Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM. Personal and population genomics of human regulatory variation. Genome Res 2012, 22:1689-1697.
88. Tennessen JA, Akey JM. Parallel adaptive divergence among geographically diverse human populations. PLoS Genet 2011, 7:e1002127.
89. Biankin AV, Waddell N, Kassahn KS, Gingras M-C, Muthuswamy LB, Johns AL, Miller DK, Wilson PJ, Patch A-M, Wu J, Chang DK, Cowley MJ, Gardiner BB, Song S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Gongora M, Pajic M, Scarlett CJ, Gill AJ, Pinho AV, Rooman I, Anderson M, Holmes O, Leonard C, Taylor D, et al. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature 2012, 491:399-405.
90. Chédotal A, Kerjan G, Moreau-Fauvarque C. The brain within the tumor: new roles for axon guidance molecules in cancers. Cell Death Differ 2005, 12:1044-1056.
91. Mehlen P, Delloye-Bourgeois C, Chédotal A. Novel roles for slits and netrins: axon guidance cues as anticancer targets?. Nat Rev Cancer 2011, 11:188-197.
92. 1000 Genome Project FTP server. ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/.
93. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, . Genomes Project Analysis G The variant call format and VCFtools. Bioinformatics 2011, 27:2156-2158. Genomes Project Analysis G.
94. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. PLINK: a tool Set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81:559-575.
95. WHAMM. http://coruscant.itmat.upenn.edu/whamm/index.html.
96. Matise TC, Chen F, Chen W, De La Vega FM, Hansen M, He C, Hyland FCL, Kennedy GC, Kong X, Murray SS, Ziegle JS, Stewart WCL, Buyske S. A second-generation combined linkage-physical map of the human genome. Genome Res 2007, 17(12):1783-1786.
97. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12(6):996-1006.
98. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010, 38:e164.
99. Sherry ST, Ward M-H, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001, 29(1):308-311.
100. Online Mendelian Inheritance in Man, OMIM®. http://omim.org/.
101. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30.
102. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012, 40(D1):D109-D114.
103. GeneCards database. http://www.genecards.org/.