Identification of a new susceptibility variant for multiple sclerosis in OAS1 by population genetics analysis

Human Genetics

Volumn 131, Issue 1, 2012, Pages 87-97

  Cagliani, Rachele ^a   Fumagalli, Matteo ^a   Guerini, Franca R ^b   Riva, Stefania ^a   Galimberti, Daniela ^c   Comi, Giacomo P ^c   Agliardi, Cristina ^b   Scarpini, Elio ^c   Pozzoli, Uberto ^a   Forni, Diego ^a   Caputo, Domenico ^b   Asselta, Rosanna ^c   Biasin, Mara ^c   Paraboschi, Elvezia M ^c   Bresolin, Nereo ^a,c   Clerici, Mario ^b,c   Sironi, Manuela ^a  

^a SCIENTIFIC INSTITUTE   (Italy)

^b IRCCS FONDAZIONE DON CARLO GNOCCHI   (Italy)

^c UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

2',5' OLIGOADENYLATE SYNTHETASE; 2',5' OLIGOADENYLATE SYNTHETASE 1; UNCLASSIFIED DRUG;

ADULT; ALLELE; ARTICLE; CONTROLLED STUDY; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; MAJOR CLINICAL STUDY; MALE; MULTIPLE SCLEROSIS; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

2',5'-OLIGOADENYLATE SYNTHETASE; ADULT; CASE-CONTROL STUDIES; DNA; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; GENOTYPE; HAPLOTYPES; HUMANS; ITALY; LINKAGE DISEQUILIBRIUM; MALE; MULTIPLE SCLEROSIS; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC;

EID: 84856640149     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-011-1053-2     Document Type: Article

References (47)

1. HJ Bandelt P Forster A Rohl 1999 Median-joining networks for inferring intraspecific phylogenies Mol Biol Evol 16 37 48 10331250 1:CAS:528: DyaK1MXjvVGltA%3D%3D (Pubitemid 29024937)
2. JC Barrett B Fry J Maller MJ Daly 2005 Haploview: analysis and visualization of LD and haplotype maps Bioinformatics 21 263 265 10.1093/bioinformatics/bth457 15297300 10.1093/bioinformatics/bth457 1:CAS:528:DC%2BD2MXkt1WitQ%3D%3D (Pubitemid 40202029)
3. V Bonnevie-Nielsen LL Field S Lu DJ Zheng M Li PM Martensen TB Nielsen H Beck-Nielsen YL Lau F Pociot 2005 Variation in antiviral 2′,5′- oligoadenylate synthetase (2′5′AS) enzyme activity is controlled by a single-nucleotide polymorphism at a splice-acceptor site in the OAS1 gene Am J Hum Genet 76 623 633 10.1086/429391 15732009 10.1086/429391 1:CAS:528:DC%2BD2MXisleisL0%3D (Pubitemid 40432169)
4. D Charlesworth 2006 Balancing selection and its effects on sequences in nearby genome regions PLoS Genet 2 e64 10.1371/journal.pgen.0020064 16683038 10.1371/journal.pgen.0020064
5. FC Chen TJ Chuang 2006 The effects of multiple features of alternatively spliced exons on the K(A)/K(S) ratio test BMC Bioinforma 7 259 10.1186/1471-2105-7-259 10.1186/1471-2105-7-259 (Pubitemid 44202724)
6. EO Ermakova RN Nurtdinov MS Gelfand 2006 Fast rate of evolution in alternatively spliced coding regions of mammalian genes BMC Genomics 7 84 10.1186/1471-2164-7-84 16620375 10.1186/1471-2164-7-84
7. JC Fay CI Wu 2000 Hitchhiking under positive Darwinian selection Genetics 155 1405 1413 10880498 1:STN:280:DC%2BD3cvgsVSntQ%3D%3D (Pubitemid 30463447)
8. M Fedetz F Matesanz A Caro-Maldonado O Fernandez JA Tamayo M Guerrero C Delgado JA Lopez-Guerrero A Alcina 2006 OAS1 gene haplotype confers susceptibility to multiple sclerosis Tissue Antigens 68 446 449 10.1111/j.1399-0039.2006.00694.x 17092260 10.1111/j.1399-0039.2006.00694.x 1:CAS:528:DC%2BD28XhtlCnt7vE (Pubitemid 44707058)
9. LL Field V Bonnevie-Nielsen F Pociot S Lu TB Nielsen H Beck-Nielsen 2005 OAS1 splice site polymorphism controlling antiviral enzyme activity influences susceptibility to type 1 diabetes Diabetes 54 1588 1591 15855350 10.2337/diabetes.54.5.1588 1:CAS:528:DC%2BD2MXktVCktrg%3D (Pubitemid 40586694)
10. YX Fu WH Li 1993 Statistical tests of neutrality of mutations Genetics 133 693 709 8454210 1:STN:280:DyaK3s3gt1Crsw%3D%3D
11. M Fumagalli R Cagliani U Pozzoli S Riva GP Comi G Menozzi N Bresolin M Sironi 2009 Widespread balancing selection and pathogen-driven selection at blood group antigen genes Genome Res 19 199 212 10.1101/gr.082768.108 18997004 10.1101/gr.082768.108 1:CAS:528:DC%2BD1MXhvVSjurc%3D
12. M Fumagalli U Pozzoli R Cagliani GP Comi N Bresolin M Clerici M Sironi 2010 Genome-wide identification of susceptibility alleles for viral infections through a population genetics approach PLoS Genet 6 e1000849 10.1371/journal.pgen.1000849 20174570 10.1371/journal.pgen.1000849
13. GV Glazko M Nei 2003 Estimation of divergence times for major lineages of primate species Mol Biol Evol 20 424 434 12644563 10.1093/molbev/msg050 1:CAS:528:DC%2BD3sXisFaqsbs%3D (Pubitemid 36427177)
14. RC Griffiths S Tavare 1994 Sampling theory for neutral alleles in a varying environment Philos Trans R Soc Lond B Biol Sci 344 403 410 10.1098/rstb.1994.0079 7800710 10.1098/rstb.1994.0079 1:STN:280: DyaK2M%2FpvVyqtg%3D%3D
15. RC Griffiths S Tavare 1995 Unrooted genealogical tree probabilities in the infinitely-many-sites model Math Biosci 127 77 98 7734858 10.1016/0025-5564(94)00044-Z 1:STN:280:DyaK2M3lt1Ojug%3D%3D
16. SR Grossman I Shylakhter EK Karlsson EH Byrne S Morales G Frieden E Hostetter E Angelino M Garber O Zuk ES Lander SF Schaffner PC Sabeti 2010 A composite of multiple signals distinguishes causal variants in regions of positive selection Science 327 883 886 10.1126/science.1183863 20056855 10.1126/science.1183863 1:CAS:528:DC%2BC3cXhslWis7c%3D
17. E Hamano M Hijikata S Itoyama T Quy NC Phi HT Long LD Ha VV Ban I Matsushita H Yanai F Kirikae T Kirikae T Kuratsuji T Sasazuki N Keicho 2005 Polymorphisms of interferon-inducible genes OAS-1 and MxA associated with SARS in the Vietnamese population Biochem Biophys Res Commun 329 1234 1239 10.1016/j.bbrc.2005.02.101 15766558 10.1016/j.bbrc.2005.02.101 1:CAS:528:DC%2BD2MXit1eqtrY%3D (Pubitemid 40568701)
18. J He D Feng SJ de Vlas H Wang A Fontanet P Zhang S Plancoulaine F Tang L Zhan H Yang T Wang JH Richardus JD Habbema W Cao 2006 Association of SARS susceptibility with single nucleic acid polymorphisms of OAS1 and MxA genes: a case-control study BMC Infect Dis 6 106 10.1186/1471-2334-6-106 16824203 10.1186/1471-2334-6-106 (Pubitemid 44251444)
19. S Ke XH Zhang LA Chasin 2008 Positive selection acting on splicing motifs reflects compensatory evolution Genome Res 18 533 543 10.1101/gr.070268.107 18204002 10.1101/gr.070268.107 1:CAS:528:DC%2BD1cXks1alsL4%3D (Pubitemid 351482778)
20. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
21. CZ Li N Kato JH Chang R Muroyama RX Shao N Dharel R Sermsathanasawadi T Kawabe M Omata 2009 Polymorphism of OAS-1 determines liver fibrosis progression in hepatitis C by reduced ability to inhibit viral replication Liver Int 29 1413 1421 10.1111/j.1478-3231.2009.02061.x 19515215 10.1111/j.1478-3231.2009.02061.x 1:CAS:528:DC%2BD1MXht1GntL3I
22. JK Lim A Lisco DH McDermott L Huynh JM Ward B Johnson H Johnson J Pape GA Foster D Krysztof D Follmann SL Stramer LB Margolis PM Murphy 2009 Genetic variation in OAS1 is a risk factor for initial infection with West Nile virus in man PLoS Pathog 5 e1000321 10.1371/journal.ppat.1000321 19247438 10.1371/journal.ppat.1000321
23. RJ Lin HP Yu BL Chang WC Tang CL Liao YL Lin 2009 Distinct antiviral roles for human 2′,5′-oligoadenylate synthetase family members against dengue virus infection J Immunol 183 8035 8043 10.4049/jimmunol.0902728 19923450 10.4049/jimmunol.0902728 1:CAS:528:DC%2BD1MXhsFCkt7nF
24. H Lu L Lin S Sato Y Xing CJ Lee 2009 Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments PLoS Comput Biol 5 e1000608 10.1371/journal.pcbi.1000608 20019791 10.1371/journal.pcbi.1000608
25. H Lu L Lin S Sato Y Xing CJ Lee 2009 Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments PLoS Comput Biol 5 e1000608 10.1371/journal.pcbi.1000608 20019791 10.1371/journal.pcbi.1000608
26. T Mashimo M Lucas D Simon-Chazottes MP Frenkiel X Montagutelli PE Ceccaldi V Deubel JL Guenet P Despres 2002 A nonsense mutation in the gene encoding 2′-5′-oligoadenylate synthetase/L1 isoform is associated with West Nile virus susceptibility in laboratory mice Proc Natl Acad Sci USA 99 11311 11316 10.1073/pnas.172195399 12186974 10.1073/pnas.172195399 1:CAS:528:DC%2BD38XmslSmur8%3D (Pubitemid 34920922)
27. WI McDonald A Compston G Edan D Goodkin HP Hartung FD Lublin HF McFarland DW Paty CH Polman SC Reingold M Sandberg-Wollheim W Sibley A Thompson S van den Noort BY Weinshenker JS Wolinsky 2001 Recommended diagnostic criteria for multiple sclerosis: guidelines from the International Panel on the diagnosis of multiple sclerosis Ann Neurol 50 121 127 11456302 10.1002/ana.1032 1:STN:280:DC%2BD38%2FitFOhug%3D%3D (Pubitemid 32591472)
28. B Modrek C Lee 2002 A genomic view of alternative splicing Nat Genet 30 13 19 10.1038/ng0102-13 11753382 10.1038/ng0102-13 1:CAS:528: DC%2BD38XislSisA%3D%3D
29. B Modrek A Resch C Grasso C Lee 2001 Genome-wide detection of alternative splicing in expressed sequences of human genes Nucleic Acids Res 29 2850 2859 11433032 10.1093/nar/29.13.2850 1:CAS:528:DC%2BD3MXltlejs7g%3D (Pubitemid 32685050)
30. M Nei WH Li 1979 Mathematical model for studying genetic variation in terms of restriction endonucleases Proc Natl Acad Sci USA 76 5269 5273 291943 10.1073/pnas.76.10.5269 1:CAS:528:DyaL3cXitVWn (Pubitemid 10236121)
31. M O'Brien R Lonergan L Costelloe K O'Rourke JM Fletcher K Kinsella C Sweeney G Antonelli KH Mills C O'Farrelly M Hutchinson N Tubridy 2010 OAS1: a multiple sclerosis susceptibility gene that influences disease severity Neurology 75 411 418 10.1212/WNL.0b013e3181ebdd2b 20679634 10.1212/WNL. 0b013e3181ebdd2b
32. AA Perelygin SV Scherbik IB Zhulin BM Stockman Y Li MA Brinton 2002 Positional cloning of the murine flavivirus resistance gene Proc Natl Acad Sci USA 99 9322 9327 10.1073/pnas.142287799 12080145 10.1073/pnas.142287799 1:CAS:528:DC%2BD38XlsVGgsbw%3D (Pubitemid 34764612)
33. M Plass E Eyras 2006 Differentiated evolutionary rates in alternative exons and the implications for splicing regulation BMC Evol Biol 6 50 10.1186/1471-2148-6-50 16792801 10.1186/1471-2148-6-50
34. M Pugliatti G Rosati H Carton T Riise J Drulovic L Vecsei I Milanov 2006 The epidemiology of multiple sclerosis in Europe Eur J Neurol 13 700 722 10.1111/j.1468-1331.2006.01342.x 16834700 10.1111/j.1468-1331.2006.01342.x 1:STN:280:DC%2BD28vhsVOguw%3D%3D (Pubitemid 44143944)
35. Qu HQ, Polychronakos C; Type I Diabetes Genetics Consortium (2009) Reassessment of the type I diabetes association of the OAS1 locus. Genes Immun 10(Suppl 1):S69-S73. doi: 10.1038/gene.2009.95
36. SF Schaffner C Foo S Gabriel D Reich MJ Daly D Altshuler 2005 Calibrating a coalescent simulation of human genome sequence variation Genome Res 15 1576 1583 10.1101/gr.3709305 16251467 10.1101/gr.3709305 1:CAS:528:DC%2BD2MXhtF2itb7E (Pubitemid 41545011)
37. DJ Smyth JD Cooper CE Lowe S Nutland NM Walker DG Clayton JA Todd 2006 No evidence for association of OAS1 with type 1 diabetes in unaffected siblings or type 1 diabetic cases Diabetes 55 1525 1528 16644715 10.2337/db05-1452 1:CAS:528:DC%2BD28XksFahurk%3D (Pubitemid 44195397)
38. M Stephens P Scheet 2005 Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation Am J Hum Genet 76 449 462 10.1086/428594 15700229 10.1086/428594 1:CAS:528:DC%2BD2MXhsFKrsbg%3D (Pubitemid 40250525)
39. M Stephens NJ Smith P Donnelly 2001 A new statistical method for haplotype reconstruction from population data Am J Hum Genet 68 978 989 10.1086/319501 11254454 10.1086/319501 1:STN:280:DC%2BD3M3kslWgsA%3D%3D (Pubitemid 32289743)
40. F Tajima 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism Genetics 123 585 595 2513255 1:CAS:528: DyaK3cXhslentA%3D%3D (Pubitemid 19274682)
41. R Development Core Team (2008) R: a language and environment for statistical computing. Vienna, Austria
42. MC Tessier HQ Qu R Frechette F Bacot R Grabs SP Taback ML Lawson SE Kirsch TJ Hudson C Polychronakos 2006 Type 1 diabetes and the OAS gene cluster: association with splicing polymorphism or haplotype? J Med Genet 43 129 132 10.1136/jmg.2005.035212 16014697 10.1136/jmg.2005.035212 1:CAS:528: DC%2BD28XitF2hu74%3D (Pubitemid 43259624)
43. K Thornton 2003 Libsequence: a C++ class library for evolutionary genetic analysis Bioinformatics 19 2325 2327 14630667 10.1093/bioinformatics/btg316 1:CAS:528:DC%2BD3sXpvVSjurc%3D (Pubitemid 37483994)
44. GA Watterson 1975 On the number of segregating sites in genetical models without recombination Theor Popul Biol 7 256 276 1145509 10.1016/0040-5809(75) 90020-9 1:STN:280:DyaE2M7pvFSquw%3D%3D
45. SI Wright B Charlesworth 2004 The HKA test revisited: a maximum-likelihood-ratio test of the standard neutral model Genetics 168 1071 1076 10.1534/genetics.104.026500 15514076 10.1534/genetics.104.026500 (Pubitemid 39491480)
46. Y Xing C Lee 2005 Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences Proc Natl Acad Sci USA 102 13526 13531 10.1073/pnas.0501213102 16157889 10.1073/pnas.0501213102 1:CAS:528:DC%2BD2MXhtVygtr7M (Pubitemid 41420882)
47. XH Zhang LA Chasin 2006 Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons Proc Natl Acad Sci USA 103 13427 13432 10.1073/pnas.0603042103 16938881 10.1073/pnas.0603042103 1:CAS:528: DC%2BD28XpvVaktr0%3D (Pubitemid 44380124)