Validation of TaqMan® SNP genotyping specificity for rs12979860 of IL-28B: Modeling primer specificity in vitro

Journal of Virological Methods

Volumn 203, Issue , 2014, Pages 39-47

  Thomas, Brad S ^a   Joyce, Michael A ^a   Levin, Aviad ^a   Tyrrell, D Lorne J ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

HCV; IL 28B IFN 3; Off target amplification; QRT PCR; Rs12979860; SNP genotyping

Indexed keywords

IL28B PROTEIN, HUMAN; INTERLEUKIN DERIVATIVE;

GENETICS; GENOTYPING TECHNIQUE; HUMAN; PROCEDURES; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; TEMPERATURE; VALIDATION STUDY;

GENOTYPING TECHNIQUES; HUMANS; INTERLEUKINS; POLYMORPHISM, SINGLE NUCLEOTIDE; REAL-TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; TEMPERATURE;

EID: 84898667183     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2014.03.016     Document Type: Article

References (54)

1. 2013-05-07. http://www.ebi.ac.uk/compneur-srv/melting/.
2. 2013-05-08. http://mobyle.pasteur.fr/cgi-bin/portal.py.
3. Amanzada A., Goralczyk A.D., Schneider S., Moriconi F., Lindhorst A., Mihm S., Van Thiel D.H., Ramadori G. High predictability of a sustained virological response (87%) in chronic hepatitis C virus genotype 1 infection treatment by combined IL28B genotype analysis and gamma-glutamyltransferase/alanine aminotransferase ratio: a retrospective single-center study. Digestion 2012, 86:218-227. 10.1159/000339879.
4. Anthony D.D., Conry S.J., Medvik K., Sandhya Rani M.R., Falck-Ytter Y., Blanton R.E., Lederman M.M., Rodriguez B., Landay A.L., Sandberg J.K. Baseline levels of soluble CD14 and CD16+56- natural killer cells are negatively associated with response to interferon/ribavirin therapy during HCV-HIV-1 coinfection. J. Infect. Dis. 2012, 206:969-973. 10.1093/infdis/jis434.
5. Bensadoun P., Rodriguez C., Soulier A., Higgs M., Chevaliez S., Pawlotsky J.M. Genetic background of hepatocyte cell lines: are in vitro hepatitis C virus research data reliable?. Hepatology 2011, 54:748. 10.1002/hep.24278.
6. Cariani E., Critelli R., Rota C., Luongo M., Trenti T., Villa E. Interleukin 28B genotype determination using DNA from different sources: a simple and reliable tool for the epidemiological and clinical characterization of hepatitis C. J. Virol. Methods 2011, 178:235-238. 10.1016/j.jviromet.2011.08.021.
7. Charlton M.R., Thompson A., Veldt B.J., Watt K., Tillmann H., Poterucha J.J., Heimbach J.K., Goldstein D., McHutchison J. Interleukin-28B polymorphisms are associated with histological recurrence and treatment response following liver transplantation in patients with hepatitis C virus infection. Hepatology 2011, 53:317-324. 10.1002/hep.24074.
8. Cisse I.I., Kim H., Ha T. A rule of seven in Watson-Crick base-pairing of mismatched sequences. Nat. Struct. Mol. Biol. 2012, 19:623-627. 10.1038/nsmb.2294.
9. de Rueda P.M., Lopez-Nevot M.A., Saenz-Lopez P., Casado J., Martin-Casares A., Palomares P., Quiles R., Gila A., Romero-Gomez M., Pavon E.J., Munoz J.A., Carazo A., Sanz-Cameno P., Moreno-Otero R., Diago M., Leon J., Ruiz-Extremera A., Salmeron J. Importance of host genetic factors HLA and IL28B as predictors of response to pegylated interferon and ribavirin. Am. J. Gastroenterol. 2011, 106:1246-1254. 10.1038/ajg.2011.82.
10. Del Campo J.A., Ampuero J., Rojas L., Conde M., Rojas A., Maraver M., Millan R., Garcia-Valdecasas M., Garcia-Lozano J.R., Gonzalez-Escribano M.F., Romero-Gomez M. Insulin resistance predicts sustained virological response to treatment of chronic hepatitis C independently of the IL28b rs12979860 polymorphism. Aliment. Pharmacol. Ther. 2013, 37:74-80. 10.1111/apt.12113.
11. Diaz-San Segundo F., Weiss M., Perez-Martin E., Koster M.J., Zhu J., Grubman M.J., de los Santos T. Antiviral activity of bovine type III interferon against foot-and-mouth disease virus. Virology 2011, 413:283-292. 10.1016/j.virol.2011.02.023.
12. Dolezel J., Bartos J., Voglmayr H., Greilhuber J. Nuclear DNA content and genome size of trout and human. Cytometry A 2003, 51:127-128. (Author Reply 129). 10.1002/cyto.a.10013.
13. Donnelly R.P., Kotenko S.V. Interferon-lambda: a new addition to an old family. J. Interferon Cytokine Res. 2010, 30:555-564. 10.1089/jir.2010.0078.
14. Doyle S.E., Schreckhise H., Khuu-Duong K., Henderson K., Rosler R., Storey H., Yao L., Liu H., Barahmand-pour F., Sivakumar P., Chan C., Birks C., Foster D., Clegg C.H., Wietzke-Braun P., Mihm S., Klucher K.M. Interleukin-29 uses a type 1 interferon-like program to promote antiviral responses in human hepatocytes. Hepatology 2006, 44:896-906. 10.1002/hep.21312.
15. Dumousseau M., Rodriguez N., Juty N., Le Novere N. MELTING, a flexible platform to predict the melting temperatures of nucleic acids. BMC Bioinform. 2012, 13:101. 10.1186/1471-2105-13-101.
16. Feld J.J., Hoofnagle J.H. Mechanism of action of interferon and ribavirin in treatment of hepatitis C. Nature 2005, 436:967-972. 10.1038/nature04082.
17. Fiorina L., Paolucci S., Papadimitriou S., Baldanti F. Comparison of three different methods for the evaluation of IL28 and ITPA polymorphisms in patients infected with HCV. J. Virol. Methods 2012, 184:103-105. 10.1016/j.jviromet.2012.05.006.
18. Firpi R.J., Dong H., Clark V.C., Soldevila-Pico C., Morelli G., Cabrera R., Norkina O., Shuster J.J., Nelson D.R., Liu C. CC genotype donors for the interleukin-28B single nucleotide polymorphism are associated with better outcomes in hepatitis C after liver transplant. Liver Int. 2013, 33:72-78. 10.1111/liv.12013.
19. Fried M.W., Shiffman M.L., Reddy K.R., Smith C., Marinos G., Goncales F.L., Haussinger D., Diago M., Carosi G., Dhumeaux D., Craxi A., Lin A., Hoffman J., Yu J. Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection. N. Engl. J. Med. 2002, 347:975-982. 10.1056/NEJMoa020047.
20. Ge D., Fellay J., Thompson A.J., Simon J.S., Shianna K.V., Urban T.J., Heinzen E.L., Qiu P., Bertelsen A.H., Muir A.J., Sulkowski M., McHutchison J.G., Goldstein D.B. Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 2009, 461:399-401. 10.1038/nature08309.
21. Hadziyannis S.J., Koskinas J.S. Differences in epidemiology, liver disease and treatment response among HCV genotypes. Hepatol. Res. 2004, 29:129-135. 10.1016/j.hepres.2004.02.011.
22. Higuchi R. Rapid, efficient DNA extraction for PCR from cells or blood. Amplifications: A Forum for PCR Users 1989, 1-3.
23. Ito K., Higami K., Masaki N., Sugiyama M., Mukaide M., Saito H., Aoki Y., Sato Y., Imamura M., Murata K., Nomura H., Hige S., Adachi H., Hino K., Yatsuhashi H., Orito E., Kani S., Tanaka Y., Mizokami M. The rs8099917 polymorphism, when determined by a suitable genotyping method, is a better predictor for response to pegylated alpha interferon/ribavirin therapy in Japanese patients than other single nucleotide polymorphisms associated with interleukin-28B. J. Clin. Microbiol. 2011, 49:1853-1860. 10.1128/JCM.02139-10.
24. Kamal S.M., El Kamary S.S., Shardell M.D., Hashem M., Ahmed I.N., Muhammadi M., Sayed K., Moustafa A., Hakem S.A., Ibrahiem A., Moniem M., Mansour H., Abdelaziz M. Pegylated interferon alpha-2b plus ribavirin in patients with genotype 4 chronic hepatitis C: the role of rapid and early virologic response. Hepatology 2007, 46:1732-1740. 10.1002/hep.21917.
25. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Gage D., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., LeVine R., McEwan P., McKernan K., Meldrim J., Mesirov J.P., Miranda C., Morris W., Naylor J., Raymond C., Rosetti M., Santos R., Sheridan A., Sougnez C., Stange-Thomann N., Stojanovic N., Subramanian A., Wyman D., Rogers J., Sulston J., Ainscough R., Beck S., Bentley D., Burton J., Clee C., Carter N., Coulson A., Deadman R., Deloukas P., Dunham A., Dunham I., Durbin R., French L., Grafham D., Gregory S., Hubbard T., Humphray S., Hunt A., Jones M., Lloyd C., McMurray A., Matthews L., Mercer S., Milne S., Mullikin J.C., Mungall A., Plumb R., Ross M., Shownkeen R., Sims S., Waterston R.H., Wilson R.K., Hillier L.W., McPherson J.D., Marra M.A., Mardis E.R., Fulton L.A., Chinwalla A.T., Pepin K.H., Gish W.R., Chissoe S.L., Wendl M.C., Delehaunty K.D., Miner T.L., Delehaunty A., Kramer J.B., Cook L.L., Fulton R.S., Johnson D.L., Minx P.J., Clifton S.W., Hawkins T., Branscomb E., Predki P., Richardson P., Wenning S., Slezak T., Doggett N., Cheng J.F., Olsen A., Lucas S., Elkin C., Uberbacher E., Frazier M., Gibbs R.A., Muzny D.M., Scherer S.E., Bouck J.B., Sodergren E.J., Worley K.C., Rives C.M., Gorrell J.H., Metzker M.L., Naylor S.L., Kucherlapati R.S., Nelson D.L., Weinstock G.M., Sakaki Y., Fujiyama A., Hattori M., Yada T., Toyoda A., Itoh T., Kawagoe C., Watanabe H., Totoki Y., Taylor T., Weissenbach J., Heilig R., Saurin W., Artiguenave F., Brottier P., Bruls T., Pelletier E., Robert C., Wincker P., Smith D.R., Doucette-Stamm L., Rubenfield M., Weinstock K., Lee H.M., Dubois J., Rosenthal A., Platzer M., Nyakatura G., Taudien S., Rump A., Yang H., Yu J., Wang J., Huang G., Gu J., Hood L., Rowen L., Madan A., Qin S., Davis R.W., Federspiel N.A., Abola A.P., Proctor M.J., Myers R.M., Schmutz J., Dickson M., Grimwood J., Cox D.R., Olson M.V., Kaul R., Raymond C., Shimizu N., Kawasaki K., Minoshima S., Evans G.A., Athanasiou M., Schultz R., Roe B.A., Chen F., Pan H., Ramser J., Lehrach H., Reinhardt R., McCombie W.R., de la Bastide M., Dedhia N., Blocker H., Hornischer K., Nordsiek G., Agarwala R., Aravind L., Bailey J.A., Bateman A., Batzoglou S., Birney E., Bork P., Brown D.G., Burge C.B., Cerutti L., Chen H.C., Church D., Clamp M., Copley R.R., Doerks T., Eddy S.R., Eichler E.E., Furey T.S., Galagan J., Gilbert J.G., Harmon C., Hayashizaki Y., Haussler D., Hermjakob H., Hokamp K., Jang W., Johnson L.S., Jones T.A., Kasif S., Kaspryzk A., Kennedy S., Kent W.J., Kitts P., Koonin E.V., Korf I., Kulp D., Lancet D., Lowe T.M., McLysaght A., Mikkelsen T., Moran J.V., Mulder N., Pollara V.J., Ponting C.P., Schuler G., Schultz J., Slater G., Smit A.F., Stupka E., Szustakowski J., Thierry-Mieg D., Thierry-Mieg J., Wagner L., Wallis J., Wheeler R., Williams A., Wolf Y.I., Wolfe K.H., Yang S.P., Yeh R.F., Collins F., Guyer M.S., Peterson J., Felsenfeld A., Wetterstrand K.A., Patrinos A., Morgan M.J., de Jong P., Catanese J.J., Osoegawa K., Shizuya H., Choi S., Chen Y.J. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921. International Human Genome Sequencing C. 10.1038/35057062.
26. Le Novere N. MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics 2001, 17:1226-1227. 10.1093/bioinformatics/17.12.1226.
27. Lee I.C., Lin C.H., Huang Y.H., Huo T.I., Su C.W., Hou M.C., Huang H.C., Lee K.C., Chan C.C., Lin M.W., Lin H.C., Lee S.D. IL28B polymorphism correlates with active hepatitis in patients with HBeAg-negative chronic hepatitis B. PLoS ONE 2013, 8:e58071. 10.1371/journal.pone.0058071.
28. Liu M.Q., Zhou D.J., Wang X., Zhou W., Ye L., Li J.L., Wang Y.Z., Ho W.Z. IFN-lambda3 inhibits HIV infection of macrophages through the JAK-STAT pathway. PLoS ONE 2012, 7:e35902. 10.1371/journal.pone.0035902.
29. Malhotra S., Morcillo-Suarez C., Brassat D., Goertsches R., Lechner-Scott J., Urcelay E., Fernandez O., Drulovic J., Garcia-Merino A., Martinelli Boneschi F., Chan A., Vandenbroeck K., Navarro A., Bustamante M.F., Rio J., Akkad D.A., Giacalone G., Sanchez A.J., Leyva L., Alvarez-Lafuente R., Zettl U.K., Oksenberg J., Montalban X., Comabella M. IL28B polymorphisms are not associated with the response to interferon-beta in multiple sclerosis. J. Neuroimmunol. 2011, 239:101-104. 10.1016/j.jneuroim.2011.08.004.
30. Manns M.P., McHutchison J.G., Gordon S.C., Rustgi V.K., Shiffman M., Reindollar R., Goodman Z.D., Koury K., Ling M., Albrecht J.K. Peginterferon alfa-2b plus ribavirin compared with interferon alfa-2b plus ribavirin for initial treatment of chronic hepatitis C: a randomised trial. Lancet 2001, 358:958-965. 10.1016/S0140-6736(01)06102-5.
31. McCluskie M.J., Weeratna R.D. Novel adjuvant systems. Curr. Drug Targets Infect. Disord. 2001, 1:263-271.
32. Moghaddam A., Melum E., Reinton N., Ring-Larsen H., Verbaan H., Bjoro K., Dalgard O. IL28B genetic variation and treatment response in patients with hepatitis C virus genotype 3 infection. Hepatology 2011, 53:746-754. 10.1002/hep.24154.
33. Montes-Cano M.A., Garcia-Lozano J.R., Abad-Molina C., Romero-Gomez M., Barroso N., Aguilar-Reina J., Nunez-Roldan A., Gonzalez-Escribano M.F. Interleukin-28B genetic variants and hepatitis virus infection by different viral genotypes. Hepatology 2010, 52:33-37. 10.1002/hep.23624.
34. Pagliaccetti N.E., Chu E.N., Bolen C.R., Kleinstein S.H., Robek M.D. Lambda and alpha interferons inhibit hepatitis B virus replication through a common molecular mechanism but with different in vivo activities. Virology 2010, 401:197-206. 10.1016/j.virol.2010.02.022.
35. Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001, 29:e45. 10.1093/nar/29.9.e45.
36. Pol S., Aerssens J., Zeuzem S., Andreone P., Lawitz E.J., Roberts S., Younossi Z., Foster G.R., Focaccia R., Horban A., Pockros P.J., Van Heeswijk R.P., De Meyer S., Luo D., Botfield M., Beumont M., Picchio G. Limited impact of IL28B genotype on response rates in telaprevir-treated patients with prior treatment failure. J. Hepatol. 2013, 58:883-889. 10.1016/j.jhep.2012.12.023.
37. Reynolds J.M., Paciga S.A., Sanders F.A., Hyde C.L., Loomis A.K., Johnston G.I. Sequence analysis of the IL28A/IL28B inverted gene duplication that contains polymorphisms associated with treatment response in hepatitis C patients. PLoS ONE 2012, 7:e29983. 10.1371/journal.pone.0029983.
38. Ritz C., Streibig J.C. Bioassay analysis using R. J. Stat. Softw. 2005, 12:1-22.
39. Robek M.D., Boyd B.S., Chisari F.V. Lambda interferon inhibits hepatitis B and C virus replication. J. Virol. 2005, 79:3851-3854. 10.1128/JVI.79.6.3851-3854.2005.
40. Ruiz-Extremera A., Munoz-Gamez J.A., Salmeron-Ruiz M.A., de Rueda P.M., Quiles-Perez R., Gila-Medina A., Casado J., Belen Martin A., Sanjuan-Nunez L., Carazo A., Pavon E.J., Ocete-Hita E., Leon J., Salmeron J. Genetic variation in interleukin 28B with respect to vertical transmission of hepatitis C virus and spontaneous clearance in HCV-infected children. Hepatology 2011, 53:1830-1838. 10.1002/hep.24298.
41. Stattermayer A.F., Stauber R., Hofer H., Rutter K., Beinhardt S., Scherzer T.M., Zinober K., Datz C., Maieron A., Dulic-Lakovic E., Kessler H.H., Steindl-Munda P., Strasser M., Krall C., Ferenci P. Impact of IL28B genotype on the early and sustained virologic response in treatment-naive patients with chronic hepatitis C. Clin. Gastroenterol. Hepatol. 2011, 9. 344-350 e2. 10.1016/j.cgh.2010.07.019.
42. Stenkvist J., Sonnerborg A., Weiland O. HCV RNA decline in chronic HCV genotype 2 and 3 during standard of care treatment according to IL28B polymorphism. J. Viral Hepat. 2013, 20:193-199. 10.1111/j.1365-2893.2012.01645.x.
43. Sugiyama M., Kimura T., Naito S., Mukaide M., Shinauchi T., Ueno M., Ito K., Murata K., Mizokami M. Development of specific and quantitative real-time detection PCR and immunoassays for lambda3-interferon. Hepatol. Res. 2012, 42:1089-1099. 10.1111/j.1872-034X.2012.01032.x.
44. Sugiyama M., Tanaka Y., Wakita T., Nakanishi M., Mizokami M. Genetic variation of the IL-28B promoter affecting gene expression. PLoS ONE 2011, 6:e26620. 10.1371/journal.pone.0026620.
45. Suppiah V., Moldovan M., Ahlenstiel G., Berg T., Weltman M., Abate M.L., Bassendine M., Spengler U., Dore G.J., Powell E., Riordan S., Sheridan D., Smedile A., Fragomeli V., Muller T., Bahlo M., Stewart G.J., Booth D.R., George J. IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy. Nat. Genet. 2009, 41:1100-1104. 10.1038/ng.447.
46. Tajir M., Elmachad M., Kabbaj N., Laarabi F.Z., Barkat A., Amrani N., Sefiani A. Frequency of IL28B rs12979860 single-nucleotide polymorphism alleles in newborn infants and in patients with chronic hepatitis C in Morocco. Genet. Test. Mol. Biomarkers 2012, 16:981-983. 10.1089/gtmb.2011.0353.
47. Tanaka Y., Nishida N., Sugiyama M., Kurosaki M., Matsuura K., Sakamoto N., Nakagawa M., Korenaga M., Hino K., Hige S., Ito Y., Mita E., Tanaka E., Mochida S., Murawaki Y., Honda M., Sakai A., Hiasa Y., Nishiguchi S., Koike A., Sakaida I., Imamura M., Ito K., Yano K., Masaki N., Sugauchi F., Izumi N., Tokunaga K., Mizokami M. Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C. Nat. Genet. 2009, 41:1105-1109. 10.1038/ng.449.
48. Thomas D.L., Thio C.L., Martin M.P., Qi Y., Ge D., O'Huigin C., Kidd J., Kidd K., Khakoo S.I., Alexander G., Goedert J.J., Kirk G.D., Donfield S.M., Rosen H.R., Tobler L.H., Busch M.P., McHutchison J.G., Goldstein D.B., Carrington M. Genetic variation in IL28B and spontaneous clearance of hepatitis C virus. Nature 2009, 461:798-801. 10.1038/nature08463.
49. Tillmann H.L., Thompson A.J., Patel K., Wiese M., Tenckhoff H., Nischalke H.D., Lokhnygina Y., Kullig U., Gobel U., Capka E., Wiegand J., Schiefke I., Guthoff W., Grungreiff K., Konig I., Spengler U., McCarthy J., Shianna K.V., Goldstein D.B., McHutchison J.G., Timm J., Nattermann J. A polymorphism near IL28B is associated with spontaneous clearance of acute hepatitis C virus and jaundice. Gastroenterology 2010, 139. German Anti, D.S.G., 1586-1592, 1592e1. 10.1053/j.gastro.2010.07.005.
50. Urban T.J., Thompson A.J., Bradrick S.S., Fellay J., Schuppan D., Cronin K.D., Hong L., McKenzie A., Patel K., Shianna K.V., McHutchison J.G., Goldstein D.B., Afdhal N. IL28B genotype is associated with differential expression of intrahepatic interferon-stimulated genes in patients with chronic hepatitis C. Hepatology 2010, 52:1888-1896. 10.1002/hep.23912.
51. van den Berg C.H., Grady B.P., Schinkel J., van de Laar T., Molenkamp R., van Houdt R., Coutinho R.A., van Baarle D., Prins M. Female sex and IL28B, a synergism for spontaneous viral clearance in hepatitis C virus (HCV) seroconverters from a community-based cohort. PLoS ONE 2011, 6:e27555. 10.1371/journal.pone.0027555.
52. Watkins N.E., SantaLucia J. Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Res. 2005, 33:6258-6267. 10.1093/nar/gki918.
53. Weibull W. A statistical distribution function of wide applicability. J. Appl. Mech. 1951, 293-297.
54. Wiegand J., Neumann K., Bohm S., Weich V., Teuber G., Klinker H., Moller B., Rasenack J., Hinrichsen H., Gerlach T., Spengler U., Buggisch P., Sarrazin C., Berg T. Importance of minimal residual viremia for relapse prediction in patients with chronic hepatitis C genotype 1 infection. Clin. Infect. Dis. 2011, 53:1111-1114. 10.1093/cid/cir670.