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Cis acting expression loci in multiple sclerosis
Journal of Neuroimmunology 162 (2005) 3 – 4 www.elsevier.com/locate/jneuroim
Letter to the Editor Cis acting expression loci in multiple sclerosis Keywords: Multiple sclerosis; Genetics; Expression loci
Dear Sir, In their recent publication, Morley et al. (Morley et al., 2004) combined microarray expression analysis with whole genome linkage screening in order to localise genetic determinants influencing gene expression (bregulatorsQ). Using a stringent linkage significance threshold, they identified a total of 142 such regulator regions, 27 of which are located within 5Mb of the regulated gene (referred to by the authors as cis acting regulators). Extended analysis of these cis acting loci revealed 14 where the tested marker also showed evidence of association with expression, indicating that the typed variants either directly influence expression or are in linkage disequilibrium with nearby variants primarily responsible for this functional effect. Seven of these loci (rs1061810, rs1506440, rs2030364, rs2280714, rs4128767, rs4869311 and rs6547625) regulate genes of immunological importance and could therefore be expected to influence functions of the immune system. Given the higher prior probability that functionally important variants influence susceptibility to complex disease such as multiple sclerosis (Tabor et al., 2002), we decided to study the relevance of these seven SNPs in the context of multiple sclerosis. Association was sought by typing each variant in 938 trio families (an affected
individual and both parents) using TaqMan methodology (Holland et al., 1991). These assays were performed on a 7900HT Sequence Detection System according to the manufacturerTs standard conditions. The TRANSMIT program (Clayton, 1999) was used to search for evidence of transmission distortion (Table 1). In each case, 163 samples were typed in duplicate to test genotyping accuracy and only one inconsistency was observed (in marker rs1506440). Mendelian inheritance was consistent across all families for each marker except rs1061810 (where three inconsistencies were observed) and rs4869311 (where two inconsistencies were observed). These data indicate that the overall genotyping error rate is b 0.1%. None of the markers showed deviation from Hardy Weinberg equilibrium. Even without Bonferroni correction, none of the SNPs show any statistically significant evidence of association. In conclusion, we have found no evidence that the variants we have tested from these functionally important and immunologically relevant loci influence susceptibility to multiple sclerosis. However, we cannot confidently exclude these genes as potential candidate susceptibility genes as it is possible that other variants within or near to these genes might influence susceptibility to multiple sclerosis.
Acknowledgements We thank members of the Association of British Neurologists for notifying families. This work was supported by the Wellcome Trust (grant 057097), the Multiple
Table 1 Immunological cis regulator SNPs in multiple sclerosis Marker
ABI Assay ID
Gene Symbol
Genotyping ratea %
Heterozygosity %
Minor allele frequency %
Uncorrected p-value
rs1061810 rs1506440 rs2030364 rs2280714 rs4128767 rs4869311 rs6547625
C___8695157_10 C___8340608_1_ C__11224873_10 C___2691243_1_ C____110200_10 C___2846789_20 C___2091642_1_
HSD17B12 RPS26 PPAT TNPO3 IL16 LRAP VAMP8
95.9 96.5 98.2 98.9 99.4 96.4 98.9
41.2 50.0 49.3 43.4 42.8 49.8 48.8
29.5 41.1 48.4 34 30.9 48.9 43.2
0.55 0.87 0.33 0.56 0.88 0.32 0.57
a
The proportion of potential genotypes successfully determined.
0165-5728/$ - see front matter D 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.jneuroim.2005.02.007
4
Letter to the Editor
Sclerosis Society of the United States (grant RG3500-A-1) and the Multiple Sclerosis Society of Great Britain and Ireland (grant 730/02). References Clayton, D., 1999. A generalization of the transmission/disequilibrium test for uncertain-haplotype transmission. Am. J. Hum. Genet. 65, 1170 – 1177. Holland, P.M., Abramson, R.D., Watson, R., Gelfand, D.H., 1991. Detection of specific polymerase chain reaction product by utilizing the 5V–3V exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 88, 7276 – 7280. Morley, M., Molony, C.M., Weber, T.M., Devlin, J.L., Ewens, K.G., Spielman, R.S., Cheung, V.G., 2004. Genetic analysis of genome-wide variation in human gene expression. Nature 430, 743 – 747. Tabor, H.K., Risch, N.J., Myers, R.M., 2002. Candidate-gene approaches for studying complex genetic traits: practical considerations. Nat. Rev., Genet. 3, 1 – 7.
Maria BanT Mel Maranian Tai Wai Yeo Julia Gray Alastair Compston Stephen Sawcer University of Cambridge Neurology Unit, Level 6, bAQ Department of Clinical Neurosciences, Addenbrooke’s Hospital, Box 165, Hills Road, Cambridge CB2 2QQ, UK E-mail address: [email protected]. TCorresponding author. Tel.: +44 1223 217842; fax: +44 1223 336941. 18 January 2005
Letter to the Editor Cis acting expression loci in multiple sclerosis Keywords: Multiple sclerosis; Genetics; Expression loci
Dear Sir, In their recent publication, Morley et al. (Morley et al., 2004) combined microarray expression analysis with whole genome linkage screening in order to localise genetic determinants influencing gene expression (bregulatorsQ). Using a stringent linkage significance threshold, they identified a total of 142 such regulator regions, 27 of which are located within 5Mb of the regulated gene (referred to by the authors as cis acting regulators). Extended analysis of these cis acting loci revealed 14 where the tested marker also showed evidence of association with expression, indicating that the typed variants either directly influence expression or are in linkage disequilibrium with nearby variants primarily responsible for this functional effect. Seven of these loci (rs1061810, rs1506440, rs2030364, rs2280714, rs4128767, rs4869311 and rs6547625) regulate genes of immunological importance and could therefore be expected to influence functions of the immune system. Given the higher prior probability that functionally important variants influence susceptibility to complex disease such as multiple sclerosis (Tabor et al., 2002), we decided to study the relevance of these seven SNPs in the context of multiple sclerosis. Association was sought by typing each variant in 938 trio families (an affected
individual and both parents) using TaqMan methodology (Holland et al., 1991). These assays were performed on a 7900HT Sequence Detection System according to the manufacturerTs standard conditions. The TRANSMIT program (Clayton, 1999) was used to search for evidence of transmission distortion (Table 1). In each case, 163 samples were typed in duplicate to test genotyping accuracy and only one inconsistency was observed (in marker rs1506440). Mendelian inheritance was consistent across all families for each marker except rs1061810 (where three inconsistencies were observed) and rs4869311 (where two inconsistencies were observed). These data indicate that the overall genotyping error rate is b 0.1%. None of the markers showed deviation from Hardy Weinberg equilibrium. Even without Bonferroni correction, none of the SNPs show any statistically significant evidence of association. In conclusion, we have found no evidence that the variants we have tested from these functionally important and immunologically relevant loci influence susceptibility to multiple sclerosis. However, we cannot confidently exclude these genes as potential candidate susceptibility genes as it is possible that other variants within or near to these genes might influence susceptibility to multiple sclerosis.
Acknowledgements We thank members of the Association of British Neurologists for notifying families. This work was supported by the Wellcome Trust (grant 057097), the Multiple
Table 1 Immunological cis regulator SNPs in multiple sclerosis Marker
ABI Assay ID
Gene Symbol
Genotyping ratea %
Heterozygosity %
Minor allele frequency %
Uncorrected p-value
rs1061810 rs1506440 rs2030364 rs2280714 rs4128767 rs4869311 rs6547625
C___8695157_10 C___8340608_1_ C__11224873_10 C___2691243_1_ C____110200_10 C___2846789_20 C___2091642_1_
HSD17B12 RPS26 PPAT TNPO3 IL16 LRAP VAMP8
95.9 96.5 98.2 98.9 99.4 96.4 98.9
41.2 50.0 49.3 43.4 42.8 49.8 48.8
29.5 41.1 48.4 34 30.9 48.9 43.2
0.55 0.87 0.33 0.56 0.88 0.32 0.57
a
The proportion of potential genotypes successfully determined.
0165-5728/$ - see front matter D 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.jneuroim.2005.02.007
4
Letter to the Editor
Sclerosis Society of the United States (grant RG3500-A-1) and the Multiple Sclerosis Society of Great Britain and Ireland (grant 730/02). References Clayton, D., 1999. A generalization of the transmission/disequilibrium test for uncertain-haplotype transmission. Am. J. Hum. Genet. 65, 1170 – 1177. Holland, P.M., Abramson, R.D., Watson, R., Gelfand, D.H., 1991. Detection of specific polymerase chain reaction product by utilizing the 5V–3V exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 88, 7276 – 7280. Morley, M., Molony, C.M., Weber, T.M., Devlin, J.L., Ewens, K.G., Spielman, R.S., Cheung, V.G., 2004. Genetic analysis of genome-wide variation in human gene expression. Nature 430, 743 – 747. Tabor, H.K., Risch, N.J., Myers, R.M., 2002. Candidate-gene approaches for studying complex genetic traits: practical considerations. Nat. Rev., Genet. 3, 1 – 7.
Maria BanT Mel Maranian Tai Wai Yeo Julia Gray Alastair Compston Stephen Sawcer University of Cambridge Neurology Unit, Level 6, bAQ Department of Clinical Neurosciences, Addenbrooke’s Hospital, Box 165, Hills Road, Cambridge CB2 2QQ, UK E-mail address: [email protected]. TCorresponding author. Tel.: +44 1223 217842; fax: +44 1223 336941. 18 January 2005