DNA sequence variation and haplotype structure of the ICAM1 and TNF genes in 12 ethnic groups of India reveal patterns of importance in designing association studies

Annals of Human Genetics

Volumn 68, Issue 6, 2004, Pages 574-587

  Sengupta, S ^a   Farheen, S ^a   Mukherjee, N ^a   Dey, B ^a   Mukhopadhyay, B ^a   Sil, S K ^b   Prabhakaran, N ^c   Ramesh, A ^c   Edwin, D ^d   Usha Rani, M V ^d   Mitra, M ^e   Mahadik, C T ^f   Singh, S ^g   Sehgal, S C ^g   Majumder, P P ^a  

^a INDIAN STATISTICAL INSTITUTE   (India)

^b TRIPURA UNIVERSITY   (India)

^c UNIVERSITY OF MADRAS   (India)

^d BHARATHIAR UNIVERSITY   (India)

^e PT RAVISHANKAR SHUKLA UNIVERSITY   (India)

^f B J Wadai Hosp Children/Res Centre   (India)

^g INDIAN COUNCIL OF MEDICAL RESEARCH   (India)

Author keywords

Genetic affinity; Genetic structure; Linkage disequilibrium; Single nucleotide polymorphism

Indexed keywords

DNA; INTERCELLULAR ADHESION MOLECULE 1; TUMOR NECROSIS FACTOR;

ARTICLE; BLOOD SAMPLING; CASE CONTROL STUDY; CHROMOSOME 19P; CHROMOSOME 6P; CONTROLLED STUDY; DNA SEQUENCE; ENDEMIC DISEASE; ETHNIC DIFFERENCE; ETHNIC GROUP; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; HUMAN CELL; INDIA; MAJOR CLINICAL STUDY; MALARIA; PLASMODIUM MALARIAE; POLYMERASE CHAIN REACTION; POPULATION GENETICS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; GENE FREQUENCY; HAPLOTYPES; HUMANS; INDIA; INTERCELLULAR ADHESION MOLECULE-1; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; RESEARCH DESIGN; TUMOR NECROSIS FACTOR-ALPHA; VARIATION (GENETICS);

EID: 19944382764     PISSN: 00034800     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1529-8817.2003.00126.x     Document Type: Article

References (17)

1. Basu, A., Mukherjee, N., Roy, S., Sengupta, S., Banerjee, S., Chakraborty, M., Dey, B., Roy, M., Roy, B., Bhattacharyya, N. P., Roychoudhury, S. & Majumder, P. P. (2003) Ethnic India: a genomic view, with special reference to peopling and structure. Genome Res 13 2277-2290.
2. Bjornsdottir, U. S. & Cypcar, D. M. (1999) Asthma: An inflammatory mediator soup. Allergy 54, 55-61.
3. Carlson, C. S., Eberle, M. A., Reider, M. J., Smith, J. D., Kruglyak, L. & Nickerson, D. A. (2003) Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet 33, 518-521.
4. Chattopadhyay P., Patkis, A. J., Mukherjee, N., Iyengar, S., Odunsi, A., Okonofua, F., Bonne-Tamir, B., Speed, W., Kidd, J. R. & Kidd, K. K. (2003) Global survey of haplotype frequencies and linkage disequilibrium at the RET locus. Eur J Hum Genet 10, 760-769.
5. Dobbie, M. S., Hurst, R. D., Klein, N. J. & Surtees, R. A. (1999) Upregulation of intercellular adhesion molecule-1 expression on human endothelial cells by tumour necrosis factor-alpha in an in vitro model of the blood-brain barrier. Brain Res 830, 330-336
6. Fernandez-Reyes, D., Craig, A. G., Kyes, S. A., Peshu, N., Snow, R. W., Berendt, A. R., Marsh, K. & Newbold, C. I. (1997) A high frequency African coding polymorphism in the N-terminal domain of ICAM-1 predisposing to cerebral malaria in Kenya. Hum Mol Genet 6, 1357-1360.
7. Gimenez, F., de Lagerie, S. B., Fernandez, F., Pino, P. & Mazier, D. (2003) Tumor necrosis factor α in the pathogenesis of cerebral malaria. Cell Mol Life Sci 60, 1623-1635.
8. Knight, J. C., Udalova, I., Hill, A. V., Greenwood, B. M., Peshu, N., Marsh, K. & Kwiatkowski, D. (1999) A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria. Nat Genet 22, 145-150.
9. Majumdar, P. & Majumder, P. P. (1999) HAPLOPOP: A computer program package to estimate haplotype frequencies from genotype frequencies via the EM algorithm. AHGU Tech Rep. Indian Statistical Institute, Kolkata.
10. Mattila, K. M., Hiltunen, M., Rinne, J. O., Mannermaa, A., Röyttä, M., Alafuzoff, I., Laippala, P., Soininen, H. & Lehtimäki, T. (2003) Absence of association between an intercellular adhesion molecule 1 gene E469K polymorphism and Alzheimer's disease in Finnish patients. Neurosci Lett 337, 61-63.
11. McGuire, W., Knight, J. C., Hill, A. V., Allsopp, C. E., Greenwood, B. M. & Kwiatkowski, D. (1999) Severe malarial anemia and cerebral malaria are associated with different tumor necrosis factor promoter alleles. J Infect Dis 179, 287-289
12. Meager, A. (1999) Cytokine regulation of cellular adhesion molecule expression in inflammation. Cytokine Growth Factor Rev 10, 27-39.
13. Pola, R., Flex, A., Gaetani, E., Papaleo, P., De Martini, D., Gerardino, L., Serricchio, M., Pola, P. & Berbabei, R. (2003) Intercellular adhesion molecule-1 K469E gene polymorphism and Alzheimer's disease. Neurobiol Aging 24, 385-387.
14. Reich, D. E., Gabriel, S. B. & Altshuler, D. (2003) Quality and completeness of SNP databases. Nat Genet 33, 457-458.
15. Saitou, N. & Nei, M. (1998) The neighbour-joining method: a new method for reconstrucing phylogenetic trees. Mol Biol Evol 4 406-425
16. Striz, I., Mio, T. & Adachi, Y. (1999) IL-4 induces ICAM-1 expression in human bronchial epithelial cells and potentiates TNF-alpha. Am J Physiol 277, L58-64.
17. Wilson, A. G., Symons, J. A., McDowell, T. L., McDevitt, H. O., Duff, G. W. (1997) Effects of a polymorphism in the human tumor necrosis factor alpha promoter on transcriptional activation. Proc Natl Acad Sci USA 94, 3195-3199.