Background & Objectives: Studying several linked markers provides more information on locating disease genes locus by using genetic association analysis.  The aims of this study were to introduce Multimarker Family Base Association Tests (FBAT-MM) and its Linear Combination (FBAT-LC) in multimarker genetic association analysis and to examine the association of selected microsatellites with HDL-C in an Iranian population.
Methods: One hundred twenty five (125) families having at least one member with metabolic syndrome and at least two members with low HDL-C were selected from participants of the Tehran Lipid and Glucose Study (TLGS). Multimarker genetic association of HDL-C level with some microsatellites in the chromosomes 8, 11, 12, and 16 were examined using FBAT-MM and FBAT-LC methods.
Results: The families consisted of 563 individuals (269 males and 294 females). FBAT-MM showed significant genetic association only between HDL-C and three microsatellites in Chromosome 11 (P<0.05). The microsatellite D11S1304 was found as the significant factor for multimarker genetic association.
Conclusion: FBAT-MM and FBAT-LC did not show shortcomings such as excessive conservatism and low power which are, usually, observed in other multimarker methods.  Finding microsatellites associated with HDL-C level can provide background for further researches on the role of predisposing genes in metabolic syndrome.

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