Frequency and distribution in three ethnic populations of single nucleotide polymorphisms in the MICA gene

The Homo sapiens major histocompatibility complex (MHC) class 1 chain related gene A (MICA) was scanned for novel single nucleotide polymorphisms (SNPs) using a panel of DNA samples from African-, Japanese- and Mexican-Americans. Overlapping primer-pairs were used to amplify products in the size range of 300 to 400 bp that were sequenced and scanned for SNPs using Phred, Phrap, Polyphred and Consed sequence analysis programs. A total of 16 SNPs were detected, six of which represent new variant nucleotides in the Homo sapiens MICA gene. Three of the variants also represent amino acid changes in the MICA protein. Differences among the three ethnic panels in the frequency of the variant nucleotides observed were inconsistent, but significant for seven of the SNPs detected. Though a small sample size, this study represents the first multi-population based analysis of the frequency and distribution of SNPs in the MICA gene, a locus that may be essential in the antigenic recognition by gammadelta T cells.