title: Direct determination of MUC5B promoter haplotypes based on the method of single-strand conformation polymorphism and their statistical estimation.
abstract: Haplotype-based human genome research is important in identifying disease susceptibility genes efficiently. Although haplotype reconstruction by statistical methods is widely used, direct haplotype determination by molecular techniques has also been developed as a complementary method for statistical estimation. In this study, we demonstrate a molecular haplotyping method making use of single-strand conformation polymorphism (SSCP) gels. We identified 10 common SNPs and a dinucleotide insertion/deletion polymorphism within 2-kb region upstream of the transcription initiation site of MUC5B and determined haplotype structure, dividing the region into two DNA fragments. Real haplotypes were determined unambiguously by our SSCP-based analysis with fragments longer than 1 kb. Haplotypes reconstructed from diploid genotypes in the same region by the statistical methods including EM algorithm were also evaluated. Direct comparison between statistical estimation and direct determination of haplotypes revealed that major haplotypes containing multiple marker sites showing strong LD are estimated in great accuracy but that a variety of haplotypes reflecting weak LD are not reconstructed precisely enough. Our data can be helpful in implementing molecular haplotyping or statistical estimation, since usage of these methods may be determined depending on the haplotype structures.
authors.affiliation: Department of Respiratory Diseases, Research Institute, International Medical Center of Japan, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan.
authors.forename: Koichiro
authors.initials: K
authors.lastname: Kamio
authors.forename: Ikumi
authors.initials: I
authors.lastname: Matsushita
authors.forename: Goh
authors.initials: G
authors.lastname: Tanaka
authors.forename: Jun
authors.initials: J
authors.lastname: Ohashi
authors.forename: Minako
authors.initials: M
authors.lastname: Hijikata
authors.forename: Koh
authors.initials: K
authors.lastname: Nakata
authors.forename: Katsushi
authors.initials: K
authors.lastname: Tokunaga
authors.forename: Arata
authors.initials: A
authors.lastname: Azuma
authors.forename: Shoji
authors.initials: S
authors.lastname: Kudoh
authors.forename: Naoto
authors.initials: N
authors.lastname: Keicho
mesh_terms: D001483:Base Sequence; D001499:Bayes Theorem; D017931:DNA Primers; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D007564:Japan; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D055257:Mucin-5B; D009077:Mucins / Q000235:genetics*; D018807:Polymorphism, Single-Stranded Conformational; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D017931:DNA Primers; C524578:MUC5B protein, human; D055257:Mucin-5B; D009077:Mucins