title: Haplotyping using a combination of polymerase chain reaction-single-strand conformational polymorphism analysis and haplotype-specific PCR amplification.
abstract: A single nucleotide polymorphism (SNP) may have an impact on phenotype, but it may also be influenced by multiple SNPs within a gene; hence, the haplotype or phase of multiple SNPs needs to be known. Various methods for haplotyping SNPs have been proposed, but a simple and cost-effective method is currently unavailable. Here we describe a haplotyping approach using two simple techniques: polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP) and haplotype-specific PCR. In this approach, individual regions of a gene are analyzed by PCR-SSCP to identify variation that defines sub-haplotypes, and then extended haplotypes are assembled from the sub-haplotypes either directly or with the additional use of haplotype-specific PCR amplification. We demonstrate the utility of this approach by haplotyping ovine FABP4 across two variable regions that contain seven SNPs and one indel. The simplicity of this approach makes it suitable for large-scale studies and/or diagnostic screening.
authors.affiliation: Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
authors.forename: Huitong
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
authors.forename: Shaobin
authors.initials: S
authors.lastname: Li
authors.affiliation: Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
authors.forename: Xiu
authors.initials: X
authors.lastname: Liu
authors.affiliation: Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
authors.forename: Jiqing
authors.initials: J
authors.lastname: Wang
authors.affiliation: Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China. Electronic address: luoyz@gsau.edu.cn.
authors.forename: Yuzhu
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand. Electronic address: jon.hickford@lincoln.ac.nz.
authors.forename: Jon G H
authors.initials: JG
authors.lastname: Hickford
mesh_terms: D000818:Animals; D001483:Base Sequence; D016172:DNA Fingerprinting / Q000379:methods*; D050556:Fatty Acid-Binding Proteins / Q000235:genetics; D006239:Haplotypes; D006801:Humans; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques; D016133:Polymerase Chain Reaction; D018807:Polymorphism, Single-Stranded Conformational; D012756:Sheep
chemical_list: D050556:Fatty Acid-Binding Proteins
keywords: Haplotype-specific PCR amplification; Haplotyping; PCR–SSCP; SNP haplotype