Iyengar S, Seaman M, Deinard A S, Rosenbaum H C, Sirugo G, Castiglione C M, Kidd J R, Kidd K K
Dept. of Genetics, Yale University School of Medicine, Yale University, New Haven, CT 06520, USA.
DNA Seq. 1998;8(5):317-27. doi: 10.3109/10425179809034076.
In numerous population genetic and disease association studies decisions about the ancestry of polymorphic alleles are often made based on the relative frequency of the alleles in the extant populations with the most frequent allele being deemed as ancestral. However, the frequency of an allele in a population is generally not a perfect indicator of its ancestral status. A more accurate method to assess ancestral/derived status of polymorphic alleles involves identification of shared alleles between species. We used this strategy to examine genomic regions homologous to several human polymorphisms in four species of non-human primates. Cross species polymerase chain reaction (CS-PCR), with primers designed from human sequence, was used to investigate regions of interest. Nineteen polymorphisms at six loci (DRD2, HOXB@, PAH, D4S10, RBP3, and RET) were examined either by restriction fragment length analysis of PCR products (PCR-RFLP) or by direct sequencing. At seventeen of the eighteen PCR-RFLPs, non-human primates were monomorphic and identical to each other for either lack of restriction enzyme site or presence of the site. Thus, at these seventeen polymorphic sites the shared alleles are most likely to be the ancestral ones in humans. In several cases we have used sequence data to further demonstrate that the nucleotide at the site of the polymorphism is conserved between species confirming the hypothesis of a single ancestral allele. However, not all human alleles can be simply resolved into ancestral and derived; sequence data from one PCR-RFLP (in an intron of the PAH locus) and a single strand conformational polymorphism (SSCP) in the 3' untranslated region (UTR) of the DRD2 gene illustrate this point.
在众多群体遗传学和疾病关联研究中，关于多态性等位基因的祖先状态的判定通常是基于现存群体中等位基因的相对频率，其中最常见的等位基因被视为祖先型。然而，一个群体中等位基因的频率通常并非其祖先状态的完美指标。一种更准确地评估多态性等位基因的祖先/衍生状态的方法涉及识别物种间共享的等位基因。我们运用这一策略来检测与几种人类多态性同源的非人类灵长类动物四个物种的基因组区域。利用从人类序列设计的引物进行跨物种聚合酶链反应（CS-PCR），以研究感兴趣的区域。通过对PCR产物的限制性片段长度分析（PCR-RFLP）或直接测序，检测了六个位点（DRD2、HOXB@、PAH、D4S10、RBP3和RET）的19个多态性。在18个PCR-RFLP中的17个中，非人类灵长类动物要么因缺乏限制性酶切位点，要么因存在该位点而呈单态且彼此相同。因此，在这17个多态性位点，共享的等位基因很可能是人类中的祖先型等位基因。在一些情况下，我们利用序列数据进一步证明，多态性位点处的核苷酸在物种间是保守的，从而证实了单一祖先等位基因的假说。然而，并非所有人类等位基因都能简单地分为祖先型和衍生型；来自一个PCR-RFLP（PAH位点的一个内含子中）的序列数据以及DRD2基因3'非翻译区（UTR）中的一个单链构象多态性（SSCP）说明了这一点。
