生活於台灣地區八個族群之COI及MTCYB基因序列變化之分析

Abstract

背景和目的 粒線體DNA的分析是法醫案件調查的重要工具之一，粒線體DNA非轉譯區，變異頻率最高的高變異區一及高度變異區二已有資料庫可供比對，進一步分析粒線體DNA轉譯區的多型性，可以增加多型性資料，提升粒線體DNA在法醫分子生物學領域應用的價值。 粒線體上轉譯區的COI基因及MTCYB基因序列被發現有相當多的變異性，可以被用於物種鑑別，但是人類的COI基因及MTCYB基因序列的變化，鮮少有人研究，本研究目的為分析在台灣生活的不同族群的人的COI基因及MTCYB基因序列多型性，進而探討這兩個基因序列在法醫學上的應用。 研究材料和方法 本研究以DNA排序方法，分析在台灣生活的8個族群共565個個案的COI及MTCYB基因序列，這些個案分別屬於台灣漢人(120人)、台灣本島原住民(148人)、蘭嶼的達悟族(53人)、中國大陸人(56人)、菲律賓人(55人)、泰國人(51人)、越南人(51人)及高加索種人(31人)，把各檢體的DNA序列與修正的劍橋參考序列( revised Cambridge Reference Sequence)作比較，列出序列不同處，且依此作型別分析。 計算各族群的型別 (haplotype)頻率，找出族群特異性序列，統計各族群依COI序列、MTCYB序列或合併COI及MTCYB序列所統計得到的型別變異型 (haplotype diversity)、核苷酸變異性 (nucleotide diversity) 及鑑別能力 (discrimination power)。計算各族群之間依COI序列、MTCYB序列、或COI及MTCYB之合併序列之Fst共祖係數，再依Reynolds’遺傳距離作多方向尺度圖(multidimensional scaling plot)。 主要結果 在這565個個案中，與修正的劍橋參考序列比較，總共發現264個粒線體DNA序列位置有變異，共有223種序列型別，COI基因序列的核苷酸變異位置有126個，其中3處有兩種核苷酸取代，故共有129種核苷酸取代，MTCYB基因序列的核酸變異位置有138處，其中1處有兩種核苷酸取代，故共有139種核苷酸取代，在223種序列型別中， 160種型別只出現1次，而最常見的一種型別則出現於6個亞洲族群的31個案中。 依COI基因、MTCYB基因及合併兩個基因序列，其綜合鑑別能力各為0.9150、 0.9385及0.9830。在大多數族群MTCYB序列的鑑別能力較COI序列為高，但在泰國人及越南人族群，COI序列的鑑別能力較MTCYB序列高，COI及MTCYB基因序列在本研究中的達悟族及高加索族群，在與本研究中其他亞洲族群比較時，有族群特異性的多型性變化。 分別依COI或MTCYB序列計算之各族群間之Fst係數不同，而依合併COI及MTCYB序列計算之Reynolds’遺傳距離作成的多方向尺度圖，可以呈現母系的遺傳在此地理區域分佈的次結構。 結論 總之，COI基因及MTCYB基因序列在各族群皆有相當多的DNA序列多型性，且在某些族群有特異性，可應用於輔助法醫學人身鑑別、族群鑑別及母系親緣鑑別，或應用於法醫人類學之母系族群遺傳距離評估。

Background and purpose The analysis of mitochondrial DNA (mtDNA) sequence has become a very powerful tool in forensic casework. Many databases of mtDNA hypervariable region 1 (HV1) and hypervariable region 2 (HV2) in the non-coding region have been established. Nevertheless, assessing variations in the coding region can provide additional genotyping information and improve forensic discrimination. The cytochrome c oxidase I gene (COI) and cytochrome b gene (MTCYB) within the coding region of mtDNA have been found to be polymorphic and have been used in species identification. However, limited data of polymorphisms of the COI and MTCYB in human populations have been described. The aim of this study was to present the sequence polymorphisms of the COI and MTCYB among different population groups living in Taiwan , and to evaluate their possible applications in forensic genetics. Materials and Methods DNA sequences of a total of 565 DNA samples from 120 Taiwanese Han, 148 indigenous Taiwanese of Taiwan Island, 53 Orchid Islanders, 56 mainland Chinese, 55 Filipinos, 51 Thais, 51 Vietnamese, and 31 Caucasian, were analyzed. All of the sequences were compared with the rCRS and nomenclatured accordingly. Haplotype frequencies were calculated and specific haplotypes among populations were identified. Characteristic parameters for population, including haplotype diversity, nucleotide diversity and discrimination power were calculated based on COI, MTCYB, and combination of both sequences as haplotypes. The pairwise comparisons between the population groups performed using Fst (coanestry coefficient) values were explored. Multidimensional scaling plots were illustrated based on Reynolds’ genetic distance between groups of population. Main Outcome There were 129 nucleotide substitutions (at 126 positions) and 139 nucleotide substitutions (at 138 positions) found in COI and MTCYB, respectively. The 565 analyzed samples presented a total of 264 positions that varied from the rCRS with a total of 223 haplotypes. One hundred and sixty haplotypes were noted only once. The most common haplotype was shared by 31 individuals among 6 Asian population groups. The discrimination power of MTCYB sequence was higher than that of the COI sequence in most of the populations except in Thais and Vietnams. Based on COI, MTCYB, and combination of both gene sequences, the discrimination power was 0.9150, 0.9385, and 0.9830, respectively. Specific polymorphisms were identified in Tao and Caucasian populations. The pairwise Fsts between population groups based on COI and MTCYB were different. The multidimensional scaling plot based on Reynolds’ genetic distance between populations presents a clear matrilineal genetic sub-structure in this area. Conclusion There are sufficient sequence polymorphisms of COI and MTCYB in individuals of different population groups. Specific polymorphisms of these two genes were identified in particular population groups. Analysis of the sequences of COI and MTCYB provide informative data for further characterization of individual haplotype in forensic casework and subclassification of matrilineal ethnic groups.