STR遗传多态性调查中样本量和采样方式选择初探

目的对STR基因座进行遗传学调查时样本量大小和采样方式进行考察分析。方法用DNA Typer~(TM)19试剂盒对血卡样本进行直扩,ABI3730型遗传分析仪电泳检测,Genemapper ID v3.2软件进行等位基因分型,根据公式计算群体遗传学参数。计算样本量在50、100、150、200、250、300、350、400、450、500十个水平上遗传多态性水平,并评估与总体的差异。计算常见的四种采样方法(整群采样、随机采样、系统采样、分层采样)所抽取样本遗传多态性水平,并评估抽样误差。结果 18个STR基因座在河北地区16 058份随机样本共检出317种等位基因,基因频率分布在3.114e-5~0.515。18个STR基因座在河北群体水平上PM为6.04e-14,TDP为0.999 999 999 999 94,CEP为0.999 999 987 514 828。PM值、CEP值在样本量大于200后中值基本稳定。四种抽样方法的抽样误差大小是:整群抽样≥单纯随机抽样≥系统抽样≥分层抽样。结论 DNATyper~(TM)19试剂盒的18个STR基因座在河北地区具有较高的遗传多态性水平。在小范围内进行人群频率调查时,可随机选择200份样本代表当地遗传多态性水平。在相对较大范围或遗传背景复杂的区域,可采用分层抽样的方法降低抽样误差。

A preliminary study on sample size and sampling methods in the STR polymorphism survey

Objective Evaluation of sample size requirements and proper sampling methods in the STR polymorphism survey. Methods Dried blood cards were amplified using DNA TyperTM 19 kit. ABI3730 genetic analyzer and Genemapper ID v3.2 software were used to genotype. Allele frequencies and population genetic parameters were calculated according to the formula. The genetic parameters were calculated when randomly subsampling 50, 100, 150, 200, 250, 300, 350, 400, 450 and 500 individuals, and the differences were evaluated. Four sampling methods (cluster sampling, random sampling, systematic sampling, stratified sampling) were also evaluated. Results 317 alleles of 18 STR loci were detected from 16058 random samples from Hebei province. The distributions of allele frequency were 3.114e-5~0.515. PM were 6.04e-14, TDP were 0.99999999999994, CEP were 0.999999987514828 on the 18 STR loci in Hebei. The changing rate of PM and CEP value reduced as the sample size increased, and gradually came to a standstill after the sample size greater than 200. Compared with the total population, the sampling error was in the order of cluster sampling ≥ random sampling ≥ systematic sampling ≥ stratified sampling. Conclusion 18 STR loci of DNATyperTM19 kit had a high level of genetic polymorphism in Hebei region. Random sampling 200 individuals is suitalbe to survey genetic polymorphism in a small scale. Stratified sampling can be used to reduce the sampling error in a relatively large scale or area with complex genetic background.