SNP查找及SNP的几种研究方法

SNP位点的选择
1，如果是检测基因的所有已知的SNP，那么首先要去了解并查询到这些SNP位点，SNP 位点可以通过查询dbSNP数据库（/SNP/）和TSC（The SNP Consortium）数据库（/），可以获知基因及上下游邻近序列的SNP位点。

2，至于挑选的原则，可以介绍一下Hap Map的正规化标准：
SNP Selection Criteria
Category 1 "verified"
This contains all SNPs for which we have allele frequency or genotyping data. This includes SNPs from the TSC allele frequency project, as well as SNPs characterized by JSNP. These SNPs were generated from those rs clusters in which at least one of the SNPs in the cluster contains genotype or allele frequency data and the minor allele must have been seen in at least two individuals.
Category 2 "two-hit"
These are true double-hit SNPs, produced in collaboration with Jim Mullikin and Sarah Hunt. A double-hit SNP must be seen twice, in two different DNA samples which must have produced two alleles. TSC trace data was only allowed to contribute one hit per allele because the individual source DNA for a trace could not be identified.
Category 3 "jsnp-verified/perlegen-verified"
This category contains two groups: SNPs that JSNP certifies are likely to be real based on manual inspection of their data (but have not been genotyped)，and SNPs that Perlegen verified independently.
Category 4 "bac-overlap"
These are SNPs from BAC overlaps that do not fall into category 1 or 2 above.
我的经验：
也可以从文献中查找，找好几个SNP位点，如果你样本量很大，那么很容易出有意义的结果。

有以下三种方法可供选择：
1、提取EDTA抗凝全血中的DNA，荧光定量PCR法。

用ABI的SNP分型试剂盒，只要你提供位点，买来试剂盒就上仪器，成本也不高，效果还可靠。

2、提取EDTA抗凝全血中的DNA，普通PCR扩增（需设计引物，可自己设计或者让公司设计），限制性内切酶分型（在引物设计的同时找到合适的酶切位点），分出基因型，统计SPSS 卡方检验
3、提取EDTA抗凝全血中的DNA，高分辨溶解曲线，一次性即可完成PCR扩增及基因分
型，统计SPSS 卡方检验。