From previous study, I think there is an SNP in the definite locus of Human Chromosome. I want to be sure about existence of the SNP in that locus. Would you please give me suggestion about the procedure to complete the work.
The HapMap describes the common patterns of genetic variation in humans. It includes the chromosome regions with sets of strongly associated SNPs:
https://hapmap.ncbi.nlm.nih.gov/whatishapmap.html
About 10 million SNPs exist in human populations for which the rarer SNP allele has a frequency of at least 1 percent. Alleles of SNPs that are close together tend to be inherited together. A set of associated SNP alleles in a region of a chromosome is called a haplotype. Most chromosome regions have only a few common haplotypes, which account for most of the variation from person to person in a population. A chromosome region may contain many SNPs, but researchers can use only a few "tag" SNPs to obtain most of the information on the pattern of genetic variation in the region.
One of the simplest ways would be Sanger sequencing.
1. Pull up the genome of the area of interest on the chromosome.
2. Use the genome sequence to build PCR amplicons. If it is a large region, make the amplicons overlap.
3. Do a DNA extraction on the individual you think has this SNP.
4. PCR amplify the DNA.
5. Clean up the PCR product.
6. Send cleaned PCR product and PCR primers in for Sanger sequencing.
7. Align to reference genome with a bioinformatics tool like DNAsp, MEGA or CLCworkbench and find SNPs.
Hi, Firstly screen dbSNP (http://www.ncbi.nlm.nih.gov/snp). If it is there you probably identified existing variant in your sample or samples. If not , then it is either a new rare variant or an artefact - in either case Sanger sequencing, as suggested by D Kang, would be good starting point to verify your original data. Good luck.
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