Recently, a friend asked for the difference between a SNP and genotype. After some babbling on my part, here is a summary.
|SNP||Positions of the genome that have a mutation|
|Genotype||Alleles of at a given SNP|
Typically we only call a mutation if is seen above a certain frequency (typically > 0.1%) across the population. Otherwise, these are known as private mutations.
Confused? Here is a simple analogy. A metabolic disease called diabetes exists but not everyone has diabetes. A medical diagnosis is required to determine the diabetic status of an individual.
Similarly, genotyping is the process of determining the SNP alleles. Here is example for three individuals:
|Position||Individual 1||Individual 2||Individual 3|
Nucleotides in positions 1 – 3 are identical across all individuals and therefore not considered a SNP in this sample. The nucleotide in position 4 is a SNP. The genotype for individual 001 at position 4 is C/T.
More generally, in the human genome, there are approximately 40 million SNPs which represent about 1.25% of the genome. In other words, the genomes of two unrelated individuals are identical at around 99% of the nucleotides.