文档介绍：Single nucleotide polymorphisms
Usman Roshan
SNPs
DNA sequence variations that occur when a single nucleotide is altered.
Must be present in at least 1% of the population to be a SNP.
Occur every 100 to 300 bases along the 3 billion-base human genome.
Many have no effect on cell function but some could affect disease risk and drug response.
Toy example
SNPs on the chromosome
Perl exercise
Determining SNPs from a pairwise genome alignment:
Can we solve this problem with a Perl script?
Bi-allelic SNPs
Most SNPs have one of two nucleotides at a given position
For example:
A/G denotes the varying nucleotide as either A or G. We call each of these an allele
Most SNPs have two alleles (bi-allelic)
Perl exercise
Determining SNP type from a multiple genome alignment.
SNP genotype
We inherit two copies of each chromosome (one from each parent)
For a given SNP the genotype defines the type of alleles we carry
Example: for the SNP A/G one’s genotype may be
AA if both copies of the chromosome have A
GG if both copies of the chromosome have G
AG or GA if one copy has A and the other has G
The first two cases are called homozygous and latter two are heterozygous
SNP genotyping
Perl exercise
SNP encoding:
Convert SNP genotype from a character sequence to numeric one