Introduction to Genetic Variation

Genetic Variation

• Genetic variation refers to the differences in DNA sequences between individuals or populations.
• There are several types of genetic variation, including:
  • Base pair variations
  • Tandem repeats
  • Structural variations

DNA Polymorphisms

• Polymorphism is the presence of two or more variations in a DNA sequence.
• Types of polymorphisms include:
  • Single Nucleotide Polymorphism (SNP)
  • Insertion-deletion polymorphism (Indel)
  • Tandem repeats
  • Structural variation and copy number variation (CNV)

Single Nucleotide Polymorphism (SNPs)

• SNPs are single base substitutions that occur throughout the genome.
• They are the most abundant type of polymorphism in the human genome.
• SNPs occur once in every 1-2 kilobase (kb) of DNA.
• Some SNPs are associated with phenotypic differences, but most are not.
• Almost all SNPs have only two alleles (bi-allelic).

Potential Functional Effect of SNPs

• SNPs can have a direct functional effect on the genome.

Genotypes and Allele Frequency

• Genotypes are the measured expression of a gene.
• Allele frequency is the calculated proportion of different alleles in a population.
• Example: The genotype of SNP rs9416742 has alleles G or A.
  • Genotypes in Europeans (n=503): GG = 339, GA = 155, AA = 9
  • Allele frequency: G allele = 83%, A allele = 17%

Linkage Disequilibrium

• Close SNPs are not independent and may be correlated.
• Allele A at SNP1 may be associated with allele G at SNP2.
• Knowing the allele at SNP 1 gives information on the allele at SNP2.

Haplotypes and Phase

• Haplotypes are a set of SNPs that are inherited together.
• Phase refers to the specific combination of alleles at multiple SNPs.
• Determining the phase of a set of SNPs is important for understanding genetic variation.

Tandem Repeat Polymorphisms

• Tandem repeat polymorphisms occur when repeat elements are present within non-coding DNA.
• These repeats can vary in length and are often found in non-coding regions of the genome.