5.4.3 SNP Flashcards
Population genetics
- Study of how the gene pool of a population changes over time, leading to the evolution of a species
- Examines gene pool, genetic diversity, and genetic variability
Allele frequency formula
Frequency of an allele G: no. of copies of allele G in the population / no. of copies of allele G + g in the population
SNP
- Single nucleotide polymorphism
- Genome: set of 23 human chromosomes
- Genome is composed of 3 billion base pairs
- SNP: variations of a single base pair, single base pair substitution. Arises as a result of mistakes in DNA replication.
- There are around 10,000,000 SNPs, occurring ~300 nucleotides. Most lead to no observable differences between people because they are located in non-coding regions of DNA, but those that do account for most of the phenotypic variations between individuals, e.g. response to medications, susceptibility to disease
- Not considered a “mutation” per se because it is present in more than 1% of the population. It is instead called a “variant”
- Happens in a large number of people. For example, in a population, 28% of people may have an A SNP instead of a G SNP in one location
- Mostly found between genes, acting as genetic markers.
Will be a data question in the exam
SNP association with disorders
- Computer technology can be used to rapidly scan genetic markers across genomes of many people to find genetic variations associated with a particular disease
- Currently, a data bank of SNP genetic markers is being built to determine if particular SNPs may be associated with diseases
- To find an association between SNPs and a response to a medication, scientists have to look at multiple SNPs across a longer stretch of DNA
Haplotypes
- A combination of SNPs
- In real life, only some of the possible haplotypes actually exist in a population
- One haplotype comes from the mother, the other from the father. Each individual thus has a haplotype pair.
- Two haplotypes in a pair can be different or the same
HapMap project
- Haplotype Mapping: a worldwide collaboration between scientists to study SNPs and human diseases
- Goal is to identify common genetic variations and patterns among people, in particular how they respond to drugs, diseases, or environmental factors
Coding vs non-coding SNPs
- Coding: will change the amino acid sequence, affecting phenotype
- Non-coding will change the amount of protein produced
- Linked SNPs and Causative SNPs don’t affect phenotype (?)
SNP data limitations
- Technically difficult to collate SNP data on a large scale
- If the regions of the genome are evenly distributed, biological questions can be answered using smaller regions
- Some genetic markers are far apart, making it more difficult to produce accurate data
- Haplotype studies look at SNPs that have been inherited from one parent and doesn’t consider crossing over during meiosis
Genotyping
Identifying genetic variations in individuals
Sequencing
Finding the exact nucleotide sequence of a certain length of DNA
SNP v. Allele
Similarities:
* Variations within DNA, and can affect traits and phenotypes.
* Both can have functional affects (e.g. disease risk, physical traits)
* Found on specific loci on the genome
SNP:
* Single nucleotide difference
* More than 1% of population.
* Used for markers of genetic studies - as often between genes.
* E.g. adenine vs. guanine at a specific base.
Allele:
* Any variant of a gene, which could be SNP or larger changes.
* There is no frequency threshold; rare mutations are still alleles.
* These gene variants influence traits directly.
* E.g. blood type
If there are two SNPs, how many haplotypes
4
