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The genome and pharmacogenetics

Barbara Jennings describes the human genome, the human genome project & how our understanding of genetic variation can be applied to pharmacogenetics
Hello. This is Barbara Jennings. Welcome to your tutorial. This is all about defining terms. By the end of the session, you’ll be able to describe the human genome and genetic variation, and you’ll be able to define the terms pharmacogenetics and pharmacogenomics. When we look at people, we see an enormous amount of individual variation. So we see variation in appearance, in personality, in IQ, and of course, we also see variation in the tendency to get particular diseases, and also in response to medicines and other therapies. So if we see what we call, phenotypic variation, we expect to find genetic variation too. Mutation is the source of genetic variation between individuals.
So every time a cell divides, or every time an egg or a sperm is produced, DNA molecules will be copied between the generations of cells ,and this copying can result in errors that are not repaired. The upshot is mutation. Talking about genetic variation brings me to the human genome. So I now want to introduce you to the human genome. So, the genome is simply the DNA sequence or content of an organism or cell. Within an egg or a sperm we find a haploid human genome and this is a 3 billion base pair sequence that’s packaged within 24 possible human chromosomes.
And human genomes are 99.9% identical between individuals of each sex, and the landscape of the genome is interesting because it contains far fewer protein coding genes than we once envisaged. So somewhere between 20 and 21 thousand of these, but these protein coding genes complex. Gene and transcript sequences can be spliced in many ways. So there are actually far fewer genes than potential protein sequence. Even more complexity is possible through sequences that are transcribed from the genome into non-coding RNAs. The roles of these non-coding RNAs are varied but some are critical for fine tuning gene expression, and a few have key roles in early development, or in cancer development too.
So as discussed, mutation is the source of genetic variation between individuals and there are several types of common genetic variation that we find within our DNA sequences. For instance, we see satellites of tandem repeat sequences - these are short sequences of DNA that are repeated in a head to tail fashion. They’re known as mini satellites and micro satellites, and variable number tandem repeats are very polymorphic. So this means that there are many possible alleles, or variations, of a particular gene sequence at any given locus in the chromosome. So these sites within our chromosomes are exploited for DNA fingerprinting and for the purpose of forensics. Other types of variant can be described as small insertions and small deletions in dell mutations.
And much larger regions of the genome that can be increased in copy number. So we see copy number variants too. But the genetic variation that explains most phenotypic variation is due to single nucleotide variants, or single nucleotide polymorphisms, referred to as SNPs. If we use the term polymorphism, we should be defining that as a genetic variant that affects more than 1% of chromosomes in a given population. So this is the usual definition. And the frequency of a genetic variation will depend on its selective advantage, so whether it affects the fitness of an individual carrying that variant, but also human history. So we see variations in frequency because of population drift.
Now in 1990, an international effort was undertaken to sequence an entire human genome and to identify the position of each human gene on the 24 chromosomes. So I want to spend a bit of time discussing what we’ve discovered from the human genome project. So the first phase of human genome mapping was all about producing a consensus map and reference sequence derived from the genomes of just a few individuals. But over the last decade or so, we’ve become much more interested in sequence variation between our genomes. So, what makes us unique at the DNA level?
Genome mapping defined a reference human genome DNA sequence of about 3 billion base pairs for us and mapped the position of more than 20,000 genes to loci on each human chromosome. But the project led to spin-off initiatives. The hapmap project is a catalogue of common genetic variants that are linked in human beings. It describes what these variants are, where they occur in our DNA, and how they are distributed among people within populations, and between populations of different ethnicities. The single nucleotide polymorphisms discussed earlier are also being mapped. These are the most common type of genetic variant among people.
SNPs are found once in every three hundred nucleotides, on average, which means there are roughly 10 million SNPs in a human genome. Most commonly these variations are found in the DNA between genes which makes them less functionally important. So the distribution of genetic variants within human populations has been shaped by our history and global migrations. So we know that approximately 100,000 years ago some humans migrated out of East Africa to the rest of Africa, to Asia, and from there to the rest of the world. With great population expansions over time, mutations have arisen throughout human history.
Because SNPs account for most of our genetic variation, resulting in our phenotypic variation, I want to focus on their functional importance for a moment. So SNV’s or SNPs arise because of point mutations or single base substitutions and not all SNPs are of equal importance to medical scientists. So most don’t even occur in coding DNA and won’t affect the proteins produced by a cell, largely. But even if we look at those that do occur in a gene, they will be of variable significance. Let us look at how mutations might affect this codon CAG. Within the exons of genes, Triplets of bases encode individual amino acids.
This codons CAG encodes the amino acid glutamine for example, but some mutations to that particular sequence will be silent, so the change in base from CAG to CAA doesn’t affect the amino acid encoded. Other mutations may have a profound effect. So TAG is actually a stop codon. So translation of the gene sequence into an amino acid sequence will be truncated at this site. But the mutations that we probably give most attention to will change this codon to one that alters the final amino acid sequence. So while CAG encodes glutamine CTG encodes leucine. So mutations of this type that just alter a singular amino acid sequence are called mis-sense mutations.
Now they can be associated with profound alterations and protein functions and in some cases with disease, And in other situations, the change may be more neutral to the functional effect of the gene. So let’s look at how some types of mutation that we’ve discussed will impact on enzyme activity. Now, the enzyme that I’ve chosen to use as an example here is from the cytochrome p450 family and it plays a critical role in the metabolism of many commonly prescribed medicines. So,let’s tabulate some different variants of the gene that encodes the CYP2D6 enzyme. So in the first column of this table, I have given you the nomenclature for common genetic variants of that enzyme.
In the second column, I described the respective class of mutation. By looking at the mutation class, we can often predict how profound the functional effect will be. For instance, frameshift and nonsense mutations are often functionally very important, and in the third column, we see that they result in no activity, in this really important metabolising enzyme. It can be harder to predict the importance of mis-sense mutations as I said. We need to know something about which domain of the protein has an altered amino acid in it. So discussing cytochrome p450 enzymes brings us on to the topic of this whole module, which is of course pharmacogenetics.
Now the terms pharmacogenetics and pharmacogenomics are used pretty interchangeably to indicate an ability to use and exploit genetic variation to predict response to medicines. But to be a bit more precise, pharmacogenetics is the use of particular genetic variants to predict response to medicine, or to guide prescribing, and pharmacogenomics can be defined as the use of genome wide variance in an individual, or a population, to identify those markers that might predict response. So, in summary, since the completion of the first phase of a human genome mapping project, there has been a successful effort to identify common genetic variations within our DNA sequences.
Pharmacogenetics, or pharmacogenomics, makes use of this information to identify those markers that can guide prescribing and predict response to medicine.
In this 12 minute tutorial, Barbara Jennings describes the human genome, the human genome project and how our understanding of genetic variation can be applied to pharmacogenetics.
You can download a PDF glossary of terminology that will be used throughout the articles and tutorials over the next three weeks. You will find it at the bottom of this page in the Downloads section.
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Using Personalized Medicine and Pharmacogenetics

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