So there are a lot of different variations that exist between and within an individual's genome. Mine and your genome differ a lot, which is why we aren't clones of each other, and that exists for every human organism and also every other organism on Earth. Now, let me talk about some of the genomic variations that are found in humans. And we've mentioned most of these before briefly, but I want to go over a little bit more detail about what they are, how we identify them, and how frequent they are in just some more detail. So one of them is called a single nucleotide polymorphism, or a SNP for short, and these are exactly what they sound like. They are single nucleotide changes, so an "a" to a "c" or a "g" to a "t" or something like that, any kind of switch that's made. Now, they're actually fairly frequent in the human genome. About 1 in every 1000 bases is altered, which is a ton of SNPs, if you think of how many bases there are in the human genome. And then, there are about 18,000,000 total SNPs in humans as a whole. So, if you took all human genomes and just threw them together, there'd be about 18,000,000 SNPs. That's a lot of time. Because there are so many, it makes sense that the majority of SNPs are actually in silent regions. They're not changing a protein, they're not changing an amino acid. They’re not having any effect on proteins, which makes sense because the vast majority of the human genome isn't protein coding. Only about 2% of the human genome codes for proteins. Therefore, most of the SNPs are going to be in regions that do not code for proteins. But they're still important because that allows us to tell the difference between DNA between individuals. If we do sequencing, it helps us identify, sort of evolutionary timescales. Even though they're not affecting proteins, they're still really important for scientists. How do people identify SNPs? There's a lot of different ways. One is called a southern blot, and that's just a way to visualize different lengths of DNA. So, if you are going to identify a SNP with different lengths of DNA, how you do it is you use proteins called restriction enzymes. What restriction enzymes do is they cut DNA at one specific region. So some people will have SNPs that allow the DNA to be cut, and some people will have SNPs that don't allow the DNA to be cut. And so, if you take the DNA from those two types of individuals and expose them to this restriction enzyme, it'll chop up their DNA, but it'll chop up their DNA differently, and therefore, they'll have different DNA lengths if you run a southern blot. And so, by running a southern blot, you can take DNA that's been cut by restriction enzymes and say, oh well, this person has different SNPs than this person because there are different DNA lengths after I exposed it to the cutting enzymes. So that's one example. You can use PCR, and also the restriction enzymes with that. It works the exact same way. But a big one is also DNA microarrays, which are just these plates that can bind to different DNA sequences. And, they can be so specific that they won't bind to a DNA sequence with one simple change in it. And that would identify a SNP, which has a single change in it. So, like I said, there are multiple different ways to do this. So here's an example of a single nucleotide polymorphism. Notice that this sequence is the same except for this nucleotide in red. And so this is just one single change. It might be in a protein-coding region, it might not. And so, these types of SNPs are found very frequently throughout the human genome. So that's kind of the most common, so let's get to some more or less common sequences. So, one of them is a deletion insertion polymorphism, which can also be shortened as a dip or an indel, mostly indel, but I did see it as a dip in a couple of your textbooks. But essentially, what these are is exactly what they sound right. Luckily, these things are named very well. So they're small deletions or insertions of some kind of genetic material. They can range from a single base pair to 517, which is the longest identified, and there are nearly 300,000 in the human genome. So about 1 in every 10 kilobases, so 10,000 bases, differs in a deletion or an indel, between two individuals. So this, like I said, can be an insertion of 1 nucleotide, or a removal of 1 nucleotide, a removal of 20 nucleotides, insertion of 20, all the way up to 517. So it's just little sequences that are inserted or deleted, and they're found throughout the genome. Another type of genomic variant is simple sequence repeats, and these are generally 1, 2, or 3 bases, so not very long, but they're repeated 15 to 100 times, normally. Sometimes they cause disease and when they cause the disease, they're repeated much more often than that, but normally, 15 to 100 times. So a really common one is actually the CA repeat. And this is the repeat of these two nucleotides, "CA," over and over and over again. And it's found about once every 30,000 base pairs in mammalian gene genomes. And generally, they arise through some type of DNA replication error, which started, you know, trying to replicate 50 CAs, but then accidentally did 75. And so, they are, like I said before, they're associated with certain diseases. Huntington disease is one of them, but those are actually a simple sequence repeat of CAG for Huntington's. So here's just an example of a CA repeat. Right? It's just "CA," "CA," "CA" over and over and over again, and it continues 15 to 100 times, and they're found sprinkled throughout the genome fairly frequently, about once every 30,000 base pairs. So finally, let's get to the last one where the last couple we're going to talk about, and those are mini satellites. Mini satellites are repeats, this is supposed to say base pairs about 500 base pairs to 20 kilobases, and so 20,000 base pairs. So these are much bigger than what we've been talking about before. And these are repeats of these long sequences that are scattered throughout the genome. Now, we have taken advantage of these through what's called a DNA fingerprint. And crime scene investigators use DNA fingerprints all the time. And what they do is they look at these mini satellites and they look at the length of them and how frequently they're found throughout the genome. And when you just identify how frequently these regions are repeated throughout the genome, it produces a pattern that's specific to you. So how many mini satellites you have and how frequently they are throughout the genome. And when you look at that, you have a unique pattern. And every individual on Earth has a unique pattern when they look at the length of those on some type of gel, which I'll show you in a second. And so this is how scientists identify whether the crime scene DNA that they found at the crime scene is the same DNA as somebody else in the system or somebody that the suspect that they brought in. And they do it through DNA fingerprinting by looking at the pattern of these mini satellites in an individual. So that's a really cool thing. I'll show you an example of that in a second. But first, I want to talk about large scale deletions, which are exactly what they sound like, these large regions that are deleted. And they can also differentiate human genomes. And an example of a large scale deletion is actually a copy number variant. And this is just, you know, numbers of copies of alleles or number of copies of large allele sections, because they're large scale deletions, of up to 1 megabase in length. And so, this is another one that's pretty frequent. So what does a DNA fingerprint look like? Well, this is what it looks like. These are different DNA links, depending on the microsatellites that are present. So if this DNA here was picked up at the crime scene and you have 3 suspects here that you had also done the DNA fingerprint on, which one would be most likely? Which one is the one whose DNA was at the crime scene? Would it be the one that matches this pattern? So if we look across, this one has the same. This one is the same, for this one, and this one has it, this one and this one has it, and this one and this one has it. So if we look at the pattern, number 2 would be the suspect that we would go with, because this is the pattern, the microsatellite pattern, that most resembles the DNA found at the crime scene. That's kind of how that works, so a little view into CSI for you. But, with that, let's now move on.
Genomic Variation - Online Tutor, Practice Problems & Exam Prep
Created using AIGenomic variations, such as single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (indels), and simple sequence repeats, contribute to genetic diversity among individuals. SNPs occur frequently, with about 18 million identified in humans, primarily in non-coding regions. Indels can range from single base pair changes to larger segments, while simple sequence repeats, like CA repeats, can be associated with diseases. Techniques like Southern blotting and DNA fingerprinting utilize these variations for identification and forensic analysis, highlighting their significance in genetics and evolutionary studies.
Genomic Variation
Video transcript
Which of the following is NOT an example of large genomic variations between two individual genomes?
Which of the following genomic variations can be detected through DNA fingerprinting?
Which of the following genomic variations is most common in human genomes?
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What are single nucleotide polymorphisms (SNPs) and how are they identified?
Single nucleotide polymorphisms (SNPs) are variations at a single nucleotide position in the DNA sequence among individuals. They occur approximately once every 1,000 bases in the human genome, resulting in about 18 million SNPs in humans. SNPs are primarily found in non-coding regions of the genome. They can be identified using several techniques, including Southern blotting, which uses restriction enzymes to cut DNA at specific sites, and DNA microarrays, which can detect single nucleotide changes by binding to specific DNA sequences. These methods help scientists study genetic diversity, evolutionary biology, and disease associations.
Created using AIWhat are deletion insertion polymorphisms (indels) and how do they differ from SNPs?
Deletion insertion polymorphisms (indels) are genomic variations where small segments of DNA are inserted or deleted. Indels can range from a single base pair to 517 base pairs in length and are found about once every 10,000 bases in the human genome. Unlike SNPs, which involve a single nucleotide change, indels involve the addition or removal of multiple nucleotides. Indels can affect gene function and regulation, and they contribute to genetic diversity among individuals. Techniques like PCR and DNA sequencing are commonly used to identify indels.
Created using AIWhat are simple sequence repeats (SSRs) and how are they associated with diseases?
Simple sequence repeats (SSRs), also known as microsatellites, are short sequences of 1-3 base pairs that are repeated 15 to 100 times in the genome. A common example is the CA repeat. SSRs can arise from DNA replication errors and are found about once every 30,000 base pairs in mammalian genomes. Some SSRs are associated with diseases; for instance, the CAG repeat is linked to Huntington's disease. When the number of repeats exceeds a certain threshold, it can disrupt normal gene function, leading to disease. SSRs are useful in genetic studies and forensic analysis due to their high variability among individuals.
Created using AIHow is DNA fingerprinting used in forensic science?
DNA fingerprinting is a technique used in forensic science to identify individuals based on their unique genetic patterns. It involves analyzing mini satellites, which are long sequences of repeated DNA ranging from 500 base pairs to 20 kilobases. By examining the length and frequency of these repeats, scientists can create a unique DNA profile for each individual. This profile is compared to DNA samples from crime scenes to identify suspects. The process involves techniques like gel electrophoresis to visualize the DNA patterns, making it a powerful tool for criminal investigations and paternity testing.
Created using AIWhat are large scale deletions and how do they contribute to genomic variation?
Large scale deletions are significant genomic variations where large regions of DNA, up to 1 megabase in length, are deleted. These deletions can result in the loss of multiple genes or regulatory elements, potentially affecting gene function and contributing to genetic diversity. One example of large scale deletions is copy number variants (CNVs), which involve variations in the number of copies of a particular gene or genomic region. Large scale deletions can be identified using techniques like comparative genomic hybridization (CGH) and next-generation sequencing (NGS), and they play a role in various genetic disorders and evolutionary studies.
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