[Kicks]

What are Single Nucleotide Polymorphisms ?

[doublebarr]

From this site:

SNP Fact Sheet


What are SNPs?

Single nucleotide polymorphisms or SNPs (pronounced "snips") are DNA sequence variations that occur when a single nucleotide (A,T,C,or G) in the genome sequence is altered. For example a SNP might change the DNA sequence AAGGCTAA to ATGGCTAA. For a variation to be considered a SNP, it must occur in at least 1% of the population. SNPs, which make up about 90% of all human genetic variation, occur every 100 to 300 bases along the 3-billion-base human genome. Two of every three SNPs involve the replacement of cytosine (C) with thymine (T). SNPs can occur in both coding (gene) and noncoding regions of the genome. Many SNPs have no effect on cell function, but scientists believe others could predispose people to disease or influence their response to a drug.
Although more than 99% of human DNA sequences are the same across the population, variations in DNA sequence can have a major impact on how humans respond to disease; environmental insults such as bacteria, viruses, toxins, and chemicals; and drugs and other therapies. This makes SNPs of great value for biomedical research and for developing pharmaceutical products or medical diagnostics. SNPs are also evolutionarily stable --not changing much from generation to generation --making them easier to follow in population studies.
Scientists believe SNP maps will help them identify the multiple genes associated with such complex diseases as cancer, diabetes, vascular disease, and some forms of mental illness. These associations are difficult to establish with conventional gene-hunting methods because a single altered gene may make only a small contribution to the disease.
Several groups worked to find SNPs and ultimately create SNP maps of the human genome. Among these groups were the U.S. Human Genome Project (HGP) and a large group of pharmaceutical companies called the SNP Consortium or TSC project. The likelihood of duplication among the groups was small because of the estimated 3 million SNPs, and the potential payoff was high.
In addition to the pharmacogenomic, diagnostic, and biomedical research implications, SNP maps are helping to identify thousands of additional markers along the genome, thus simplifying navigation of the much larger genome map generated by researchers in the HGP.
How can SNPs be used as risk factors in disease development?
SNPs do not cause disease, but they can help determine the likelihood that someone will develop a particular disease. One of the genes associated with Alzheimer's, apolipoprotein E or ApoE, is a good example of how SNPs affect disease development. This gene contains two SNPs that result in three possible alleles for this gene: E2, E3, and E4. Each allele differs by one DNA base, and the protein product of each gene differs by one amino acid.
Each individual inherits one maternal copy of ApoE and one paternal copy of ApoE. Research has shown that an individual who inherits at least one E4 allele will have a greater chance of getting Alzheimer's. Apparently, the change of one amino acid in the E4 protein alters its structure and function enough to make disease development more likely. Inheriting the E2 allele, on the other hand, seems to indicate that an individual is less likely to develop Alzheimer's.
Of course, SNPs are not absolute indicators of disease development. Someone who has inherited two E4 alleles may never develop Alzheimer's, while another who has inherited two E2 alleles may. ApoE is just one gene that has been linked to Alzheimer's. Like most common chronic disorders such as heart disease, diabetes, or cancer, Alzheimer's is a disease that can be caused by variations in several genes. The polygenic nature of these disorders is what makes genetic testing for them so complicated.
The answer to this question is based on information provided by the Genome News Network.

[Lexy]

I read that and several other things.... I STILL don't know what it is.

[doublebarr]

LOL, I know!!!! That's why I just posted it and didn't add anything. I still don't really know exactally what an SNP is, LOL!

[Kicks]

I'm more 'conflusalated' than I was already. Probably should give a bit more info as to why I'm asking and put it in the "Breeding" section.

My App stallion is in a research study (blood and hair samples) through a USA University in regards to the "Origins of Apps" as he traces traces very heavily to old App blood lines. As I understand it SNP's are being used. Blood and follicles are being sent to the University.

Does that make any more sense?

[ladida]

I'll help explain it in simpler terms.

DNA is coded by the letters TAGC and three letters together is called a codon...so TAG would be a codon. Each one of these codons represents an amino acid, and combined together they make a protein.

When there this type of mutation occurs, also called base-pair substitution, the codon TAG would then become TTG instead. Usually this does not change the gene expressed at all, because there are only 20 amino acids but many more combinations of codons available...so they repeat.

The way they are tracing lines then is they look for this mutation in your stallions genes. If he has it, his blood is from after the mutation. If he doesn't have the mutation, chances are he contains blood from a line that did not mutate.

Mutations are passed on genetically.

Do you get it? I can still help if need be.

[ryu2832]

SNPs are as everyone else has said single base changes in a DNA sequence.

For what they are doing with the appaloosa lines think of it this way.

You make a photocopy (think of each photocopy as a generation). You take the copy and make a photocopy of that, the copy had a piece of lint on it that shows up on each subsequent copy of it. You make a copy of the second copy another speck of lint.

Eventually, if you keep making copies of copies, these little changes accumulate. If you lay all of them out infront of you, you can tell the earlier copies from the later copies.

So now imagine that you have two copiers (representing two different lines), one has a scratch on the glass that you can see on all the copies made from that machine. If you put a copy from machine 1 into machine 2 and make a copy--the scratch shows up. You can tell by looking at the copied pages, exactly what page was the first that used machine 2 because of the distinct mark left by it.

So back to the DNA. The SNPs are small changes that accumulate over time to the horses genome. You can create a molecular lineage by tracking the changes through a known pedigree, like making copies from copies. You can also track different lines by identifying the distinct markers that they have from each other, like the scratch on the glass.

Clear as mud?

[Lexy]

Bravo Ladida and Ryu....... you have a gift.

This is kinda like trigonometry. You either get it or you don't or you get it but couldn't explain it if your life depended on it.

Hopefully no one will ever hold a gun to my head wanting me to help them understand SNPs........ I get it, but couldn't explain it!

[Kicks]

Originally Posted by ryu2832

SNPs are as everyone else has said single base changes in a DNA sequence.

For what they are doing with the appaloosa lines think of it this way.

You make a photocopy (think of each photocopy as a generation). You take the copy and make a photocopy of that, the copy had a piece of lint on it that shows up on each subsequent copy of it. You make a copy of the second copy another speck of lint.

Eventually, if you keep making copies of copies, these little changes accumulate. If you lay all of them out infront of you, you can tell the earlier copies from the later copies.

So now imagine that you have two copiers (representing two different lines), one has a scratch on the glass that you can see on all the copies made from that machine. If you put a copy from machine 1 into machine 2 and make a copy--the scratch shows up. You can tell by looking at the copied pages, exactly what page was the first that used machine 2 because of the distinct mark left by it.

So back to the DNA. The SNPs are small changes that accumulate over time to the horses genome. You can create a molecular lineage by tracking the changes through a known pedigree, like making copies from copies. You can also track different lines by identifying the distinct markers that they have from each other, like the scratch on the glass.

Clear as mud?

Think I understand it a bit now. Am I right - they are sort of doing the reverse by starting with the 'final' copy (the horses in the study) and trying to remove the 'layers' back to the 'original' (Nez Perce) horses?

[Morri]

This site has a lot of good info written in less complicated scientific terms
SNPs: Variations on a Theme

Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources