Sept 11

EVERY ____ KB PAIRS IN THE HUMAN GENOME, THERE IS A SNP

3

Wha is a frame shift mutation

It is a genetic mutation caused by the indels of a number of nucleotides that is not evenly divisible by 3 from the dna sequence. due to the triple nature of gene expression by codons, the insertiona dn deletion can change the reading frame of the codon resultin in a diff translation from the original. The earlier in the sequence the deletion or insertion occurs, the more altered the protein is.

What are some phenotypic consequences of mutations

Loss of function mutations include: Point mutation and truncation Point mutation: A point mutation, or single base substitution, is a type of mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic material (nonsense, misense, framshift) , DNA or RNA. The term point mutation also includes insertions or deletions of a single base pair. Trucation results in deletion Gain of function muation: enhanced activity. Dominant effect. Conditional Loss of function: i.e. a particular protein hs a normal functionality at one temperature but not a normal functionatliy on other.

If the mutation occurs in a wobble base, it is going to result in

a silent mutation

A missense mutation is when

a single DNA base change is changed resulting in a codon that codes for a different AA

Once you have the data from a SNP chip assay, you can subject it to

a varity of statsical steps! Like the Manhattan Plot

In order for a polymorphism to be described as a SNP it must occur in how much of population?

1 percent of the sample population

So, what are the phenotypic consequences of having various mutations in genes:

1. gain of function mutation 2. Loss of function mutation

There are ___ amino acids and

64 possible codons.

A nonsense mutation is when

A single DNA base mutation in a sequence of DNA that results ina premature stop codon or a nonsense codon

what is a SNP

A single nucleotide polymorphism

Insertions and deletions also called indels produce this kind of mutation

frameshift mutation

Overactivity mutation is also knonw as

gain of function mutation

Are gain of function mutations dominant or recessive

Dominant

A gain of function mtuation example

Oncogene mutations are gain of function mutations. They make the cell proliferate more rapidly.

Insertions and deletions are also called

Indels

Silent mutations occur at

the wobble base

Classes of DNA mtuations

somatic Germline And in those classes you have DNA mtuations called 1. Single DNA base mutation 2. Insertions and Deletions

What is a frameshift mutation

A genetic mutation caused by insertions or deletions of a number of nucleotides.

A silent mutation is when

A single DNA base mutation occurs at the wobble base. 1. It may result in the same amino acid if it is within the exon 2. It may occur in the noncoding regions of the protein

A frame shift is what kind of mutation?

An insertion and Deletoin (Indels)

Single DNA base mutations include

Base Pair substitutions: Misense, nonsense, silent Single DNA subsitution Mutations: Transition Transversion

What are polymorphisms?

Deviations from normal allele sequences. They provide no loss or gain of function. they serve as molecular markers for new genes.

What is a dominant negative mutation

Dominant negative mutation: If you have one copy of gain of function mtuation from moma nd one cipy of dominant gain of functio from dad, this dominant negative mutaiton is going to turn the protein into a poison.

What occurs more transition or transversion?

Even though transversion can result in more DNA variety (dissimialr shape changes), transition will be more frequent because of the molecular mehcniams responsible for generating transition mutations.

What is a gain of function mutation

Example is like a single mutation event in a normal cell will create an oncogene (a gene that has the potential to cause cancer). Activating mutation enables oncogene to stimulate cell proliferation.

FUNCTIONAL CLASSIFICATION OFA SNP INCLUDES ITS PLACE IN A

GENE REGION SYNONOMYS NON SYNOMOMYS (BOTH ABOVE ARE RNA ENCODING REGIONS) UNTRANSLATED INTRON SPLICE JUNCTION

What are the problems with the GWAS assays?

GWAS studies are suceptible to false pos and false neg failure to screen sample pops may influence results Improper statsical analysis can skew results

iNTERNATIONAL HAP MAP PROJECT

HAPLOTYPE: A SET OF SNPS ONA CHROMOSOME THAT ARE STATSIFCALLY ASSOCIATED AND MAY SERVE AS DISEASE MARKERS. THE GOAL OF THE INTERNATIONAL HAPMAP PROJECT IS TO COMPARE THE GENETIC SEQUENCES OF DIFFERENT INDIVIDUALS TO ID CHROMOSOMAL REGIONS WHERE GENETIC VARIANTS ARE SHARED.

How can SNPs be used as risk factors in disease development?

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 illness. One of the genes associated with Alzheimer's disease, apolipoprotein E or ApoE, is a good example of how SNPs affect disease development. ApoE 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 a person who inherits at least one E4 allele will have a greater chance of developing Alzheimer's disease. 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 a person 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 disease, 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.

Explain loss of function mutatoins

In normal cells, tumor suppresor genes have a dampening or repressive effect on the regulation of hte cell cycle or apoptosis. In a loss of function mutation involving a tumor suppresor gene (which codes for a protein acting as a stp singal fro a cell), you need 2 mutated alleles to mutate the tumor suppresor gene. So a normal cell can hav a mutation event that inactivates the tumor suppresor gene. Becasue it is recessive, it will have NO effect in the mutation in one gene copy. However, a second mutation event will inactivate the second gene copy which will eliminate the tumor suppresor geneand stimulate cell proliferation.

Why are insertions and deletions also called Indels

Indels are a mutation class including inertions deletions and the combination thereof.

How do haplotypes help at all in finding the genetic sequences of different indviduals and identifying chromsomal regions where genetic variants are shared?

Many SNPS ona single chromsome inherited together is called a haplotype. If a known halotype on a chromsome is known to cause a disease, we can create a marker for that haplotype and figure out the genes on it and thus, figure out whcih genes correlate with whcih disease. For example. Say a researcher wants to find some genetic variants, or polymporhisms that are associated with high bp. He could look at all the SNPS in the persons DNA and see where they differ among regular people, and if these peopel have similar snps, but researcher can also say, okay, i wnt to look at Gene A B and E for high BP located on chromosome 4. So if you know the collectoin of haplotypes you are looking for you can make a marker for just the tag SNPS on the haplotype to find chromsomal regions that may be associated with the disease. If people with high bp share a particualr haplotype, variants contributing to the disease might be somewhere within or near that haplotype.

WHAT KIND OF AMINO ACID SEQUENCE CHANGE RESULTS FROM SNPS?

NONE. SNPS CAUSE NO CHANGE IN AMINO ACID SEQUENCE BECAUSE OF CODON REDUNDANCY (WOBBLE BASE)

IN ORDER FOR A POLYMORPHISM TO BE CLASSIFED AS A SNP IT MUST OCCUR IN

ONE PERCENT OF HTE SAMEPLE POPUATION

Transition Mutations is when

Purine goes to Purine Or Pyrimidine goes to Pyrimidine (similar shape changes)

Transversion mutation is when

Purine goes to pyrimdine (or disimilar shape changes)

How to ID disease cuasing genes

SNP analysis CNV GWAC High Throuput Sequencing

What are soeme of the polymorphisms discussed?

SNP--SINGLE NUCLEOTIDE POLYMORPHISM STR--SHORT TANDEM REPEAT DNP--DINUCLEOTIDE POLYMORPHISM TNP--TRINUCLEOTIDE POLYMORPHISM

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. SNPs can occur in 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.

Do SNPS always result in changes to the genetic code?

Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions (regions between genes). SNPs within a coding sequence do not necessarily change the amino acid sequence of the protein that is produced, due to degeneracy of the genetic code.

What is the manhattan plot

So you take a group of people with thyroid cancer a group of people without take their dna, cut it up, fragment, ligate, pcr, hybridize. We now have that labeled piece of dna with a known snp. Ok, so this will ligate itself somewhere onto SNP microarray. But the diseased people will have the diseased SNPS light up int he microarrays and the nondiseased will have the nondiseasedlight up in the microarray. now all the data are subject o testss. So you take all this data and you make it a manhattan plot A low P value means that it is statiscally signficant. It can be associated with the certain snps you are looking for. Then you can see the genes associated with that particular snp and then decide if that is the reason for your disease.

How do we use the snp microarrays?

Take the patients dna cut the patients dna witha frequent cutter restriction enzyme run it through a column to get rid of the long pieces of dna ligate it with an adaptor do pcr clean up fragment and label it with a marker

Info about SNPS

The HapMap is a catalog of common genetic variants that occur 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 among populations in different parts of the world. The International HapMap Project is not using the information in the HapMap to establish connections between particular genetic variants and diseases. Rather, the Project is designed to provide information that other researchers can use to link genetic variants to the risk for specific illnesses, which will lead to new methods of preventing, diagnosing, and treating disease. The genetic sequences of different people are remarkably similar. When the chromosomes of two humans are compared, their DNA sequences can be identical for hundreds of bases. But at about one in every 1,200 bases, on average, the sequences will differ (Figure 1). One person might have an A at that location, while another person has a G, or a person might have extra bases at a given location or a missing segment of DNA. Each distinct "spelling" of a chromosomal region is called an allele, and a collection of alleles in a person's chromosomes is known as a genotype. Differences in individual bases are by far the most common type of genetic variation. These genetic differences are known as single nucleotide polymorphisms, or SNPs (pronounced "snips"). By identifying most of the approximately 10 million SNPs estimated to occur commonly in the human genome, the International HapMap Project is identifying the basis for a large fraction of the genetic diversity in the human species. For geneticists, SNPs act as markers to locate genes in DNA sequences. Say that a spelling change in a gene increases the risk of suffering from high blood pressure, but researchers do not know where in our chromosomes that gene is located. They could compare the SNPs in people who have high blood pressure with the SNPs of people who do not. If a particular SNP is more common among people with hypertension, that SNP could be used as a pointer to locate and identify the gene involved in the disease. However, testing all of the 10 million common SNPs in a person's chromosomes would be extremely expensive. The development of the HapMap will enable geneticists to take advantage of how SNPs and other genetic variants are organized on chromosomes. Genetic variants that are near each other tend to be inherited together. For example, all of the people who have an A rather than a G at a particular location in a chromosome can have identical genetic variants at other SNPs in the chromosomal region surrounding the A. These regions of linked variants are known as haplotypes (Figure 2). . The International HapMap Project is identifying these common haplotypes in four populations from different parts of the world. It also is identifying "tag" SNPs that uniquely identify these haplotypes. By testing an individual's tag SNPs (a process known as genotyping), researchers will be able to identify the collection of haplotypes in a person's DNA. The number of tag SNPs that contain most of the information about the patterns of genetic variation is estimated to be about 300,000 to 600,000, which is far fewer than the 10 million common SNPs. Once the information on tag SNPs from the HapMap is available, researchers will be able to use them to locate genes involved in medically important traits. Consider the researcher trying to find genetic variants associated with high blood pressure. Instead of determining the identity of all SNPs in a person's DNA, the researcher would genotype a much smaller number of tag SNPs to determine the collection of haplotypes present in each subject. The researcher could focus on specific candidate genes that may be associated with a disease, or even look across the entire genome to find chromosomal regions that may be associated with a disease. If people with high blood pressure tend to share a particular haplotype, variants contributing to the disease might be somewhere within or near that haplotype.

How can SNPS be used as molecular markers?

The co-inheritance of SNPs with genes of interest (i.e. disease genes) is a phenomenon that allows for SNPs to be used as markers for potential disease genes. If a SNP occurs in more than 1% of the population, you can use to ddiagnose a disease.

Additionally, there is more single base pair mutations

There are promoter mutations and splice site mutations. Splicing at different places leads to different mrna and different protein. A single base change in the promoter region can result in a different promoter region A single base pair chang in the splice site can result in a splice site mutation

Molecular techniques to analyze DNA variation it he human genome?

There are traditional techniques like gel fractiation, southern blot, dna ybridxation, pcr and genomic and cDNA libraries.... butttttt it takes too long... instead do... snp analysis cnv analysis genomic wide associatioin studies high throuput sequencing Using these, we can id disease causing genes easily

What is a manhattan plot

This is a "Manhattan" plot -- so named because of how the groupings of dots look like skyscrapers on the Manhattan skyline. This plot is based on a small sample of children (less than 200) who took part in our study and is for illustration purposes only. This plot shows differences between the extreme high and extreme low groups for genetic variants across the human genome. Each dot represents the results of a statistical test run for a specific genetic variant. On the X (horizontal) axis of this plot are locations of chromosomes across the human genome (22 chromosome pairs, plus sex-determining pairs). The differences between the high and low groups can be found on the Y (vertical) axis which displays how significant, or meaningful, these differences are according to our statistical analyses. The higher the value, the stronger the genetic association. If the result lies above the dotted line, it is considered statistically significant after accounting for all of the many tests that have been performed. The power, or strength, of our statistical analyses will be much greater once we have finished data collection and we have a full sample. We anticipate that multiple results will cross the dotted line, or be significant!

How are genome-wide association studies conducted?

To carry out a genome-wide association study, researchers use two groups of participants: people with the disease being studied and similar people without the disease. Researchers obtain DNA from each participant, usually by drawing a blood sample or by rubbing a cotton swab along the inside of the mouth to harvest cells. Each person's complete set of DNA, or genome, is then purified from the blood or cells, placed on tiny chips and scanned on automated laboratory machines. The machines quickly survey each participant's genome for strategically selected markers of genetic variation, which are called single nucleotide polymorphisms, or SNPs. If certain genetic variations are found to be significantly more frequent in people with the disease compared to people without disease, the variations are said to be "associated" with the disease. The associated genetic variations can serve as powerful pointers to the region of the human genome where the disease-causing problem resides. However, the associated variants themselves may not directly cause the disease. They may just be "tagging along" with the actual causal variants. For this reason, researchers often need to take additional steps, such as sequencing DNA base pairs in that particular region of the genome, to identify the exact genetic change involved in the disease.

Most SNPS are a consequence of?

Transition mutations

WHAT IS A HAPLOTYPE?

WHEN SNPS ARE INHERTIED TOGETHER ON A SINGLE CHROMOSOME WE CALL IT A HAPLOTYPE. WE CAN TAKE THESE VARIOUS HAPLOTYPES AND SEE IF THEY ARE ASSOCIATED WITH A PARTICULAR DISEASE WITH THE HELP OF THE INTERNATIONA HAPMAP PROKECT

What is permuation analsys

When you are evaluating a particualr interesting result with very low P values (high on manahhatn plot), it is neessary to see how often they arise by chance if the study was repeated and if there were no true positibe findings.... like if no p values were actually out of the loop statiscally... none were so high.... because theres lots of them, so statiscall, thye should all be low. So what do you do? All of the statistics of interest are claculated int he control group and in the case group. No biologically meaningful association should be observed in the permuted data because the case and control labels, the phenotypic values, have been shuffeled. If they do, you know that your snp just is rare or something.

What is a genome wide association study?

You can take disea specific snps that you KNOW to be associated with disease, put them on microarrays and put the patientss DNA with it. You can buy microarrays with all human snps on silicon wafers. Then you can comapre this diseased patientss DNA hybridized to snps to patientss without the dsiease an also put their dna ona silicon wafer with all teh snps on it and compre. Now you can see if the disease associates with certain snps

What is a GWAS

an examination of many common genetic variants in different individuals to see if any variant is associated with a trait. GWAS typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major diseases. Steps: Take a group of pople with a disease cut their DNA up Put it on a SNP microarray Take another group of people without disease CUt their DNA up (with sepcifc frequent cutter) Put it on a SNP microarray then do statstical analysis and witht he manahttan plot, determine if there is any sorts of low P value associated with any snp... if low p value, means statsically sig. You know where that snp came from, so it must be associted wtiha certain gene. Then you can suggest that X disease is associated with X snp.

For example, human chromsome three has SNPs that surround the XPC gene. SNPS can either be

around the gene or on the gene Around: Indirect association On gene: Direct association

underactivity mutation is also known as

loss of function mutation

Single DNA base mutations:

missense, nonsense, silent Misesne: different aa nonsense: stop silent: snps (occurs in wobble base)

Loss of function mutations are considered

recessive

Because transitions are changing purine to purine and pyrimidine to pyrimidine, they are less likely to what

result in a amino acid substituion, and are more likely to persist in the genome as SILENT mutations. Most single nucleotide polymorphisms are consequence of transition mutations.