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SNP ppt.pptx
- 1. CREDIT SEMINAR ON SINGLE NUCLEOTIDEPOLYMORPHISM (SNP)
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- 3. INTRODUCTION SNPs isa variation in a single nucleotide occur at specific position in the genome among individuals.
- 4. INTRODUCTION SNPs aremost common type of genetic variation among organisms. Each SNP location in genome have 4 version- one for each nucleotide A,G,T,C.
- 5. In cattle,SNP profiles for individual animals are generated using a small plastic chip that is diagnostic for up to 50 000 SNPs spaced throughout the genome. Phenotypes, usually averaged over offspring of bulls, are matched with SNP profiles of bulls mathematically so that animals can be ranked for siring desirable phenotypes via their SNP profiles. The value of these systems is very dependent on the number of accurate phenotypes matched with SNP profiles Increasing the number of North American Holstein bulls evaluated from 1151 to 3576 quadrupled the additional genetic gain in net merit from this approach. Once a valid SNP evaluation system is developed, any animal in that population, including embryos, can be evaluated with similar accuracy. Contemporary Relevance
- 6. The studyon Goat Population reveled 16 million single-nucleotide polymorphisms (SNPs) as well as 123,577 insertions and deletions. Contemporary Relevance
- 7. PROPERTIES SNPs arefound in coding and non-coding both regions. Occurs with a very high frequency. The abundance of SNPs and the ease with which they can be measured make these genetic variations significant. SNP is commonly biallelic.
- 8. PROPERTIES SNPs aremost widespread type of sequence variation in genome. Widespread use because these are numerous, more stable, potentially easier to score than microsatellite repeats. In many organisms most polymorphisms result from changes in single nucleotide position (point mutation) has led to the development of technique to study single nucleotide polymorphisms. Have power to reveal hidden polymorphism not detected with other marker or method.
- 9. CLASSIFICATON SNPs Linked SNPs CausativeSNPs Non-coding SNPs Coding SNPs Synonymous Non- synonymous Missense Nonsense
- 11. LINKED SNPs Alsoknown as indicative SNPs. They do not resides within genes and do not affect protein function. Nevertheless, they do correspond to a particular drug response or to the risk for getting a certain disease.
- 12. Causative SNPs Foundinside genes. Causative SNPs affect the way a protein functions, correlating with a disease or influencing a person’s response to medication. Further divided in 2 types : a) NON-CODING REGION b) CODING REGION
- 13. NON-CODING REGION SNPs A segment of DNA that does comprise a gene and thus does not code for a protein. This region located within the gene’s sequences, change the timing , location, or level of gene expression.
- 14. CODING REGION SNPs This is region of DNA that code for proteins. Located within the region of a gene, change the amino acid sequence of the gene’s protein product and thus alter the protein structure made by coding region. These are of 2 types- a) Synonymous b) Non-synonymous
- 15. SYNONYMOUS A SNPin which both forms lead to the same polypeptide sequence is termed as Synonymous (sometimes called a silent mutation). This do not affect the protein sequence.
- 16. NON-SYNONYMOUS A SNPin which both forms form different polypeptide sequence, they are Non- synonymous. This SNPs change the amino acid sequence of protein. Missense change results in a different amino acid while Nonsense change result in premature stop codon.
- 17. eSNP That isexpression SNP. SNPs that are not present in the protein-coding region may still affect gene splicing, transcription factor binding, messenger RNA degradation, or the sequence of non coding RNA. Gene expression affected by this type of SNP is referred as an eSNP. These may be present upstream or downstream from the gene.
- 18. What are effectsof SNPs
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- 27. How to identifySNPs Using Sequencing Data Genotyping with SNP Microarrays Filtering SNPs
- 28. Identified SNPs TillDate Cattle : Buffalo : Goat : Sheep : Pig : HUMAN : 2 million SNPs
- 29. ADVANTAGES SNP markersare useful in gene mapping. Helps in detection of mutations at molecular level. SNP are useful in positional cloning of mutant locus. SNP markers are useful in detection of disease causing genes. High genomic abundance. Potential for high throughout analysis. Relatively low genotyping error. Locus specificity.
- 30. DISADVANTAGE Most ofSNPs are biallelic and less informative than SSRs. Multiplexing is not possible for all loci. SNP assay technique is costly. Development of SNP markers are labour oriented. More SNP are required in preparing genetic maps than SSRs markers.
- 31. APPLICATIONS For manytraits in dairy cattle, the rate of genetic improvement can be nearly doubled when SNP information is used in addition to current methods of genetic evaluation. In Livestock SNPs helps to Design conservation strategy, aids in breed management, genetic improvement, and utilization programs. Gene discovery and Mapping Association based candidate polymorphism testing Diagnostics profiling/ disease diagnosis Drug response predication Homogeneity testing/ study design Gene function identification Drug discovery and development
- 32. REFERENCES Brookes, AJ.(1999). The essence of SNPs. Gene,234: 177-186. Dawson, E. (1999). SNP maps: more markers needed? Molecular medicine todays, 5: 419-420. Nachman and Michel W. (2001). “Single nucleotide polymorphisms and recombination rate in humans”. Trends in genetics, 17(9) : 481-485. Wang, D. G., Siao, C.J. and Berno (1998). Large scale identification, mapping and genotyping of single nucleotide polymorphism in the human genome. Science, 280: 1077-1082.
- 33. REFERENCES William, J.G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A. and Tingey, S.V. (1990). DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic acids research, 18: 6531-6535.