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Single Nucleotide Polymorphisms (SNPs)

Single Nucleotide Polymorphisms (SNPs). DNA fragment. Nitrogenous bases: A, T, G e C. In a eukaryotic cell, the DNA is localized inside of the nucleus, compacted and organized in a structure called cromosome.

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Single Nucleotide Polymorphisms (SNPs)

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  1. Single Nucleotide Polymorphisms (SNPs)

  2. DNA fragment • Nitrogenous bases: A, T, G e C. • In a eukaryotic cell, the DNA is localized inside of the nucleus, compacted and organized in a structure called cromosome.

  3. In diploid species, like humans, having 2n pairs of chromosome, where n is the number of differentes chromosomes. The genotype is the set of all chromosomes. (in humans are 46). Chromosome and Genotype

  4. In haplotypes species, have n chromosomes, only one copy. In humans the genotype is the set of 23 chromosomes from the father and another 23 from the mother. Haplotype

  5. These chromosomes are passed with very great fidelity from one generation to the next. However, occasionally a mutation has occurred and effectively changed one base to another. The variation occurred in genetics sequences are many types, but the main are mutations and polymorphisms. Evolution

  6. Polymorphism • When several chromosomes from a population are compared, a site where a mutation occurred in the past may be found, and some chromosomes will have the original base and others will have the new base, i.e. the population will be polymorphic. • The variation of DNA sequences inside of the same species and have at least two types, is called alleles. Traça (Biston betularia) branca Variante preta da traça

  7. Polymorphism • A special kind of polymorphism is the target of many researchs, because of the major variation frequence in DNA humans. • This kind of ploymorphism is called: Single Nucleotideo Polymorphism ou SNP.

  8. What are SNPs ?(Single Nucleotide Polymorphisms) • Common DNA sequence variations among individualsin genome wherein the least frequent allele has an abundance of 1% or greater. • Make up about 90% of all human genetic variation. • Some SNPs are reported to be highly related to diseases or influence cells response to a drug.

  9. What are SNPs? SNPs are DNA sequence variations that occur when a single nucleotide (A,T,C,or G) in the genome sequence is altered. 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 make up about 90% of all human genetic variation.

  10. Schematic representation

  11. Recall process to construct proteins

  12. If there is a change in the DNA…

  13. SNPs with no change

  14. SNPs with small changes

  15. SNPs causing changes in shape

  16. Some protein changes are eventual

  17. But when they happen, they can lead to diseases

  18. Another disease Sickle-cell disease Glu -> GTG Val -> GAG

  19. What are SNPs? SNPs 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.

  20. G/T G/T G/C Type 2 transcript Type 3 transcript Type 2 protein M D V L V S E S S A Type 3 protein SNPs have various functions promoter GU AG 3’UTR 5’UTR atggacgtactggtg tctgagtgctccgcg TFBS A/G G/T Type 1 transcript Transcrip. Factor Binding Sites • Altering the encoded protein • Alternative splicing • Premature termination • Transcription regulation Type 1 protein M D V L V S E C S A

  21. Important SNP Resource SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences Areum Han, Hyo Jin Kang, Yoobok Cho, Sunghoon Lee, Young Joo Kim and Sungsam Gong NAR 2006 34(Web Server issue):W642-W644 doi: http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W642 SNP@Domain Site: http://snpnavigator.net/

  22. dbSNP: the NCBI database of genetic variationSherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K.Nucleic Acids Research (NAR) 2001; 29:308-311.

  23. Recent SNPs Sites and BDs • Uzun, C. M. Leslin, A. Abyzov, and V. IlyinStructure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathwaysNAR, July 13, 2007; 35(suppl_2): W384 - W392. • J. Park, S. Hwang, Y. S. Lee, S.-C. Kim, and D. LeeSNP@Ethnos: a database of ethnically variant single-nucleotide polymorphismsNAR, January 12, 2007; 35(suppl_1): D711 - D715.

  24. Árvores Filogenéticas

  25. Árvores Filogenéticas Árvores filogenéticas são árvores que representam as relações evolucionárias entre as diferentes espécies. Cada nó com descendentes é considerado o ancestral comum mais recente destes descendentes. Muitas vezes o comprimento das arestas representa a distância em tempo de evolução. Há várias formas de representação.

  26. Árvore Filogenética Phylogenetic tree showing the relationship between the archaea and other forms of life. Eukaryotes are colored red, archaea green and bacteria blue. Adapted from Ciccarelli et al. 2006

  27. Árvores Filogenéticas São construídas - Com base em distâncias (diferenças) entre seqüências de DNA das espécies envolvidas. - Sob a hipótese de que todas evoluíram de um ancestral comum. Muitas vezes são representadas através de dendogramas.

  28. Phylogeny From the Tree of the Life Website,University of Arizona Orangutan Human Gorilla Chimpanzee

  29. A Árvore da Vida da SCIENCE A revista Science tem uma Árvore da Vida on-line: http://www.sciencemag.org/feature/data/tol/

  30. Evolução Convergente e Divergente Evolução é dita convergente quando organismos que não são fortemente relacionados desenvolvem características similares de forma independente. Ex: Asas de insetos, aves e morcego. Evolução é dita divergente quando organismos que são fortemente relacionados desenvolvem características diferentes.

  31. Terminologia 0 0 0 0 1 0 1 0 0 0 1 1 0 0 0 1 1 0 1 1 0 0 1 1 0 0 1 no homoplasy back-mutation parallel evolution

  32. Filogenia Perfeita Um conjunto de seqüências S tem uma filogenia perfeita se existe uma árvore filogenética sobre S tal que: - Cada estado de cada caracter ocupa uma sub-árvore, ou - Nenhum caracter tem back-mutation ou evolução paralela.

  33. A=(0,0), B=(0,1), C=(1,0), D=(1,1) não tem uma filogenia perfeita. Intuitivamente, - O 1o. elemento associa (A, B) e (C,D) - O 2o. elemento associa (A, C) e (B, D) Exemplo

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