VRIJE UNIVERSITEIT                     BRUSSEL             IPMB:1 st        Year  “SINGLE NUCLEOTIDE POLYMORPHYSIM”       ...
Single Nucleotide Polymorphisms (SNPs)Overview  Introduction  General information & principles    SNP detection techniques...
INTRODUCTIONThe word” polymorphism is a generic term that means “many shapes” i.e. ability to appear in different form.S...
Introduction (cont…)Some Facts:In human beings, 99.9% bases are same (Cooper et al., 1985).Remaining 0.1 % makes a perso...
Introduction (cont…)SNP Facts:►Occur with a very high frequency.   About 1 in 1000 bases to 1 in 100 to 300    bases.►The...
Introduction (cont…)Differ on single base nucleotides at a given position.DNA sequence variation occurring when a single...
Introduction (cont…) Surprisingly, human genome  sequence is 99.9% identical  in all people. This is true of everyone,  ...
Introduction (cont…)Two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a...
Introduction (cont…)For example, here in the       Table 1: sequence from chromosome                                     ...
SNP OCCURRENCE For a variation to be considered a SNP, it must occur in  at least 1% of the population. SNPs occur norma...
How many SNPs?Table 2: Occurrence of SNP in human population (Natural genetics,         2001)                Nickerson and...
SNP DETECTION TECHNIQUES• Sequence genomes of a large number of people.  Compare the bases sequences to discover SNPs.• Ge...
SNP DETECTION TECHNIQUESAnyone may obtain a SNP report from one of several on-line genome scanning companies.           ...
Table 3: Different methods for detecting SNPs (Approach            ExamplesEnzymatic           oRestriction fragment lengt...
Importance &            application(Cont..) SNP is found                   » Noncoding                   » intergenic    ...
Importance & application(Cont..)Researchers use SNPs in Personalized medicine individual’s response.              – Pharm...
SUMMARY Each individual has many single nucleotide  polymorphisms that together create a unique DNA  pattern for that per...
REFERENCES• Botstein D, White RL, Skolnick M, and Davis RW, 1980.  Construction of a genetic linkage map in man using  res...
REFERENCES(Cont..)• Nickerson and Kruglyak, Nature Genetics, 2001• Primrose ,S and Twyman, R(2006), Principles of  gene ma...
AKNOWLEDGMENTInstructor Steven Odongo.IPMB staffClassmates12/21/2012          seminar   20
12/21/2012   seminar   21
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Seminar presentation on snp (mulualem & janvier)

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Seminar presentation on snp (mulualem & janvier)

  1. 1. VRIJE UNIVERSITEIT BRUSSEL IPMB:1 st Year “SINGLE NUCLEOTIDE POLYMORPHYSIM” By MULUALEM TESHOME & JANVIER HABINSHUTI12/21/2012 Seminar presentation 1
  2. 2. Single Nucleotide Polymorphisms (SNPs)Overview Introduction General information & principles SNP detection techniques SNP importance and applications in sciences Reference12/21/2012 seminar 2
  3. 3. INTRODUCTIONThe word” polymorphism is a generic term that means “many shapes” i.e. ability to appear in different form.Single(Simple) nucleotide polymorphisms or SNP (pronounced “snips”), are the most common type of genetic variation among peoples.A SNP is defined as a single base change in a DNA sequence that occurs in a significant proportion (more than 1 percent) of a large population. 12/21/2012 seminar 3
  4. 4. Introduction (cont…)Some Facts:In human beings, 99.9% bases are same (Cooper et al., 1985).Remaining 0.1 % makes a person unique.  Different attributes.  Characteristics .  Traits.  How a person looks.  Diseases he or she develops.12/21/2012 seminar 4
  5. 5. Introduction (cont…)SNP Facts:►Occur with a very high frequency. About 1 in 1000 bases to 1 in 100 to 300 bases.►The abundance of SNPs & the ease with which they can be measured make these genetic variations significant.►SNPs close to particular gene acts as a marker for that gene.12/21/2012 seminar 5
  6. 6. Introduction (cont…)Differ on single base nucleotides at a given position.DNA sequence variation occurring when a single nucleotide A, T, C, or G in the genome differs between members of a species . 12/21/2012 seminar 6
  7. 7. Introduction (cont…) Surprisingly, human genome sequence is 99.9% identical in all people. This is true of everyone, regardless of race or heritage However, there are certain positions (Fig.1) where some people have one nucleotide pair, while others have another. These positions are known asSNPs (pronounced "snips"). Fig 1: Typical example of SNP of two 12/21/2012 strands.
  8. 8. Introduction (cont…)Two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide.In this case we say that there are two alleles: C & T & almost all common SNPs have only two alleles. We use the term allele (pronounced ull-leel) to identify which nucleotide is present at a SNP.12/21/2012 seminar 8
  9. 9. Introduction (cont…)For example, here in the Table 1: sequence from chromosome that has a SNP. (Table 1), is a segment of sequence from chromosome 1 that has a SNP. Paul & Julia have the G allele on both of their copies of this chromosome. However, Jose has one G & one A allele, & Roger has two C alleles. 12/21/2012
  10. 10. SNP OCCURRENCE For a variation to be considered a SNP, it must occur in at least 1% of the population. SNPs occur normally throughout a person’s DNA.They occur once in every 300 nucleotides on average, which means there are roughly 10 million SNPs in the human genome (three billion DNA base pair if haploid); diploid ?Most commonly, these variations are found in the DNA between genes. 12/21/2012 seminar 10
  11. 11. How many SNPs?Table 2: Occurrence of SNP in human population (Natural genetics, 2001) Nickerson and Kruglyak, Nature Genetics, 2001
  12. 12. SNP DETECTION TECHNIQUES• Sequence genomes of a large number of people. Compare the bases sequences to discover SNPs.• Generate a single map of the human genome containing all possible SNPs.• Today the International HapMap Project is an organization that aims to develop a haploide map (HapMap) of the human Genome describe the common patterns of human genetic variation.12/21/2012 seminar 12
  13. 13. SNP DETECTION TECHNIQUESAnyone may obtain a SNP report from one of several on-line genome scanning companies.  One simply sends in a sample of saliva or a cheek swab (together with a fee).  A week or two later, the company sends back the report.SNP detection technologies are used to scan for new polymorphisms & to determine the allele(s) of a known polymorphism in target sequences. 12/21/2012 seminar 13
  14. 14. Table 3: Different methods for detecting SNPs (Approach ExamplesEnzymatic oRestriction fragment length polymorphisms (RFLP) oAmplified fragment length polymorphisms (AFLP) oCleavase fragment length polymorphisms (CFLP) o Randomly amplified polymorphic DNA (RAPD)Electrophoretic Single-strand conformation polymorphism (SSCP)  DNA sequencingSolid Phase o Oligonucleotide arraysChromatographic oDenaturing high performance liquid chromatography (DHPLC) 12/21/2012 seminar Primrose &Twyman, 2006
  15. 15. Importance & application(Cont..) SNP is found » Noncoding » intergenic » Rare exons regions Presence of SNPs • Harmless » change in phenotype » pigmentation » livestock breeding Programs. • Harmful » diabetes, cancer, » Huntington’s, » Parkinson Alzheimers disease12/21/2012 seminar 15
  16. 16. Importance & application(Cont..)Researchers use SNPs in Personalized medicine individual’s response. – Pharmacogenomics – Pharmacogenetics...Tracking inheritance of disease genes within families.Determine Genotype and Phenotypes in many individuals. 12/21/2012 seminar 16
  17. 17. SUMMARY Each individual has many single nucleotide polymorphisms that together create a unique DNA pattern for that person (some people have one nucleotide, while others have another). SNPs have four possible alleles: A, T, G, and C. Modern techniques make it possible to determine the status of large numbers of SNPs very efficiently. SNPs promise to significantly advance our ability to understand and treat human disease. 12/21/2012 seminar 17
  18. 18. REFERENCES• Botstein D, White RL, Skolnick M, and Davis RW, 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet32:314–331.• Brower, V. Genome II: the next frontier.Nat.Biotechnology.16,1004(1998)• Cooper, D.N., Smith, B.A., Cooke, H.J., Niemann, S., and Schmidtke, J. 1985. An estimate of unique DNA sequence heterozygosity in the human genome. Hum. Genet. 69: 201-205.• Indiana, 24th November, 2003(SNP and Human genome)• Manish Anand, Nihar Sheth and Jim Costello,Univ. of12/21/2012 seminar 18
  19. 19. REFERENCES(Cont..)• Nickerson and Kruglyak, Nature Genetics, 2001• Primrose ,S and Twyman, R(2006), Principles of gene manipulation and genomics.7th Ed.Blackwell.USA• Wang DG,FanJ-B,Siao C-J,Berno A,Young P,Sapolsky R, Ghandour G, et al (1998) Large Scale identification, mapping and genotyping of Single-nucleotide Polymorphisme in the human genome.Science 280:1077-1082.• http://www.genome.gov/10001634• http://www.nature.com/ng/index.html12/21/2012 seminar 19
  20. 20. AKNOWLEDGMENTInstructor Steven Odongo.IPMB staffClassmates12/21/2012 seminar 20
  21. 21. 12/21/2012 seminar 21

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