1. VRIJE UNIVERSITEIT
BRUSSEL
IPMB:1 st Year
“SINGLE NUCLEOTIDE POLYMORPHYSIM”
By
MULUALEM TESHOME
&
JANVIER HABINSHUTI
12/21/2012 Seminar presentation 1

2. Single Nucleotide Polymorphisms (SNPs)
Overview
Introduction
General information & principles
SNP detection techniques
SNP importance and applications in sciences
Reference
12/21/2012 seminar 2

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.
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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.
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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.
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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 .
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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
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strands.

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.
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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.
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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. How many SNPs?
Table 2: Occurrence of SNP in human population (Natural genetics,
2001)
Nickerson and Kruglyak, Nature Genetics, 2001

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.
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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.
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14. Table 3: Different methods for detecting SNPs (
Approach Examples
Enzymatic 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 sequencing
Solid Phase o Oligonucleotide arrays
Chromatographic oDenaturing high performance liquid chromatography
(DHPLC)
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Primrose &Twyman, 2006

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 Alzheimer's disease
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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.
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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.
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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. of
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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.html
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20. AKNOWLEDGMENT
Instructor Steven Odongo.
IPMB staff
Classmates
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21. 12/21/2012 seminar 21