A brief introduction about single nucleotide polymorphism

1. GENETIC MARKER
SINGLE NUCLEOTIDE
POLYMORPHISM
(SNP)
by
Saloni Arora
SNP
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2. A Genetic marker is a gene or
DNA sequence with a known
location on chromosome that
can be used to identify
individuals or species.
A genetic marker may be a
short DNA sequence
surrounding a single base-pair
change ( SNP ), or a long one
like, minisatellites.
SNP
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http://isaaa.org/siteimages/pocketkimages
/clip_image002_0018.jpg

3. The world polymorphism is a generic term that
means “many shapes” i.e. ability to appear in
different forms .
SNP is defined as a single base change in DNA
sequence that occurs in a significant proportion (
more than 1% ) of a large population .
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4. Human genome sequence
is 99.9% identical in all
people .
However , there are certain
positions (Fig.1) where
some people have one
nucleotide pair , while others
have another
These positions are known
as SNPs .
www. learn.genetics.com

5. SNPs are the most frequent forms
among various genetic variations .
> 90% of human genetic
variations come from SNPs.
 SNP has become preferred markers
for association studies .
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6.  The nucleotide on SNP locus is called
> a major allele
> a minor allele
94% ---- A C T T A G C T G - G : major allele
6% ---- A C T T A G C T T - T: minor allele
http://projects.nfstc.org/pdi/Subject09/images/pdi_s09_m02_01_c.jpg
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7. Non-coding region
Coding region
NON-CODING REGION
A segment of DNA that does comprise a gene and thus does
not code for a protein .
SNP
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8. CODING REGION
Regions of DNA/RNA sequence that
code for proteins
SYNONYMOUS
A SNP in which both forms lead to the same polypeptide
sequence is called synonymous .
( sometimes called silent mutations )
NON-SYNONYMOUS
If a different polypeptide sequence is produced they are non
synonymous .
A non synonymous change may either be missense or
nonsense
• a missense change results in a different amino acid .
• a nonsense change results in a premature stop codon .
SNP
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9. SNP
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http://learn.genetics.utah.edu/content/precision/snips/images/snp-types.jpg

10. For a variation to be considered a SNP, it
must occur in at least 1% of the population.
They occur once in every 300~600
nucleosides on average , which means 10
million SNPs in the human genome .
Most commonly these variations are found in
DNA between genes .
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11. Personalized
medicines
Genetic marker
Human genetic study
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12. Sequence genomes of a large number of
people.
Compare the base sequences to discover
SNPs.
Generate a single map of the human
genome containing all possible SNPs => SNP
maps.
SNP
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13. SNP
GCAT
http://www.ubooks.pub/Books/B0/E19R191
9/MAIN/images/image036.jpg

14. Genome of each individual contain
distinct SNP pattern .
People can be grouped based on SNP
profile.
SNPs profiles are important for
identifying response to drug therapy.
There might be correlations between
certain SNP profiles and specific
responses to treatments .
SNP
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15. SNP
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.http://www.ubooks.pub/Books/B0/E19R
1919/MAIN/images/image037.jpg

16.  Primer extension is a method scientists used to
determine which version of known SNP a person has .
SNP
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http://isaaa.org/siteimages/pocketkimages/clip002_0018.jpg

17. Anyone may obtain a SNP report from
several on-line genome scanning
companies .
 SNP detection technologies are used
to scan for new polymorphism and to
determine the allele(s) of a known
polymorphism in target sequences .
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18. SNP
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19. MAY BE HARMLESS
. Change in phenotype
. Pigmentation
. Livestock breeding programs
MAY BE HARMFUL
. Diabetes , cancer
. Parkinson’s disease
. Huntington’s disease
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20. Evolution and ecological genomics
Gene discovery and mapping
Response prediction
Homogeneity testing / study design
Gene function identification
Association based candidate polymorphism
testing
Diagnostics / risk profiling
Drug discovery and development
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21. “SNPs and snails and puppy dog tails, and
that’s what people are made of …”
A Case Study on Genome Privacy
by
Debby Walser -Kuntz, Sarah Deel, and Susan Singer
Department of Biology
Carleton College, Northfield, MN
In April 1999 Terri Seargent went to her doctor with slight
breathing difficulties. A simple genetic test confirmed her worst
nightmare: she had alpha-1 deficiency, meaning that she might
one day succumb to the same respiratory disease that killed her
brother. The test probably saved Seargent’s life—the condition is
treatable if detected early—but when her employer learned of her
costly condition, she was fired and lost her health insurance.
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22. There are privacy issues with genetic Information .
Concerned scientists have requested to pass laws
that protect employees .
Over the past few years, many proposed bills failed .
One current piece of federal legislation being
considered by the U.S. House of Representatives is the
Genetic Information Nondiscrimination Act.
The following are key excerpts from the Act:
Use of Genetic Information
Acquisition of Genetic Information
 where an employer purchases documents
that are commercially and publicly available
that include family medical history.
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23. Single-nucleotide polymorphism / SNP | Learn
Science at Scitable .
Human Genome Project Information — SNP Fact
Sheet
http://www.ncbi.nlm.nih.gov/About/primer/snps.html
Carlson, Bruce (2008-06-15). "SNPs — A Shortcut
to Personalized Medicine". Genetic Engineering &
Biotechnology News. Mary Ann Liebert, Inc. 28 (12).
Retrieved 2008-07-06.
www.nature.com
www.pubmedcentral.gov.in
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