SNPs

1
SNPs

• Karthikeyan Narayanan

2
Introduction

• The human genome consists of 3 billion
  nucleotides ('base pairs') of DNA.
• Everyone shares about 99.9 per cent of this DNA.
• But 0.1 per cent difference is what makes each
  one unique.
• SNPs (pronounced snips) are a key part of this
  variation.
• The variation makes us look different

3
What are SNPs?

• Single nucleotide polymorphisms or 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.

4
Why SNPs?

• Number of Available Markers
• SNPs 1 in 1,000 bp 3,000,000 Markers
• Diallelic - Nucleotide Substitutions
• Number of High Throughput Typing Methods
• Found in Coding and Non-Coding Regions
• Potential Association with Functional Variation

5
How are SNPs generated?
6
Genetic Analysis
7
How are they identified?

• There are many methods to identify variance
• RFLP
• Single strand confirmation polymorphisms.
• Heteroduplex analysis.
• Direct DNA Sequencing.
• Variant detector Arrays.

8
SSCP

• In SSCP the DNA fragment spanning the putative
  SNP is PCR amplified, denatured and run on
  denaturing PAGE.
• During gel run the fragments attain secondary
  structure based on their sequence.
• Any change in the migration pattern is observed
  and then sequenced to find the SNPs
• It is widely used and simple technique
• It has a variable success rate of 70 95.
• Its labour intensive and low throughput.

9
Heteroduplex Analysis

• This technique relies on the detection of
  heteroduplex formation of the PCR product of a
  heterozygote after denaturation and reannealing.
• The most reliable device for detection is HPLC.
• It is simple, low cost, and the efficiency is
  about 95 100.
• Throughput is app 10minutes per sample using
  commercially available systems like transgenomic
  wave

Heteroduplexes are resolved ahead of he
homoduplexes at terperatures ranging from 54C to
58C
10
Direct DNA Sequencing
11
VDA

• It is a new tool for SNP detection
• It is like microarray
• The strength between the matched and mismatched
  oligonucleotides are measured.
• It has a high-throughput and its sensitivity is
  that of the Direct DNA sequencing method

12
Varied Detector Array(DNA Chips)
13
Recent Technologies for SNP detection

• Fluorescent Micro array based system (Affymetrix)
• Fluorescent bead based technologies
  (Luminex,illumina, Q-dot)
• Automated ELISA assays (Orchid biocomputer)
• Pyrosequencing
• Fluorescence resonance energy transfer-(FRET)
  based Cleavase assays (third wave technologies)
• Mass Spectrophotometry detection (Rapigene,
  Sequenom)

14
Applications
DRUG DISCOVERY
15
Other Applications

• Some of the other applications of SNPs are
• Health Care
• Prognosis
• Tailored medicines

16
Conclusion

• High-throughput screening of SNPs is emerging as
  an important new field
• New technologies with advantages and
  disadvantages proliferate.
• SNP genotyping technologies are maturing, and
  companies are commercializing them in the form of
  products.
• SNPs could potentially help optimize clinical
  trials through patient stratification.

17
Thank You