lecture+5+snps (1)

8/3/2019 Lecture+5+SNPs (1)

1/24

By

Syed Shujaat Ali

[email protected]

[email protected]


2/24

Single Nucleotide Polymorphism.

Variation of a single character.

For a SNP to be considered as a variation?


3/24

SNPs are variations in the sequence of DNA, thatoccurs when any of the four nucleotides get replaced

by another. Most common type of mutation.

Occurrence.

3 Million SNPs.


4/24


5/24

Coding SNPs.

Non-Coding SNPs.

Synonymous SNPs. Non-Synonymous SNPs / Replacement Polymorphism.

- Functional & Non-Functional SNPs.


6/24

Human Genome Similarity.

Impact on Human Genome.

Stability of SNPs.

Scientists thought. Human response to diseases.


7/24

Direct or Indirect impact of SNPs on Diseases.

E.g. Diabetes type 1, Diabetes type 2, Cancer,Alzheimers Disease, Parkinson Disease and many

other traits that vary between individuals.


8/24

ApoE Gene.

ApoE (Apolopoprotein).

ApoE2, ApoE3 & ApoE4.

Inheritance of any one ApoE. Probability with ApoE2 and ApoE4.


9/24

Established in 1999 by pharmaceutical companies &Welcome Trust, UK, lead by Arthur. L. Holden.

GOAL

Find and Map 300,000 SNPs. To create a widely acceptable, authentic, high-quality,

public database, using SNPs as markers, evenlydistributed throughout the human genome.


10/24

By the end of the project many more SNPs werediscovered.

DNA samples collection.

Different Ethnic / racial groups. Volunteer contributions.


11/24

TSC can be accessed from:

dbSNP database of NCBI.

HGVbase (Human Genome Variation Database).


12/24

Majority of SNPs lie outside gene.

They do not cause disease directly.

Environmental Factors.

Life style Factors. Interaction among different genes.


13/24

Most of SNPs serve as Biological Markers.

Used in gene identification, disease location etc.


14/24

Researcher 1.

Collect Blood Samples (affected and unaffectedindividuals)

Isolate DNA. Analyse DNA and SNP pattern.

Researcher 2.

Compare the obtained SNP patterns to the patterns of

the unaffected individual. Such a comparison study is called Association Study.


15/24

SNP response cannot be detected or predetermined.

Response to drug. Personalized Medicines.


16/24

15 million SNP sites in human genome.

3.8 million SNPs common among 270 individuals.

Latest Research

99.9 % human genome is same. 0.1 % dissimilarity.

AND!


17/24

Polyscan

SNPsFinder

ssahaSNP (Sequence Search and Alignment by

Hashing Algorithm) GeneVar (Gene Expression Variation)

AvadisNGS


18/24

http://snpsfinder.lanl.gov/
http://snpsfinder.lanl.gov/http://snpsfinder.lanl.gov/


19/24


20/24

Downloadwww.sanger.ac.uk

Install

Activate

Input sequence Play with different functions of the software.
http://www.sanger.ac.uk/http://www.sanger.ac.uk/


21/24


22/24


23/24


24/24

PRACTICE, PRACTICE and

PRACTICE.

lecture+5+snps (1)

Documents