1. GENETIC MARKER
OR
MOLECULAR MARKER
BY ADEELA TEHSEEN
IMMB -MMC
IST SEM:02121005
2. BIO MARKER
MARKER is a molecule or substance in the body that is used as an
indicator of a specific biological process occurring in the body.
The most common use is to find indications of disease.
For example, tumor markers include
CA-125 (in ovarian cancer),
CA 15-3 (in breast cancer),
CEA (in colon cancer),
PSA (in prostate cancer)..
4. HISTORY
1847 : first lab test on protein cancer
1960: word bio-marker appear in literature
2000 sequence of human genome
2005: part of biotechnology
5. WHY GENETICISTS INTERESTED IN DNA MARKER &
DNA POLYMORPHISM
TO LOCATE DISEASE GENES
CLOSER THE MUTANT GENE TO DISEASED GENE
ALONG CHROMOSOME CLOSER THE LINKAGE
MORE CHANCE OF INHERITED DISEASE
6. GENETIC MAPING TO INDIVIDUAL IDENTIFICATION
HUMAN POPULATION HISTORY
EPIDEMIOLOGY&FOOD SAFETY SCIENCE
ECOLOGICAL INDICATION
HISTORY OF DOMESTICATION
EVOLUTIONARY GENETICS
POPULATION STUDIES
7. ANALYSIS
GENES AND MARKERS ARE LOCATED CLOSE TO EACHOTHER ON
CHROMOSOMES
WHEN GENE IS MUTED
MARKER ANALYSIS PROVIDE INFORMATION
RELATED TO CHROMOSOMES HAVING THIS
MUTED GENE
EXAMPLE: IF YOUNG ONES INHERITED CHROMOSOME WITH
MUTED GENE HAVING GREATER CHANCES OF
DEVELOPING DISEASE.
YOUNG ONCE INHERITED CHROMOSOMES WITH
NORMAL GENE HAVING NO CHANCES OF
DEVELOPING DISEASE
9. Genetic markers are sequences of DNA which have been traced to
specific locations on the chromosomes and associated with particular
traits.
10. NEGATIVE ASPECT
ALTHOUGH THEY ARE HARMLESS ITSELF.
But THEY ALLOW POSITION OF DISEASED GENES TO BE LOCATED
ALONG CHROMOSOMES
11. FRAGMENTANALYSIS CATEGORIES
NUCLIEC ACID PCR AMPLIFICATION
HYBRIDIZATION
SMALL AMOUNT OF DNA
GREAT AMOUNT OF DNA GENOME
GENOME
LARGE FRAGMENT IDENTIFY
SMALL FRAGMENT SIZE
NO PRIOR KNOWLEDGE OF DNA
SEQUENCES SOME PRIOR KNOWLEDGE OF
DNA SEQUENCES
12. TYPES
RFLP ( Restriction fragment length polymorphism)
AFLP (Amplified fragment length polymorphism)
RAPD (Random amplification of polymorphic DNA)
SNP (SinSNP single nucleotide polymorphism)
VNTR (Variable number tandem repeat)
13. RFLP
RESTRICTIVE FRAGMENT LENGTH POLYMORPHISM
GREEK WORD :MANY SHAPES BY GRODZIKER
Definition ACCORDING TO :
Gene Tests from the University of Washington and the
National Center for Biotechnology Information
Fragment of DNA of predictable size resulting from digestion
(cutting) of a strand of DNA by a given restriction enzyme. DNA
sequence alterations (mutations) that destroy or create the
sites at which a restriction enzyme cuts DNA change the size
(and number) of DNA fragments resulting from digestion by a
given restriction enzyme
14. RESTRICTIVE ENZYME
THEY ARE PROTEIN, ISOLATED FROM BACTERIA TO CUT DNA IN
FRAGMNETS OF VARIOUS LENGTH,
SHORT LENGTH
MEDIUM LENGTH
LONG LENGTH
USES
PROTECTION FROM FOEIGN DNA
15. INDIVIDUAL A
ATTC GAATTC GAATTC
CTTAAG CTTAAG CTTAAG
RESTRICTION ENZYMES LOCATE
RESTRICTIVE SITES
INDIVIDUAL B
SITE DIFFERENCE
GAATTC AAATTC GAATTC
CTTAAG TTTAAG CTTAAG
16. G AATTC G AATTC G AATTC
CTTAA G CTTAA G CTTAA G
SHORT FRAGMENTS MEDIUM FRAGMENTS
LONG FRAGMENST
G AATTC AAATTC G AATTC
CTTA G AAATTC CTTAA G
17. These fragments are separated by gel electrophoresis
Unque patern for unique dnag fragment.
Used in forensic sci ence.
LONG SHORT
MEDIUM SHORT
E FRAGMENT FRAGMENT
L
E
C
T
R
O
P
H
E LONG FRAGMENT
R
E
S
I
S
18. ADVANTAGES DISADVANTAGES
RFLP USED AS MARKER USE LARGE AMOUNT
TO IDENTIFY OF DNA
PARTICULAR GROUP AT
RISK OF CERTAIN INTENSE LABOUR
GENETIC DISORDER REQUIRED
USED AS MARKERS ON
GENETIC MAPS.
19. 2-AFLP
AMPLIFIED FRAGMENT LENGTH POLYMORPHISM.
PCR BASED TOOL.
RESTRICTIVE ENZYMES CUTS RESTRIVE FRAGMENTS OF DNA
UNDER RERSTRICTION PROCESS.
THIS FRAGMENT IS 4-8 BAISE PAIR LONG & IN 5'_ 3' DIRECTION.
THIS FRAGMENT IS AMPLIFIED BY PRIMERS.
PRIMER SHOULD BE COMPPLIMENTARY
AMPLIFIED FRAGMENT IS THEN SEPARATED AND VISUALIZED
UNDER FLOURESCENCE.
20. USES
FAST
INEXPENSIVE
VARIABLE
RFLPS CAN BE USED TO TRACE INHERTITANCE PATTERNS,
IDENTIFY SPECIFIC MUTATIONS, AND FOR OTHER MOLECULAR
GENETIC TECHNIQUES
AFLP ANALYSIS ALLOWS THE RELIABLE IDENTIFICATION OF OVER
50 LOCI IN A SINGLE REACTION
USED IN GENETICS RESEARCH, DNA FINGERPRINTING, AND IN
THE PRACTICE OF GENETIC ENGINEERING.
21. 3- RAPD
(or Random amplification of polymorphic DNA)
1990 williams et al
IT DOESNT REQUIR SEQUENCE INFORMATION AND INVOLVED
AMPLIFIED RANDOM DNA FRAGMENTS.
PCR BASED
Its also gell based
required10mer oligonucleotide.
Dominent
22. WORKING PROCEDURE
RESTRICTIVE ENZYMES CUTS RANDOM FRAGMENT OF DNA OF
10 NUCLEOTIDE.
SHORT PRIMER (8-12 NUCLEOTIDE) IS USED .
The primer acts as both a reverse and forward primer.
From this, one gets variable length products (bands on a gel).
A large number of primers are typically sc reened early in a study, to
determine which ones are polymorphic and provide interpretable banding
patterns.
the use of many random primers, a large number of genetic markers can
be used
The products are simply run on an angrose gel ,stained and visualizedA
With the use of many random primers, a large number of genetic
23. APPLICATION OF RAPD
In wide rangef use.
Applications in many areas of biology. like:
GENETIC MAP
PLANT BREEDING
RAPDs have been used for studies of hybridization, breeding systems,
conservation issues, levels and distribution of genetic variation, genomic
and linkage mapping, identification - disease resistance, ecotypes,
cultivars, etc ).
24. ADVANTAGES DISADVANTAGES
No previous knowledge about the DNA .
sequence.
Dominant inheritance - not
Not strongly affected by the complexity appropriate to use standard
of the genome. measures of population genetics.
Small amounts of genomic DNA They have not been used widely to
required.
measure interspecific genetic
Minimal laboratory equipment and differences in plants
supplies.
Universal primer set - useful in a wide
variety of species
25. 5 SNP
Single Nucleotide Polymorphism
(1994 by JORDEN & HUMPHRIES)
Sinlge letter change in dna
Prnounced as snip
Based on nucleotide difference between two alleles.
Based on nucleotide differences between two alleles.
Locus-by-locus approach
Occur through out genome
Frequent type of polymorphism.
26. INTRODUCTION
Single Nucleotide Polymorphism. The most common
form of DNA variation, alterations to a single base.
If the SNP is in a gene, it can disrupt the gene's
function.
Most SNPs do not occur in genes but can be
associated with other types of DNA variation and so
are used effectively as markers.
Typically, SNPs are biallelic, although very rarely tri-
or tetra allelic forms can be found.
The average frequency of SNPs in the human
genome is approximately one per 1,000 BP.
27. TECHNIQUES FOR ANALYSIS
GEL-BASED :
Specific primers are designed which would cause
amplification of a positive allele due to exact match of primer.
NON GEL-BASED:
Appropriate regions are amplified and then mismatches
detected by techniques such as high performance liquid
chromatography (HPLC).
28. VNTR
BY 1995 JEFFEREYS et al
VNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem repea
29. CONCLUSION
A wide range of molecular marker technologies is now
available for genetic studies. Amongst these, RAPD, AFLP
RFLP and SSR marker systems are emerging as the lead
technologies
These new generation of markers viz. SRAP, MITE, TE-
AFLP and IMP are in the early phase of usage and are not
routines in molecular marker technology laboratories
30. REFERENCE
HAN D BOOK OF BIO MARKER BY , KL.JAIN
BIO MARKER IN DRUGS DEVELOPMENT
EDITED BY MICHAEL,R,BLEAVIAN,CLAUDIO.
GEBETICS BY DANIAL,HARL
MR MAHESHWARAN (ADVANCE BIO TECH-
TMIL NADU AGRICULTURAL UNIVERSITY COIMBATO)
UC DAVIS • DEPARTMENT OF PLANT SCIENCES-NEALE CHAPTER 4
MOLECULAR MARKERS BY Ashwani Kumar 2009
WIKIPEDIA
DESCRIPTION OF MOLECULAR MARKER TYPES (WUEMED 2006)
