GENETIC MARKER ORMOLECULAR MARKER BY ADEELA TEHSEEN IMMB -MMC IST SEM:02121005
BIO MARKERMARKER is a molecule or substance in the body that is used as anindicator 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)..
BIO MARKERMORPHOLOGICAL MARKERPHARMACEUTICAL MARKERSGENETIC MARKERS
HISTORY1847 : first lab test on protein cancer1960: word bio-marker appear in literature2000 sequence of human genome2005: part of biotechnology
WHY GENETICISTS INTERESTED IN DNA MARKER & DNA POLYMORPHISMTO LOCATE DISEASE GENES CLOSER THE MUTANT GENE TO DISEASED GENE ALONG CHROMOSOME CLOSER THE LINKAGE MORE CHANCE OF INHERITED DISEASE
GENETIC MAPING TO INDIVIDUAL IDENTIFICATIONHUMAN POPULATION HISTORYEPIDEMIOLOGY&FOOD SAFETY SCIENCEECOLOGICAL INDICATIONHISTORY OF DOMESTICATIONEVOLUTIONARY GENETICSPOPULATION STUDIES
ANALYSISGENES AND MARKERS ARE LOCATED CLOSE TO EACHOTHER ON CHROMOSOMESWHEN GENE IS MUTEDMARKER 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
LOCATIONPARTICULAR REGION OF GENOME.GENETIC MARKER DETECT BY DIRECT ANALYSIS OF DNA .
Genetic markers are sequences of DNA which have been traced tospecific locations on the chromosomes and associated with particulartraits.
NEGATIVE ASPECTALTHOUGH THEY ARE HARMLESS ITSELF.But THEY ALLOW POSITION OF DISEASED GENES TO BE LOCATED ALONG CHROMOSOMES
FRAGMENTANALYSIS CATEGORIESNUCLIEC ACID PCR AMPLIFICATION HYBRIDIZATION SMALL AMOUNT OF DNAGREAT AMOUNT OF DNA GENOME GENOMELARGE FRAGMENT IDENTIFY SMALL FRAGMENT SIZENO PRIOR KNOWLEDGE OF DNA SEQUENCES SOME PRIOR KNOWLEDGE OF DNA SEQUENCES
TYPESRFLP ( 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)
RFLPRESTRICTIVE FRAGMENT LENGTH POLYMORPHISM GREEK WORD :MANY SHAPES BY GRODZIKERDefinition 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
RESTRICTIVE ENZYMETHEY ARE PROTEIN, ISOLATED FROM BACTERIA TO CUT DNA IN FRAGMNETS OF VARIOUS LENGTH,SHORT LENGTHMEDIUM LENGTHLONG LENGTHUSESPROTECTION FROM FOEIGN DNA
G AATTC G AATTC G AATTCCTTAA G CTTAA G CTTAA G SHORT FRAGMENTS MEDIUM FRAGMENTS LONG FRAGMENST G AATTC AAATTC G AATTCCTTA G AAATTC CTTAA G
These fragments are separated by gel electrophoresisUnque 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
ADVANTAGES DISADVANTAGESRFLP USED AS MARKER USE LARGE AMOUNTTO IDENTIFY OF DNAPARTICULAR GROUP ATRISK OF CERTAIN INTENSE LABOURGENETIC DISORDER REQUIREDUSED AS MARKERS ONGENETIC MAPS.
2-AFLPAMPLIFIED FRAGMENT LENGTH POLYMORPHISM.PCR BASED TOOL.RESTRICTIVE ENZYMES CUTS RESTRIVE FRAGMENTS OF DNAUNDER RERSTRICTION PROCESS.THIS FRAGMENT IS 4-8 BAISE PAIR LONG & IN 5_ 3 DIRECTION.THIS FRAGMENT IS AMPLIFIED BY PRIMERS.PRIMER SHOULD BE COMPPLIMENTARYAMPLIFIED FRAGMENT IS THEN SEPARATED AND VISUALIZEDUNDER FLOURESCENCE.
USESFASTINEXPENSIVEVARIABLE RFLPS CAN BE USED TO TRACE INHERTITANCE PATTERNS,IDENTIFY SPECIFIC MUTATIONS, AND FOR OTHER MOLECULARGENETIC TECHNIQUESAFLP ANALYSIS ALLOWS THE RELIABLE IDENTIFICATION OF OVER50 LOCI IN A SINGLE REACTIONUSED IN GENETICS RESEARCH, DNA FINGERPRINTING, AND INTHE PRACTICE OF GENETIC ENGINEERING.
3- RAPD (or Random amplification of polymorphic DNA) 1990 williams et alIT DOESNT REQUIR SEQUENCE INFORMATION AND INVOLVEDAMPLIFIED RANDOM DNA FRAGMENTS.PCR BASEDIts also gell basedrequired10mer oligonucleotide.Dominent
WORKING PROCEDURERESTRICTIVE ENZYMES CUTS RANDOM FRAGMENT OF DNA OF10 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, todetermine which ones are polymorphic and provide interpretable bandingpatterns.the use of many random primers, a large number of genetic markers canbe usedThe products are simply run on an angrose gel ,stained and visualizedAWith the use of many random primers, a large number of genetic
APPLICATION OF RAPDIn wide rangef use.Applications in many areas of biology. like: GENETIC MAP PLANT BREEDINGRAPDs have been used for studies of hybridization, breeding systems,conservation issues, levels and distribution of genetic variation, genomicand linkage mapping, identification - disease resistance, ecotypes,cultivars, etc ).
ADVANTAGES DISADVANTAGESNo previous knowledge about the DNA .sequence. Dominant inheritance - notNot strongly affected by the complexity appropriate to use standardof the genome. measures of population genetics.Small amounts of genomic DNA They have not been used widely torequired. measure interspecific geneticMinimal laboratory equipment and differences in plantssupplies.Universal primer set - useful in a widevariety of species
5 SNP Single Nucleotide Polymorphism (1994 by JORDEN & HUMPHRIES)Sinlge letter change in dnaPrnounced as snipBased on nucleotide difference between two alleles.Based on nucleotide differences between two alleles.Locus-by-locus approachOccur through out genomeFrequent type of polymorphism.
INTRODUCTIONSingle Nucleotide Polymorphism. The most commonform of DNA variation, alterations to a single base. If the SNP is in a gene, it can disrupt the genesfunction. Most SNPs do not occur in genes but can beassociated with other types of DNA variation and soare 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 humangenome is approximately one per 1,000 BP.
TECHNIQUES FOR ANALYSISGEL-BASED : Specific primers are designed which would causeamplification of a positive allele due to exact match of primer.NON GEL-BASED: Appropriate regions are amplified and then mismatchesdetected by techniques such as high performance liquidchromatography (HPLC).
VNTR BY 1995 JEFFEREYS et alVNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem repea
CONCLUSIONA wide range of molecular marker technologies is nowavailable for genetic studies. Amongst these, RAPD, AFLPRFLP and SSR marker systems are emerging as the leadtechnologiesThese new generation of markers viz. SRAP, MITE, TE-AFLP and IMP are in the early phase of usage and are notroutines in molecular marker technology laboratories
REFERENCEHAN D BOOK OF BIO MARKER BY , KL.JAINBIO MARKER IN DRUGS DEVELOPMENTEDITED BY MICHAEL,R,BLEAVIAN,CLAUDIO.GEBETICS BY DANIAL,HARLMR MAHESHWARAN (ADVANCE BIO TECH-TMIL NADU AGRICULTURAL UNIVERSITY COIMBATO)UC DAVIS • DEPARTMENT OF PLANT SCIENCES-NEALE CHAPTER 4MOLECULAR MARKERS BY Ashwani Kumar 2009WIKIPEDIADESCRIPTION OF MOLECULAR MARKER TYPES (WUEMED 2006)