This document provides an overview of gene mapping and cloning of disease genes. It discusses genetic mapping and physical mapping techniques used to locate genes on chromosomes, including linkage mapping using polymorphic DNA markers like RFLPs, SSLPs, and SNPs. The document also describes cloning a disease gene, which involves constructing a recombinant DNA molecule containing the gene, multiplying the recombinant DNA in host cells, and obtaining numerous clones with the gene of interest. PCR and other molecular techniques are important tools in gene cloning and mapping diseases at the DNA level.

1. GENE MAPPING AND
CLONING OF DISEASE
GENE
BY
DINESH K
M PHARM PHARMACOLOGY

2. GENE MAPPING
 INTRODUCTION
Gene- a unit of heredity which is transferred
from a parent to offspring and is held to
determine some characteristic of the offspring.
The first marker to be used.
MAPPING- determining the location of elements
within a genome with respect to identifiable
landmarks.

3. Types of mapping
 Genetic mapping- linear description of DNA markers/genes on a given
chromosome with closely placed markers being inherited together more
often.
 Physical mapping- physical location on the chromosome, relating more
towards exact positioning of gene elements.
 Comparative mapping
Genome/genetic maps – graphic representation of the relative positions of genes
a DNA sequences.

4. 1. Genetic mapping
 Linkage mapping
 Pedigree
 Polymorphic markers
2. Physical mapping
 Cytogenetic mapping
 Somatic cell mapping
 Radiation hybrid mapping
 Restriction mapping- PFGE,BAC contigs, sequencing
3. Comparative mapping
 Gene sequences
 Data bases
 DNA chips

5. Genetic mapping
 A genetic map must show the positions of distinctive features.
 Requires informative markers-polymorphic and a population with known
relationships.
 Best if measured between “close” markers.
 Unit of distance in genetic maps= centiMorgans (cM)
 1 cM= 1% chance of recombination between markers.

6. DNA markers for Genetic mapping
 Genes are useful markers but not ideal.
 Mapped feature that are not genes are called DNA markers.
 DNA markers must have at least two alleles to be useful
 DNA sequence features that satisfy this requirements are-
-restriction fragment length polymorphism(RFLP)
-simple sequence length polymorphism (SSLP)
-single nucleotide polymorphism(SNP)

7. RFLP
 RFLP is the first type of DNA marker to be studied.
 Restriction enzymes cut DNA at specific recognition sequences.
 But restriction sites in genomic DNA are polymorphic and exists as two
alleles.
 The RFLP and its position in the genome map can be worked out following
the inheritance of its alleles.

8. Two methods of RFLP
• Southern hybridization
• PCR
Polymorphic restriction site
DNA (ALLELE 1) DNA (ALLELE 2)
add the restriction
endonuclease
4 fragments 2 fragments

9. Simple sequence length polymorphism
(SSLP)
 SSLPs are arrays of repeat sequences that display length variation.
 Here different alleles contain different number of repeat sequences.
 SSLPs can b multiallelic.
 Two types of SSLPs are-
-Minisatellites(VNTRs)
-Microsatellites(STRs)
 Microsatellites are more popular than minisatellites as DNA markers..

10. Single nucleotide polymorphism(SNP)
 There are some positions in the genome where some individuals have one
nucleotide while others have another.
 Some SNPs give to RFLPs but many do not.
 SNPs originate when a point mutation occurs in genome converting one
nucleotide to another.
 There are just two alleles-the original sequence and the mutated version.
 SNPs enable very detailed genome maps to be constructed.

11. Typing method of SNPs
 These are mainly based on oligonucleotide hybridization analysis. These are-
-DNA chip technology
-solution hybridization
-Oligonucleotide ligation assay
-Amplication refractory mutation assay (ARMS test)

12. LOD score
 The LOD score used for linkage analysis in human populations, and also in
animal and plant populations.
 Computerized LOD score analysis is a simple way to analyse complex family
pedigrees in order to determine the linkage between mendelian traits.
 The method briefly, works as follows:
-establish a pedigree
-make a no of estimates of recombination frequency
-calculate a LOD score for each estimate
-the estimate with the highest LOD score will be considered the best estimate.

13. LOD Score
 It is calculated as follows:
 LOD=Z=log 10 probability of birth sequence with a given linkage
probability of birth sequence with no linkage
greater than 3.0- evidence for linkage
less than 3.0 – evidence to exclude linkage

14. Demerits
 Not much sufficient for directing the sequencing phase of a genome project.
 Limited accuracy
 Depends on the no. of crossovers that have been scored.

15. Physical mapping
 The most important techniques used in physical mapping are as follows:
1. Restriction mapping
2. Fluorescent in situ Hybridization (FISH)
3. Sequence tagged site (STS) mapping

16. Restriction mapping
 Restriction mapping locates the relative positions on a DNA molecule of the
recognition sequences for restriction endonuclease.
 The simplest way to construct a restriction map is to compare the fragment
sizes produced when a DNA molecule is digested with two different
restriction enzymes that recognize different target sequences.
 Direct examination of DNA molecules for Restriction sites
a) Two ways –gel stretching
-molecular combing

17. Fluorescent in situ hybridization(FISH)
 Fish enables the position of a marker on a chromosome or extended DNA
molecule to be directly visualized.
 In optical mapping the marker is a restriction site and it is visualized as a gap
in an extended DNA fibre.
 In FISH, the marker is a DNA sequence that is visualized by hybridization with
a fluorescent probe.

18. Sequence tagged sites (STS)
 STS mapping is the most powerful physical mapping technique.
 Detailed maps are generated by STS mapping.
 A sequence tagged site (STS) is a short DNA sequence, generally between
100bp and 500bp in length.
 STS is easily recognizable and occurs once in the chromosome or genome
being studied.

19. Genetic map vs physical map
Genetic map Physical map
It is constructed using recombination
frequency calculated from the
progenies
It pertains to locating the position of
DNA sequences.
It is an indirect method of locating the
positions of genes or DNA markers
It is a direct method of locating the
positions of genes or DNA markers.
Unit of measurement of map distance is
cM
Unit of measurement of map distance is
base pair.

20. Importance of gene mapping
 It helps in the analysis of the heterogeneity and segregation of human genetic
diseases.
 It help to develop methods for gene therapy.
 It provides clinically useful information about linkage

22. Cloning of a disease gene
 Cloning – a clone is a genetically identical copy of an organism and it ay b
naturally occurring or created in the lab.
 Types of cloning
 Gene cloning
 Reproductive cloning
 Therapeutic cloning

23. Gene cloning
 Making multiple copies of a single gene
 The insertion of a fragment of DNA carrying a gene into a
cloning vector and subsequent propagation of
recombinant DNA molecules into many copies is known as
gene cloning

25. Basic steps of gene cloning
 Construction of recombinant DNA molecule
 Transport of the recombinant DNA to the host cell
 Multiplication of recombinant DNA molecule
 Division of the host cell
 Numerous cell division resulting in a clone
The gene cloning requires specialized tools and techniques
a) Vehicles
b) vector

26. PCR
 Pcr is a method of copying DNA molecules. DNA replication is common life; for
example it takes place inside your own cells every time they divide.
 PCR, or the polymerase chain reaction, add a two components to this process.
The initial reaction yields twice the number of starting molecules, but then is
immediately followed by a subsequent reaction.
 The goal of PCR reaction is commonly to replicate only a portion of the of
interest.

27. Uses of PCR
 It is used in human diagnostics
 Detecting HIV
 Detecting bacterial infections
 Genotyping
 Environmental monitering
 Scientific research

28. Three main stages of PCR
 Denaturing- when the double- stranded template DNA is heated to separate it
into two single strands
 Annealing- when the temperature is lowered to enable the DNA primers to
attach to the template DNA
 Extending- when the temperature is raised and the new strand of DNA is made
by the Taq polymerase enzyme.

29. References
 Molecular pharmacology: from DNA to Drug discovery .
John dickensonet.al
 Slide shares
 Gene mapping
 Gene cloning