Definition of genetic markers

According to Wikipedia.org, genetic markers is

defined as :
A genetic marker is a gene or DNA sequence
with a known location on a chromosome that can
be used to identify cells, individuals or species.
 It can be described as a variation (which may
arise due to mutation or alteration in the genomic
loci) that can be observed.
 A genetic marker may be a short DNA sequence,
such as a sequence surrounding a single base-pair
change (single nucleotide polymorphism, SNP),
or a long one, like minisatellites.
Genetic marker studies
Studies done in vary environment
- it keeps the genetics to remain
constant.
Objective :
1. Examine links between genetic marker
and specific disorder/traits.
2. Is a measureable human trait that
controlled by a single allele with known
chromosomal location.
Genetic epidemiology:
Study of role of genetic factors in
determining health and disease in families
and populations and as interplay of such
genetic factors with environmental
factors.
 Characteristics of genetic marker
studies.

1.Genomic abundance
2.Level of polymorphism
3.Locus specificity
4.Codominance of alleles
5.Reproducibility
6. Labor-intensity
7. Technical demands
8. Operational costs
9. Development costs
10. Quantity of DNA required
11. Amenability to automation
 Genomic abundance
 The number of markers that can be generated is determined
mainly by the frequency at which the sites of interest occur
within the genome. RFLPs and AFLPs generate abundant
markers due to the large number of restriction enzymes available
and the frequent occurrence of their recognition sites within
genomes.

 Genomic abundance is essential to studies where a large fraction

of the genome needs to be covered, e.g. for the development of
high-density linkage maps in gene mapping studies.

 In addition to genomic abundance, genome coverage is also

sought, caution should be taken in marker selection. While some
markers are known to be scattered quite evenly across the
genomes.
Level of polymorphism
 Determined by the mutation rate at the genomic sites involved
 Moreover, only mutations modifying the net electric charge and
conformation of proteins can be detected, reducing the resolving
power of allozymes.
 In contrast, mutations at minisatellite and microsatellite loci,
mainly due to changes in the number of repeat units of the core
sequence.
 The other markers presented generally show intermediate levels of
polymorphism, resulting from base substitutions, insertions or
deletions which may alter primer annealing sites and recognition
sites of restriction enzymes, or change the size of restriction
fragments and amplified products.
 In choosing the appropriate technique, the level of polymorphism
detected by the marker needs to be considered in relation to the
presumed degree of genetic relatedness within the material to be
studied.
 Locus specificity
Representing various genomic regions
Similar sized fragments may represent
alleles from different loci and not be
homologous.
In general, locus-specific markers generate
polymorphisms of known identity, however
in most cases sequencing data are needed
for their development.
Codominance of alleles
Markers for which both alleles are expressed
when co-occurring in an individual.
 Therefore, with codominant markers,
heterozygotes can be distinguished from
homozygotes, allowing the determination of
genotypes and allele frequencies at loci.
As a consequence, only an approximation of
allele frequency can be obtained by assuming
Hardy-Weinberg equilibrium in a population
and estimating allele frequency from the
proportion of individuals with the absent
phenotype (homozygous recessive).
 Reproducibility

To obtain reproducible results, the

extraction of purified, high quality DNA
is a prerequisite for the majority of the
marker techniques. For example,
degraded and/or unpurified DNA may
affect the amplification or restriction of
DNA, resulting in unspecific
polymorphisms.
Labor-intensity
 RFLPs and minisatellites are labour-intensive markers
because their analysis includes the time-consuming steps of
Southern blotting, labeling of probes and hybridization.
 Therefore, PCR-based techniques are currently preferred,
some of which can even be automated to decrease the labour-
intensity.
 PCR sequencing may still be quite labour-intensive if
performed by the old time-consuming method of performing
four separate sequence reactions per sample.
 However, automated procedures have greatly reduced labour-
intensity of PCR-sequencing.
 The labour-intensity of the other PCR-based techniques
presented varies from low to medium, depending on the
methodological procedures required in addition to PCR.
Technical demands
 RFLPs, minisatellites and manual PCR sequencing require
higher technical skills and facilities for analysis.
 RFLP and minisatellite analyses require Southern blot
hybridizations and may include radioactive labeling
 This calls for expertise and exclusive facilities needed to
comply with special legal and safety requirements.
 These technologies are therefore among the most technically
demanding markers.
 Another type of technical demand arises from the use of
polyacrylamide gels and automated equipment.
 Allozymes and PCR-based markers analyzed on agarose gels
(e.g. RAPD, SCAR and microsatellites) are the least
technically demanding.
Operational costs
 Wages, laboratory facilities, technical equipment and consumables
all contribute to the operational costs of the techniques.
 Laborious and technically demanding markers, such as RFLPs,
minisatellites, PCR sequencing, and those techniques being
performed by automated equipment, are quite expensive.
 Costs increase due to the level of the more complex technologies.
 In general, operational costs of markers will vary depending on the
methodology. Regarding automated procedures and technologies,
while purchasing the equipment is usually very expensive.
 The relative costs/benefits of outsourcing will vary in different labs
according to local labour and supply costs, availability of
equipment, the benefit of generating your own data for quality
control or educational purposes, and the legal requirements to ship
crop germplasm DNA out of a country. 
 Development costs
  Marker development may be very time-consuming and costly
when suitable probes or sequence data for primer construction
are unavailable.
 The development of site-specific PCR primers (e.g. for
microsatellite analysis) also requires the construction of
libraries, which then need to be screened to identify the
fragments of interest.
 The investment required for marker development should be
evaluated in relation to the intended range of application of
the technique.
 Alternatively, new genomic tools are allowing probes,
primers and sequence data to be obtained from genome
databases of other species, with the understanding, as in all
DNA tools, that their usefulness may decrease with
increasing evolutionary distance between the species.
Quantity of DNA required
Because only small quantities of template
DNA (5-100 ng per reaction) are required,
techniques which are based on the PCR are
currently preferred.
Intermediate quantities of DNA are needed
for AFLP-analysis (0.3-1 µg per reaction)
because restriction of the DNA precedes the
PCR reaction.
 In general, consideration should be given to
the use of PCR-based markers if only small
amounts of DNA can be obtained.
Amenability to automation
Adequate equipment and resources are available,
techniques that can be automated are highly
preferred because of the potential for high sample
throughput.
 Although considerable financial investment is
still required, automation may be cost-effective
when techniques are applied on a routine basis.
 As pointed out above, outsourcing of data
generation may also be an alternative strategy.
Nearly all techniques that are based on the PCR
are amenable to a certain degree of automation.