GENE MAPPING

POLYMORPHIC MARKERS AND LINKAGE ANALYSIS

GENERAL CONCEPTS
A prerequisite for successful linkage analysis is the availability of
a large number of highly polymorphic markers dispersed
throughout the genome. There are several classes of these
polymorphic markers and over 20,000 of these polymorphic
markers have now been identified and are available for linkage
studies.

DIFFERENT TYPES OF DNA

POLYMORPHISMS

DIFFERENT TYPES OF DNA

POLYMORPHISMS

RECOMBINATION AND LINKAGE

Linkage: Alleles of two loci that are likely to be inherited together.
M: Marker (SRTP)

2
loci

MEIOSIS

2
allele

RECOMBINATION AND LINKAGE

Crossove
r

Haplotype:
combination of alleles
on a single
chromosome.

RECOMBINATION AND LINKAGE

RECOMBINATION FREQUENCY
The closer to 0% recombination frequency is, the closer the
marker is to the gene.

The gene is LINKED to the marker; they are inherited together more than half the
cases.

RECOMBINATION
FREQUENCY
AND
Out of 6 children in generation III, one is recombinant (a1 from mother).
GENE MAPPING
Recombination frequency is 1/6 = 0.17 = 17% (distance between 2 loci)
Neurofibromatosis I
1% = 1 centiMorgan (cM) = 1 million bp
gene
A1,a2
a2,a2
Disease = A 1
Normal = a

a1,a1

A1,a2

A1,a1a1,a2
No
recombination

a1,a1
(Recombination)

LOD SCORES
LOD: Probability that the gene and the marker are linked together.
A LOD score > 3 indicates linkage.
A LOD score < 2 indicates no linkage.
The value of RF at which the highest LOD score is seen is the most likely
estimate of the recombination frequency.

GENETIC
DIAGNOSIS
INDIRECT VS DIRECT DIAGNOSIS

Direct diagnosis: Mutation itself is examined.

Indirect diagnosis: linked markers are used to infer whether individual in a
family has inherited the disease-causing allele.

Mutated
gene

PCR
Dot Blot and ASO
*RFLP
*DNA sequencing

Marke
rPCR
*RFLP
*SRTP

DOT BLOT (ASO)

ASO: Allele specific oligonucleotide.
Use 2 different ASO probes
(10 20 oligonucleotides).
1 recognize normal allele.
1 recognize mutant allele.

Hemochromatosis:
mutation in HFE gene.

H
N

C
R

H
M

(DIRECT) RFLP

150 bp
PCR
Hph1
o
114r
36

SIBLING 2 IS ALSO AFFECTED

INDIRECT DIAGNOSIS USING STRPs

SRTP marker (version 1,2,3,4) is found near Marfan syndrome gene.

Which SRTP version is

associated with the Marfan
syndrome?
If 10% recombination of marker
3, what is the probability of
develop
Marfan?
90% of
getting Marfans.
90% of getting Marfans.

INDIRECT TESTING USING RFLP

What is the best conclusion about the fetus?
What is the best conclusion about the mother of the
fetus sisters?
X
X

y
X
y

xy
X

X
x

X
X

X
X

X
X

X = Normal allele
x = Mutant allele
NO MALE TO MALE
TRANSMISSION

x
X

CLINICAL VIGNETTES

a
A

a
a

a
a

A
a

a
a

a
A

A = disease
allele
a = normal
allele

X
X
x

AA
aa

The fetus is homozygous for

Thethe
fetus
is homozygous
for
LCAD
mutation.
the LCAD mutation.