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7/31/2019 Marking the Genome-microsatellites
http://slidepdf.com/reader/full/marking-the-genome-microsatellites 1/33
Microsatellites
7/31/2019 Marking the Genome-microsatellites
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What is microsatellite
• Simple Sequence Repeats (SSR)
• 1-6 bp long
7/31/2019 Marking the Genome-microsatellites
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Classification of Microsatellites
• Simple microsatelltes
• Composite microsatellites
7/31/2019 Marking the Genome-microsatellites
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Simplemicrosatellites
containonly
onekindof
repeat
sequences:
(GT)n (AC)n (AG)n
7/31/2019 Marking the Genome-microsatellites
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Compositemicrosatellites
containmore
thanonetype
repeats
7/31/2019 Marking the Genome-microsatellites
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Molecular Basis of Microsatellite
Polymorphism
Different by 3 repeats
• Slippage of DNA polymerase is believed to be the major cause ofmicrosatellite variation
• The mutation rate can be as high as 0.1 to 0.2% per generation
7/31/2019 Marking the Genome-microsatellites
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Abundant and Even Distribution
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Abundant
• Abundance varies with species, but all speciesstudied to date have miocrosatellites
• In well studied mammal species, onemicrosatellite exist in every 30-40 kb DNA.
7/31/2019 Marking the Genome-microsatellites
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Even distribution
• On all chromosomes• On all segments of chromosomes
• With genes
• Often in introns• In exons as well
• Trinucleotide repeats and human diseases:Huntington disease, fragile X, and other mental
retardation-related human diseases
7/31/2019 Marking the Genome-microsatellites
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2
36
1
Small Locus sizes adapt them for PCR
PCR
7/31/2019 Marking the Genome-microsatellites
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Microsatellites are co-dominant
markers
AD BC
Allele A
Allele B
Allele C
Allele D
BD CD AC AB BD AC BD AB
AB CD BC CC
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Mendelian Inheritance of Microsatellites
Liu et al. 1999. Biochem. Biophys. Res Comm. 259: 190-194Liu et al. 1999. J. Heredity 90: 307-311.
Microsatellites are inherited as codominant markers accordingto Mendelian laws
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Advantages of Microsatellite Markers
AbundantEvenly
distributedHighly
polymorphic
Smallloci
Co-dominant
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Development of
microsatellite markers
7/31/2019 Marking the Genome-microsatellites
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Need
• SSR containing clones
• Sequences of the flanking regions of SSR
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Genomic DNA
Microsatellites-enriched
Small-insert DNA Libraries (I)
Digest with several 4-bp blunt endersGel fraction of 300-600 bp
Ligation to a phagemid vector
insert
Small insert
3.4 kb
insert
Small insert
3.4 kb
insert
Small insert
3.4 kb
insert
Small insert
3.4 kb
insert
Small insert
3.4 kb
insert
Small insert
3.4 kb
insert
Small insert
3.4 kb
insert
Small insert
3.4 kb
insert
Small insert
3.4 kb
micro
Small insert3.5 kb
7/31/2019 Marking the Genome-microsatellites
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insert
Small insert plasmids3.5 kb
insert
Small insert plasmids3.5 kb
insert
Small insert plasmids3.5 kb
in
micro
sert
Small insert plasmids3.5 kb
Conversion into single-stranded
phagemids using helper phage
Single-stranded phagemids
3.5 kb
Single-stranded phagemids
3.5 kb
Single-stranded phagemids
3.5 kb
micro
Single-stranded phagemids
3.5 kb
Won’t be converted to ds
will be degraded in WT host
Using dut/ung-
CJ236 strain
u
uu
u
uu
uu
uu
u
uu
Microsatellites-enriched Libraries (II)
7/31/2019 Marking the Genome-microsatellites
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micro
Single-stranded phagemids
3.5 kb
Convert into ds
using (CA)15 (e.g.)
micro
3.5 kb
micro
ds plasmids
3.5 kb
u
u
u
Transform intoWT E. coli
micro
ds plasmids
3.5 kb
Microsatellite-enriched Libraries (III)
According to Ostrander et al., 1992: PNAS 89:3419
7/31/2019 Marking the Genome-microsatellites
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Microsatellites-enriched
Libraries
CAGA
TACG
CTGT
CAACATCAG
CACCGGCGTCGCCGA
...
4 bp 5 bp
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Characterizationof Microsatellites
• Isolate plasmid DNA;
• sequence clones;
• Identify clones with enough sequencesfor primer design.
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PCR Optimization and PIC Analysis
• PCR products best <200 bp
• PCR conditions: annealing temperature, Mg++, pH,DMSO, etc.
• Polymorphism information content• Polymorphism in reference families
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Disadvantages of microsatellites
• Previous genetic information is needed
• Huge Upfront work required
• Problems associated with PCR of microsatellites
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The concept of Polymorphicinformation content
• Measures the usefulness of a marker• Informativeness in specific families
7/31/2019 Marking the Genome-microsatellites
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1. AA x AA
4. AA x AB
Not polymorphic
B segregates 1:1,A segregates with intensity 1:1
6. AØ x AB
2. AA x BB
5. AA x BØ
No segregation
A not segregateB segregates 1:1
A segregates 3:1,B segregates 1:1
3. AØ x ØØ Only 1 allelesegregating 1:1
7. AB x AB A segregates 3:1,B segregates 3:1
Microsatellite Genotyping
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Microsatellite Genotyping
8. AØ x BØ
9. AB x ØØ
10. AA x BC
11. AØ x BC
12. AB x AC
13. AB x CD
A segregates 1:1,B segregates 1:1
A segregates 1:1, B segregates1:1, A & B alternating
2 of the 3 allelessegregating 1:1
All 3 alleles segregating 1:1,2 types with only 1 allele
2 of 3 alleles segregating 1:1,the other 3:1 with a single alleleexisting for some individuals
All 4 allelessegregating 1:1
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• PIC refers to the value of a marker for detectingpolymorphism within a population
• PIC depends on the number of detectable allelesand the distribution of their frequency.
• Bostein et al. (1980) Am. J. Hum Genet. 32:314-331.
• Anderson et al. (1993). Genome 36: 181-186.
Polymorphic Information Content PIC)
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n
PICi = 1- Pij2
j=1
Where PICi is the polymorphic information contentof a marker i; Pij is the frequency
of the jth pattern for marker i and the summationextends over n patterns
Polymorphic Information Content (PIC)
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n
PICi = 1- Pij2
j=1
Example: Marker A has two alleles, first allele has afrequency of 30%, the second allele has a
frequency of 70%PICa = 1- (0.32 + 0.72) = 1- (0.09 + 0.49) = 0.42
Polymorphic Information Content PIC)
7/31/2019 Marking the Genome-microsatellites
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n
PICi = 1- Pij2
j=1
Example: Marker B has two alleles, first allele has afrequency of 50%, the second allele has a
frequency of 50%PICb = 1- (0.52 + 0.52) = 1- (0.25 + 0.25) = 0.5
Polymorphic Information Content PIC)
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n
PICi = 1- Pij2
j=1
Example: Marker C has two alleles, first allele has afrequency of 90%, the second allele has a
frequency of 10%PICc = 1- (0.92 + 0.12) = 1- (0.81 + 0.01) = 0.18
Polymorphic Information Content PIC)
7/31/2019 Marking the Genome-microsatellites
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n
PICi = 1- Pij2
j=1
Example: Marker D has 10 alleles, each allele has afrequency of 10%
PICd = 1- [10 x 0.12] = 1- 0.1 = 0.9
Polymorphic Information Content PIC)
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Allele frequency and Forensics
• Say, we have 10 marker loci
• We have done adequate population genetics toknow each one have a 10% distribution
• Test of each locus can define certain level ofconfidence as to what the probability is to obtainthe results you are obtaining.
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Allele frequency and Forensics
• Locus 1, positive
• You are included, but every one out of 10 peoplehas the chance to be positive
• locus 2, positive
• You are included, but every one out of 100people has the chance to be positive at bothlocus 1 and locus 2
• …
• Locus 10, also posive
• ...