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Searching Microsatellite Markers for Mapping a Disease Gene. 林明薇 Ming-Wei Lin, PhD 陽明大學醫學系家庭醫學科 台北榮民總醫院教學研究部. Genetic Markers. Protein marker blood group, HLA tissue types…etc.. DNA marker RFLPs (restriction fragment length polymorphisms)

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searching microsatellite markers for mapping a disease gene

Searching Microsatellite Markers for Mapping a Disease Gene

林明薇 Ming-Wei Lin, PhD

陽明大學醫學系家庭醫學科

台北榮民總醫院教學研究部

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genetic markers
Genetic Markers
  • Protein marker
    • blood group, HLA tissue types…etc..
  • DNA marker
    • RFLPs(restriction fragment length polymorphisms)
    • Minisatellites (VNTR - variable number tandem repeats)
    • Microsatellites (STR - short tandem repeats)
    • SNPs (single nucleotide polymorphisms)

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microsatellite markers
Microsatellite Markers
  • Types:
    • di- (CA)n,
    • tri- (CAG)n,
    • tetra- (GATA)n nucleotide repeats.
  • Evenly distributed through genome.

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microsatellite markers1
Microsatellite Markers

Primer 1

CA

CA

CA

Primer 2

CA

CA

CA

CA

CA

CA

CA

CA

CA

CA

CA

CA

CA

CA

CA

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genotyping results
Genotyping Results

D13S121- dinucleotide

D13S770 - trinucleotide

Child 1

Child 1

Child 2

Child 2

Child 3

Child 3

Father

Father

Mother

Mother

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applications
Applications
  • Linkage mapping and association study (linkage disequilibrium)
  • Loss of heterozygosity
  • Microsatellite instability
  • Forensic application
  • Paternity identification

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linkage mapping for disease genes
Linkage Mapping for Disease Genes
  • Linkage analysis

(Lod score method)

  • Allele-sharing methods

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linkage

Linkage

Linkage describes the phenomenon whereby allele at neighbouring loci are close to one another on the same chromosome, they will be transmitted together more frequently than chance.

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recombinant gametes

Recombinant Gametes

Crossing over between two neighbouring loci will produce recombinant gametes.

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recombination fraction

Recombination Fraction

Recombination fraction (θ) =

number of recombinant gametes

------------------------------------------

total gametes

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recombination fraction1
Recombination Fraction
  • Recombination fraction is a measure of genetic distance.
  • 1cM=1% chance of recombination between two loci.

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statistical significance of the lod score

Statistical Significance of the Lod Score

lod score > 3: evidence of linkage

2 < lod score < 3: suggestive evidence of linkage

-2 < lod score < 2: uninformative of linkage

lod score < -2: exclusion of linkage

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loss of heterozygosity

Loss of Heterozygosity

Loss of one allele at a heterozygous locus in a tumour cell, resulting in a homozygous genotype.

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microsatellite instability
Microsatellite Instability
  • Microsatellite instability is numerous or aberrant allele at a microsatellite locus.
  • Many tumours show microsatellite instability.

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microsatellite marker databases
Microsatellite Marker Databases
  • GDB: http:/www.gdb.org
  • Marshfield: http://research.marshfieldclinic.org/genetics/
  • CHLC (Cooperative Human Linkage Center): http:/www.chlc.org
  • Genethon: http://www.genethon.fr/genethon_en.html

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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GDB

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marshfield
Marshfield

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marshfield1
Marshfield

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marshfield2
Marshfield

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marshfield3
Marshfield

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marshfield4
Marshfield

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marshfield5
Marshfield

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marshfield6
Marshfield

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marshfield7
Marshfield

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marshfield8
Marshfield

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CHLC

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CHLC

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CHLC

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CHLC

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CHLC

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CHLC

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genethon
Genethon

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genethon1
Genethon

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genethon2
Genethon

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microsatellite marker databases1
Microsatellite Marker Databases
  • CEPH (Centre d’Etude du Polymorphisme Humain): http://www.cephb.fr
  • Utah: http://www.genetics.utah.edu/home.html

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CEPH

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CEPH

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CEPH

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standardized genotype data
Standardized Genotype Data
  • CEPH 1331-01
  • CEPH 1331-02
  • CEPH 1347-02

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nhri databases
NHRI Databases
  • GDB mirror site http://gdb.nhri.org.tw/

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successful examples
Successful Examples
  • Cystic fibrosis
  • Huntington disease
  • Early onset breast cancer (BRCA1, BRCA2)
  • Alzheimer disease (chr14, chr1)
  • Maturity-onset diabetes of the young (MODY) (chr12)
  • ...

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