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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. 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

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  1. 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 M-W LIN

  2. 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) M-W LIN

  3. Microsatellite Markers • Types: • di- (CA)n, • tri- (CAG)n, • tetra- (GATA)n nucleotide repeats. • Evenly distributed through genome. M-W LIN

  4. Microsatellite Markers Primer 1 CA CA CA Primer 2 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA M-W LIN

  5. Genotyping Results D13S121- dinucleotide D13S770 - trinucleotide Child 1 Child 1 Child 2 Child 2 Child 3 Child 3 Father Father Mother Mother M-W LIN

  6. Applications • Linkage mapping and association study (linkage disequilibrium) • Loss of heterozygosity • Microsatellite instability • Forensic application • Paternity identification M-W LIN

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  9. Linkage Mapping for Disease Genes • Linkage analysis (Lod score method) • Allele-sharing methods M-W LIN

  10. Linkage Analysis Family M-W LIN

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  12. 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. M-W LIN

  13. Recombinant Gametes Crossing over between two neighbouring loci will produce recombinant gametes. M-W LIN

  14. Recombination Fraction Recombination fraction (θ) = number of recombinant gametes ------------------------------------------ total gametes M-W LIN

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  17. Recombination Fraction • Recombination fraction is a measure of genetic distance. • 1cM=1% chance of recombination between two loci. M-W LIN

  18. 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 M-W LIN

  19. Loss of Heterozygosity Loss of one allele at a heterozygous locus in a tumour cell, resulting in a homozygous genotype. M-W LIN

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  21. Microsatellite Instability • Microsatellite instability is numerous or aberrant allele at a microsatellite locus. • Many tumours show microsatellite instability. M-W LIN

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  23. 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 M-W LIN

  24. GDB M-W LIN

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  45. Marshfield M-W LIN

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