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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 ( r estriction f ragment l ength p olymorphisms)

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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 YMGC Genotyping Core

  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) YMGC Genotyping Core

  3. YMGC Genotyping Core

  4. Polymorphic Markers • Heterozygosity • H= 1- (p12 + p22 + p32 + …) • Polymorphism information content (PIC) • PIC = 1-  pi2 -   2pi2pj2 YMGC Genotyping Core

  5. YMGC Genotyping Core

  6. Microsatellite Markers • Types: • di- (CA)n, • tri- (CAG)n, • tetra- (GATA)n nucleotide repeats. • Evenly distributed through genome. YMGC Genotyping Core

  7. Microsatellite Markers Primer 1 CA CA CA Primer 2 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA YMGC Genotyping Core

  8. Genotyping Results D13S121- dinucleotide D13S770 - trinucleotide Child 1 Child 1 Child 2 Child 2 Child 3 Child 3 Father Father Mother Mother YMGC Genotyping Core

  9. Applications • Linkage mapping and association study (linkage disequilibrium) • Loss of heterozygosity • Microsatellite instability • Forensic application • Paternity identification YMGC Genotyping Core

  10. Collins FS. (1992) Nature genetics 1:3-6 YMGC Genotyping Core

  11. Collins FS. (1992) Nature genetics 1:3-6 YMGC Genotyping Core

  12. Linkage Mapping for Disease Genes • Linkage analysis (Lod score method) • Allele-sharing methods YMGC Genotyping Core

  13. Linkage Analysis Family YMGC Genotyping Core

  14. Allele-Sharing Method AC AB AC BC AB CD BC BC AC AB AD BC IBD = 0 IBD = 2 IBD = 1 YMGC Genotyping Core

  15. Loss of Heterozygosity Loss of one allele at a heterozygous locus in a tumour cell, resulting in a homozygous genotype. YMGC Genotyping Core

  16. YMGC Genotyping Core

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

  18. YMGC Genotyping Core

  19. 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 YMGC Genotyping Core

  20. GDB YMGC Genotyping Core

  21. GDB YMGC Genotyping Core

  22. GDB YMGC Genotyping Core

  23. GDB YMGC Genotyping Core

  24. GDB YMGC Genotyping Core

  25. GDB YMGC Genotyping Core

  26. GDB YMGC Genotyping Core

  27. GDB YMGC Genotyping Core

  28. GDB YMGC Genotyping Core

  29. GDB YMGC Genotyping Core

  30. GDB YMGC Genotyping Core

  31. GDB YMGC Genotyping Core

  32. GDB YMGC Genotyping Core

  33. GDB YMGC Genotyping Core

  34. GDB YMGC Genotyping Core

  35. GDB YMGC Genotyping Core

  36. GDB YMGC Genotyping Core

  37. GDB YMGC Genotyping Core

  38. Marshfield YMGC Genotyping Core

  39. Marshfield YMGC Genotyping Core

  40. Marshfield YMGC Genotyping Core

  41. Marshfield YMGC Genotyping Core

  42. Marshfield YMGC Genotyping Core

  43. Marshfield YMGC Genotyping Core

  44. Marshfield YMGC Genotyping Core

  45. Marshfield YMGC Genotyping Core

  46. Marshfield YMGC Genotyping Core

  47. CHLC YMGC Genotyping Core

  48. CHLC YMGC Genotyping Core

  49. CHLC YMGC Genotyping Core

  50. CHLC YMGC Genotyping Core

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