Jan, 2003 YMGC Genotyping Core

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

Jan, 2003 YMGC Genotyping Core

Genetic Markers•Protein marker

blood group, HLA tissue types…etc..

•DNA markerRFLPs (restriction fragment length

polymorphisms)Minisatellites (VNTR - variable

number tandem repeats)Microsatellites (STR - short tandem

repeats)SNPs (single nucleotide

polymorphisms)

Jan, 2003 YMGC Genotyping Core

Jan, 2003 YMGC Genotyping Core

Polymorphic Markers• Heterozygosity

H= 1- (p12 + p2

2 + p32 + …)

• Polymorphism information content (PIC)

PIC = 1- pi2 - 2pi2pj2

Jan, 2003 YMGC Genotyping Core

Jan, 2003 YMGC Genotyping Core

Microsatellite Markers

•Types:di- (CA)n,tri- (CAG)n,tetra- (GATA)n nucleotide repeats.

•Evenly distributed through genome.

Jan, 2003 YMGC Genotyping Core

Microsatellite Markers

CA CA CA

Primer 1

Primer 2

CA CA CA CA

CA CA CA CA CA

CA CA CA CA CA CA

Jan, 2003 YMGC Genotyping Core

Genotyping Results

Child 1

Child 2

Child 3

Father

Mother

Child 1

Child 2

Child 3

Father

Mother

D13S121- dinucleotide

D13S770 - trinucleotide

Jan, 2003 YMGC Genotyping Core

Applications•Linkage mapping and association study (linkage disequilibrium)

•Loss of heterozygosity•Microsatellite instability•Forensic application•Paternity identification

Jan, 2003 YMGC Genotyping Core

Collins FS. (1992) Nature genetics 1:3-6

Jan, 2003 YMGC Genotyping Core

Collins FS. (1992) Nature genetics 1:3-6

Jan, 2003 YMGC Genotyping Core

Linkage Mapping for Disease Genes

•Linkage analysis (Lod score method)•Allele-sharing methods

Jan, 2003 YMGC Genotyping Core

Linkage Analysis Family

Jan, 2003 YMGC Genotyping Core

IBD = 2 IBD = 1 IBD = 0

AC AB

BC BC

AC BC

AC AB

AB CD

AD BC

Allele-Sharing Method

Jan, 2003 YMGC Genotyping Core

Loss of Heterozygosity

Loss of one allele at a heterozygous locus in

a tumour cell, resulting in a homozygous genotype.

Jan, 2003 YMGC Genotyping Core

Jan, 2003 YMGC Genotyping Core

Microsatellite Instability

•Microsatellite instability is numerous or aberrant allele at a microsatellite locus.

•Many tumours show

microsatellite instability.

Jan, 2003 YMGC Genotyping Core

Jan, 2003 YMGC Genotyping Core

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

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

GDB

Jan, 2003 YMGC Genotyping Core

Marshfield

Jan, 2003 YMGC Genotyping Core

Marshfield

Jan, 2003 YMGC Genotyping Core

Marshfield

Jan, 2003 YMGC Genotyping Core

Marshfield

Jan, 2003 YMGC Genotyping Core

Marshfield

Jan, 2003 YMGC Genotyping Core

Marshfield

Jan, 2003 YMGC Genotyping Core

Marshfield

Jan, 2003 YMGC Genotyping Core

Marshfield

Jan, 2003 YMGC Genotyping Core

Marshfield

Jan, 2003 YMGC Genotyping Core

CHLC

Jan, 2003 YMGC Genotyping Core

CHLC

Jan, 2003 YMGC Genotyping Core

CHLC

Jan, 2003 YMGC Genotyping Core

CHLC

Jan, 2003 YMGC Genotyping Core

CHLC

Jan, 2003 YMGC Genotyping Core

CHLC

Jan, 2003 YMGC Genotyping Core

Genethon

Jan, 2003 YMGC Genotyping Core

Microsatellite Marker Databases

• NCBI: http://www.ncbi.nlm.nih.gov/

• CEPH (Centre d’Etude du Polymorphisme Humain): http://www.cephb.fr

• Utah: http://www.genetics.utah.edu/home.html

Jan, 2003 YMGC Genotyping Core

NCBI

Jan, 2003 YMGC Genotyping Core

NCBI

Jan, 2003 YMGC Genotyping Core

CEPH

Jan, 2003 YMGC Genotyping Core

CEPH

Jan, 2003 YMGC Genotyping Core

CEPH

Jan, 2003 YMGC Genotyping Core

Standardized Genotype Data

• CEPH 1331-01

• CEPH 1331-02

• CEPH 1347-02

Jan, 2003 YMGC Genotyping Core

ABI PRISM Linkage Mapping Set

• http://home.appliedbiosystems.com/

Jan, 2003 YMGC Genotyping Core

ABI PRISM Linkage Mapping Set

Jan, 2003 YMGC Genotyping Core

ABI PRISM Linkage Mapping Set

Jan, 2003 YMGC Genotyping Core

ABI PRISM Linkage Mapping Set