SHORT TANDEM REPEATS

forensic genetics

chromosome structure and nomenclature

• marker within gene- gene name used as designation

  • e.g. TH01

• marker outside gene- chromosomal position as designation

  • D5S818

telomere → p (short arm) → centromere → q (long arm) → telomere

what are genetic markers?

• segment of DNA

• identifiable physical location

• inheritance can be followed

• exon- coding region

  • transcribed into RNA translated into protein

• intron- non-coding region

• intragenic- within

• extragenic- outside 

applications

gene mapping

• determination of relative position and distance/location of genes

• marker located close to gene and segregates with gene

molecular diagnosis of inheritable diseases

• human genetic testing 

• marker allele segregates with disease causing gene mutation → haemochromatosis 

• marker mutation causes diseases → huntingtons chorea

cancer diagnosis 

• genotype difference between normal tissue and tumor 

human identity testing

types of DNA polymorphisms 

sequence polymorphisms

• SNPs- single nucleotide polymorphisms- 1bp

length polymorphisms

• STRs- short tandem repeats 

  • microsatellites 

  • 1-6 bp

• VNTRs- variable number of short tandem repeats

  • minisatellites

  • >6-100 bp

location of forensic DNA markers

autosomal

• inherited from both parents

• STRs, VNTRs, SNPs

• kinship analysis 

Y-chromosomal

• male inherits from father 

• Y-STR, Y-SNP

• patrilinear kinship

mitochondrial

• inherited from mother

• SNPs

• matrilinear kinship 

categories for STR markers

• simple repeats

  • contains units of identical length and sequence 

  • (GATA)(GATA)(GATA)

• simple repeats with non-consensus alleles

  • (GATA)(GAT-)(GATA)

• compound repeats 

  • comprise 2 or more adjacent simple repeats 

  • (GATA)(GATA)(GACA)

• complex repeats 

  • contains several repeat blocks of variable unit length 

  • (GATA)(GACA)(—CA)(CATA)

• hypervariable repeats 

  • complex repeat with non-consensus alleles

  • (don’t even fucking attempt)

evolution of STRs

unequal crossover

slipped strand mispairing

FINISH FLASHCARD

analysis of STRs

fragment length analysis

traditional method: silver staining

• PAGE- polyacrylamide gel electrophoresis

  • determination of alleles by comparison to co-separated allelic ladder

  • visualisation by silver staining 

analysis of STRs

size calling- local southern

• based on reciprocal relationship between fragment length and fragment mobility

• determines the sizes of fragments

• fitting constants of the curve calculated for each group of 3 neighbouring points of the standard

  • curve 1→ 2 below, 1 above fragment 

  • curve 2→ 1 below, 2 above fragment 

• average of both sizes averaged

  • determine the unknown fragment length