BASIC GENETIC TERMS

BASIC GENETIC

TERMS

Parentage Testing by STR-PCR

Locus Child Mother 1 2

D3S1358 16/17 16 17 17

vWA 14/18 16/18 14/15 16/17 FGA 21/24 20/21 24 24

TH01 6 6/9.3 6/9 6/7

TPOX 10/11 10/11 8/11 8/9

CSF1PO 11/12 12 11 11/13

D5S818 11/13 10/11 13 9/13

D13S317 9/12 9 12/13 11/12

Which alleged father’s genotype has the paternal alleles?

Evidence Testing by STR-PCR

Which suspect—S1 or S2—was at the crime scene?

(V = victim, E = crime scene evidence, AL = Allelic ladder)

AL S1 S2 V E M

AL S1 S2 V E M

AL S1 S2 V E M

Locus 1 Locus 2 Locus 3

Short Tandem Repeat Polymorphisms: Y-STR

• The Y chromosome is inherited in a block without recombination.

• STR on the Y chromosome are inherited paternally as a haplotype.

• Y haplotypes are used for exclusion and paternal lineage analysis.

Single Nucleotide

Polymorphisms (SNP)

• Single-nucleotide differences between DNA sequences.

• One SNP occurs approximately every 1,250 base pairs in human DNA.

• SNPs are detected by sequencing, melt curve analysis, or other methods.

• 99% have no biological effect;

60,000 are within genes.

5′ AGTCTG 5′ AG(T/A)CTG 5′ AGACTG

T/T T/A A/A

SNP Detection by Sequencing

haplotype

~10,000 bp

SNP Haplotypes

SNPs are inherited in blocks or haplotypes.

Applications of SNP Analysis

• SNPs can be used for mapping genes, human identification, chimerism analysis, and many other applications.

• The Human Haplotype Mapping (HapMap) Project is aimed at

identifying SNP haplotypes throughout the human genome.

HV 1

(342 bp) HV 2 (268 bp)

Mitochondrial genome 16, 600 bp

P_L P_H1 P_H2

Mitochondrial DNA Polymorphisms

Sequence differences in the hypervariable

regions (HV) of the mitochondrial genome.

Mitochondrial DNA Polymorphisms

• Mitochondria are maternally inherited.

• There are an average of 8.5 base differences in the mitochondrial HV sequences of unrelated individuals.

• All maternal relatives will have the same mitochondrial sequences.

• Mitochondrial typing can be used for legal exclusion of individuals or

confirmation of maternal lineage.

Summary

•Four types of polymorphisms are used for a

variety of purposes in the laboratory: RFLP, VNTR, STR, and SNP.

•Polymorphisms are used for human identification and parentage testing.

•Y-STR haplotypes are paternally inherited.

•Polymorphisms are used to measure engraftment

after allogeneic bone marrow transplants.

Summary

•Single-nucleotide polymorphisms are detected by sequencing, melt curve analysis, or other methods.

•SNPs can be used for the same applications as other polymorphisms.

•Mitochondrial DNA typing is performed by sequencing the mitochondrial HV regions.

•Mitochondrial types are maternally inherited.