1. Chapter 8
Additional DNA Markers: Amelogenin, Y-Chromosome STRs, mtDNA, SNPs, Alu Repeats
©2002 Academic Press

2. Amelogenin Sex-Typing Marker
6 bp deletion
X = 212 bp
Y = 218 bp
X = 106 bp
Y = 112 bp
AmpFlSTR kits
PowerPlex 1.1
1:1 Mixture: 3X + 1Y
Female: X, X
Male: X, Y
©2002 Academic Press

3. Lineage Markers Mitochondrial DNA (mtDNA) Y chromosome
maternally inherited
polymorphic control region (D-loop)
multiple copies per cell; survives better
Y chromosome
paternally inherited
variety of Y STR and Y SNP markers
haplotype rather than genotype
©2002 Academic Press

4. Human Mitochondrial DNA
HV1
HV2
16024
16365
340 73
342 bases
268 bases 1
Control Region
~1100 bp
mtDNA
16,569 bp
HV1
HV2
©2002 Academic Press

5. Maternal Inheritance of mtDNA1 2 3 5 4 12 11 10 9 6 7 8 18 17 15 16 13 14
MtDNA Haplotype Groups:
2,3,6,8,11,13,15,16
4,9,10
14,17,18 A B C D E F G
©2002 Academic Press

6. mtDNA Sample Process Flow
Performed separately and preferably after evidence is completed
Extract mtDNA from evidence (Q) sample
Extract mtDNA from reference (K) sample
PCR Amplify
HV1 and HV2 Regions
PCR Amplify
HV1 and HV2 Regions
Sequence HV1 and HV2 Amplicons
(both strands)
Sequence HV1 and HV2 Amplicons
(both strands)
Confirm sequence with forward and reverse strands
Confirm sequence with forward and reverse strands
Note differences from Anderson (reference) sequence
Note differences from Anderson (reference) sequence
Compare Q and K sequences
©2002 Academic Press
Compare with database to determine haplotype frequency

7. heteroplasmic sequence
mtDNA Heteroplasmy
homoplasmic sequence
heteroplasmic sequence
©2002 Academic Press
position 6371
C/T

8. Comparison of STR and SNP Markers
Occurrence in Human Genome
~1 in every 15 kb
~1 in every 1 kb
General Informativeness
High
Low; only 20-30% as informative as STRs
Marker Type
di-, tri-, tetranucleotide repeat markers
biallelic markers
Number of Alleles
per Marker
typically >5
typically 2
Detection Methods
gel/capillary electrophoresis
sequence analysis;
microchip hybridization
Multiplex Capability
>10 markers with multiple fluorescent dyes
potential of 1000s on microchip
Characteristics
Short Tandem Repeats
(STRs)
Single Nucleotide Polymorphisms
(SNPs)
©2002 Academic Press

9. Alu insertion PCR Assay
Human Alu Repeat
(~300 bp)
AluI
Two possible alleles
400 bp
100 bp
©2002 Academic Press