This document discusses applications of Y chromosome short tandem repeat (STR) markers in forensic medicine. It provides information on the structure of the Y chromosome, commonly used Y STR markers and multiplex assays. Examples are given of how Y STR analysis was used to identify Saddam Hussein after his capture and to confirm paternal lineages in forensic investigations and ancestry research. The document also outlines the basic process of STR typing from sample collection to analysis and comparison of genetic profiles.

1. Ministry of Higher
education & scientific
Research
Al-Mustaqbal University
Collage
Department of Medical
lab. Techniques

2. • Structure of the Y Chromosome
• Advantages of Y Chromosome Markers
• Commonly Used of Y Chromosome Markers
• Y STR Multiplex Assays
• Applications of Y STR in forensic medicine

3. Structure of the Y Chromosome
p
q

5. •forensic investigations
•genealogical purposes
•evolutionary studies
•Advantages to human identity
testing
•paternal lineages

6. Autosomal
(passed on in part,
from all ancestors)
Y-Chromosome
(passed on complete, but
only by sons)
Mitochondrial
(passed on complete,
but only by daughters)
Lineage Markers
Figure 9.1, J.M. Butler (2005) Forensic DNA Typing, 2nd Edition © 2005 Elsevier Academic Press
Vertical heredity

7. • Microsatellites
• is a tract of repetitive DNA in which certain DNA motifs
(ranging in length from two to five base pairs) are
repeated, typically 5–50 times. Microsatellites occur at
thousands of locations within an organism's genome.
• STRs mostly tetranucleotide repeats
• Bi-allelic markers (unique event polymorphisms--UEP)
• SNPs (single nucleotide polymorphisms)
• Y Alu polymorphism (YAP) or other insertions/deletions
(“indels”)
• Minisatellite
• is a tract of repetitive DNA in which certain DNA motifs
(ranging in length from 10–60 base pairs) are typically
repeated 5-50 times.

8. • short tandem repeat (STR) in DNA occurs when:
• a pattern of two or more nucleotides are repeated
• the repeated sequences are directly adjacent to each
other.
• The pattern can range in length from 2 to 5 base pairs
(bp)
• is typically located in the non-coding intron region.
• A short tandem repeat polymorphism (STRP) occurs
when homologous STR loci differ in the number of
repeats between individuals.

14. Locus
Repeat
Motif
#
Repeats
#
Alleles
Allele size
ranges
(bp)
Gene
Diversity
(h)
PCR Primer Sequences
DYS19 (GATA)n 10-19 9 174-210 0.72
Primer A: CTACTG AGT TTC TGT TAT AGT
Primer B: ATG GCA TGT AGT GAG GAC A
Primer A2: GTT ATA TAT ATA TAG TGT TTAG
3)
Primer B2: GTT AAG GAG AGT GTC ACT A 3)
DYS389I 1) (GATA)n
(GACA)n
9-16 7 235-263 0.61
Primer A:CCA ACT CTC ATC TGT ATT ATC TAT
Primer B: TCT TAT CTC CAC CCA CCA GA
Primer 2B: TTA TCC CTG AGT AGT AGA AGA AT 5)
DYS389II
1) (GATA)n
(GACA)n
26-33 8 355-383 0.75 see DYS389I
DYS390
(GATA)n
(GACA)n
18-27 9 191-227 0.61
Primer A: TAT ATT TTA CAC ATT TTT GGG CC
Primer B: TGA CAG TAA AAT GAA CAC ATT GC
DYS391 (GATA)n 7-14 8 271-299 0.49
Primer A: CTA TTC ATT CAA TCATAC ACC CA
Primer B: GAT TCT TTG TGG TGG GTC TG
DYS392 (ATT)n 6-16 11 233-263 0.52
Primer A: TCA TTA ATC TAG CTT TTA AAA ACA A
Primer B: AGA CCC AGT TGA TGC AAT GT
DYS393 (GATA)n 9-16 8 108-136 0.34
Primer A: GTG GTC TTC TAC TTG TGT CAA TAC
Primer B: AAC TCA AGT CCA AAA AAT GAG G
DYS385 (GAAA)n 7-22 68 352-412 0.85
Primer A:AGC ATG GGT GAC AGA GCT A
Primer B: GGG ATG CTA GGT AAA GCT G
Primer 2B: CCA ATT ACA TAG TCC TCC TTC 4)
YCAII
2)
(CA)n 1-9 31 144 - 160 0.67
Primer A: TAT ATT AAA TAG AAG TAG TGA
Primer B: TAT CGA TGT AAT GTT ATA TTA
From Y STR Database http://ystr.charite.de/

16. Y Chromosomal Adam

17. Applications of Y STR in forensic
medicine
Sources of Biological Evidence
• Blood
• Semen
• Saliva
• Urine
• Hair
• Teeth
• Bone
• Tissue
Blood stain
Only a very small
amount of blood is
needed to obtain a
DNA profile

18. Sample Obtained from Crime Scene or Paternity
Investigation
DNA
Extraction
DNA
Quantitation
PCR Amplification
of Multiple STR markers
Biology
Separation and Detection of
PCR Products
(STR Alleles)
Technology
Sample Genotype
Determination
Genetics
Comparison of Sample
Genotype to Other Sample
Results
If match occurs, comparison of
DNA profile to population
databases
Generation of Case Report
with Probability of Random
Match

19. DNA Database
STR Typing
DNA
Extraction
Multiplex PCR Amplification
Male: 13,14-15,16-12,13-10,13-15,16
Interpretation of Results
Sample Collection
& Storage
Buccal swab
Blood Stain
DNA
Quantitation
Slot Blot
1 ng
0.3 ng
1 ng
1 ng
0.7 ng
0.5 ng
0.5 ng
No DNA

20. Capillaries
Electrodes for Injection
Figure 14.4, J.M. Butler (2005) Forensic DNA Typing, 2nd Edition © 2005 Elsevier Academic Press

21. Scanned
Gel
Image
Capillary Electropherogram
8 repeats
9 repeats

22. AMEL
D3S1358
TH01
TPOX
D2S1338
D19S433
FGA
D21S11
D18S51
CSF1PO
D16S539
D7S820
D13S317
D5S818
VWA
D8S1179
Information is tied together with multiplex PCR and data analysis
AmpFlSTR® Identifiler™ (Applied Biosystems)

23. Family Inheritance of STR Alleles (D13S317)
Father
Child #1
Child #2
Child #3
Mother
PCR product size (bp)
11 14
11
12 14
8 14
12
12
8
Adam
Marshall
Katy
Father
Mother
PATERNITY TESTING

24. Chiaroni 2009
Al-Zahery 2011 Tofanelli 2009

25. “We got him!”
Saddam Hussein’s
capture verified with
DNA testing
December 14, 2003
DNA Profile
Source: www.cnn.com; The Scientist Dec 19, 2003

26. Captured December 13, 2003
Is this man really
Sadaam Hussein?
Uday and Qusay Hussein
Killed July 22, 2003
Matching Y-STR
Haplotype Used to
Confirm Identity
(along with allele sharing
from autosomal STRs)
Butler, J.M. (2005) Forensic DNA Typing, 2nd Edition, Box 23.1, p. 534

27. Uday and Qusay Hussein
Killed
July 22, 2003
Captured December 13, 2003
Source: www.cnn.com
Suspected
Saddam
Portion of DNA Profile
“A Forensic Paternity Test”
Y-chromosome tests were also
used to verify male lineage…
DNA Used as the Ultimate Biometric
for Confirming Saddam’s Identity

29. Armed Forces DNA
Identification Laboratory
(Rockville, MD)
Identification of Skeletal Remains from
Previous Military Conflicts
Identification of
Michael J. Blassie - Vietnam Tomb of the
Unknown
>2100 Unaccounted for
from Southeast Asia
>8000 Unaccounted for
from Korea
>75,000 Unaccounted for
from WWII

30. 30
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