The prospect for more than 13 commonly used STR Tetranucleodide loci in forensic
settings
Carrie Rowland
Forensic Bioinformatic Services, Inc.
Dayton, Ohio
www.bioforensics.com
An Overview: Where are we going
• History of DNA testing• Generations of DNA tests and how performed• Current methodology• New prospects• Conclusions
Six criteria for judging a DNA profiling system
1. Discrimination power.2. Sensitivity.3. Absence of, or the ability to reconcile technical artifacts.4. Speed.5. Ability to deconvolve mixtures.
6. Amenability to database searches.
Brief History of Forensic DNA Typing
• 1980 - Ray White describes first polymorphic RFLP marker
• 1985 - Alec Jeffreys proposes multilocus VNTR probes be used forensically
• 1985 - first paper on PCR• 1988 - FBI starts DNA casework• 1991 - first STR paper• 1995 - FSS starts UK DNA database• 1998 - FBI launches CODIS database
Three generations of DNA testing
DQ-alphaTEST STRIPAllele = BLUE DOT
RFLPAUTORADAllele = BAND
Automated STRELECTROPHEROGRAMAllele = PEAK
How do they fare?
□ Discriminating power
Sensitivity
Technical artifacts
Speed□ Mixtures
□ Databasing
Discriminating power □ Sensitivity□ Technical artifacts□ Speed□ MixturesDatabasing ٱ
RFLP DQ-alpha STR
Discriminating power
Sensitivity□ Technical artifacts
Speed□ Mixtures
Databasing
RFLP technology
What we would like for them to look like.
What they often look like.
Incomplete digest
Available Kits for STR Analysis
• Kits make it easy for labs to just add DNA samples to a pre-made mix
• 13 CODIS core loci– Profiler Plus and COfiler (PE Applied Biosystems)
– PowerPlex 1.1 and 2.1 (Promega Corporation)
• Increased power of discrimination– CTT (1994): 1 in 410
– SGM Plus™ (1999): 1 in 3 trillion
– PowerPlex ™ 16 (2000): 1 in 2 x 1017
An Example Forensic STR Multiplex Kit
D3 FGAvWA 5-FAM (blue)
D13D5 D7 NED (yellow)
A D8 D21 D18 JOE (green)
GS500-internal lane standard
ROX (red)
AmpFlSTR® Profiler Plus™Kit available from PE Biosystems (Foster City, CA)
9 STRs amplified along with sex-typing marker amelogenin in a single PCR
100 bp 400 bp300 bp200 bpSize Separation
Col
or S
epar
atio
n
13 CODIS Core STR Loci with Chromosomal Positions
CSF1PO
D5S818
D21S11
TH01
TPOX
D13S317
D7S820
D16S539 D18S51
D8S1179
D3S1358
FGA
VWA
AMEL
AMEL
STR Allele Frequencies
0
5
10
15
20
25
30
35
40
45
6 7 8 9 9.3 10
Caucasians (N=427)
Blacks (N=414)
Hispanics (N=414)
TH01 Marker
*Proc. Int. Sym. Hum. ID (Promega) 1997, p. 34
Number of repeats
Fre
qu
ency
amelogenin
D19
D3
D8
TH01
VWA D21FGA
D16D18 D2
amelogeninD19
D3D8 TH01
VWA D21
FGA
D16D18 D2
Tw
o di
ffer
ent i
ndiv
idua
ls
DNA Size (base pairs)
Results obtained in less than 5 hours with a spot of blood the size of a pinhead
probability of a random match: ~1 in 3 trillion
Human Identity Testing with Multiplex STRs
Simultaneous Analysis of 10 STRs and Gender
AmpFlSTR® SGM Plus™ kit
FBI’s CODIS DNA Database
Combined DNA Index System
• Launched October 1998• Used for linking serial crimes and
unsolved cases with repeat offenders• Links all 50 states• Requires >4 RFLP markers and/or 13
core STR markers• Current backlog of > 600,000 samples
As of June, 2004• Total profiles = 1,857,093• Total forensic profiles = 85,477• Total convicted offender = 1,771,616
http://www.fbi.gov/hq/lab/codis/aidedmap.htm
STR alleles with n+4 stutter products
D21S11 D18S51
D8S1179
DNA Size (bp)
6.3% 6.2% 5.4%
Rel
ativ
e F
luor
esce
nce
Uni
ts
Schematic of Stutter Product Formation Process
Walsh et al (1996) Nucleic Acids Res. 24: 2807-2812
Slipped Strand Mispairing Model
1 2 3 4 5
1 2 3 4 5 6
Normal STR Allele Replication
Repeat unit bulges out when strand breathing occurs
Mechanism behind n+4 stutter
Walsh, et al. (1996) Nucleic Acids Research 24(14):2807
DNA polymerase
Template DNA
12345
61
2
3456
7
What is on the horizon ?
1. 14th …….locus
2. Pentanucleotide repeats
3. Mitochondrial DNA
4. Single nucleotide polymorphisms (SNPs)
Top Related