Transcript CODIS and Y-chromosome

FBI’s CODIS DNA Database
Combined DNA Index System
• Launched October 1998.
• Links to all 50 states.
• Used for linking serial crimes and
unsolved cases to repeat
offenders.
• Current backlog of >600,000
samples.
• Requires >4 RFLP markers
and/or 13 core STR markers.
Position of Forensic STR Markers
on Autosomes
13 CODIS Core STR Loci
TPOX
D3S1358
D8S1179
D5S818
FGA
CSF1PO
TH01
VWA
D7S820
AMEL
Sex-typing
D13S317
D16S539
D18S51
D21S11
AMEL
Information on 13 CODIS STRs
Locus
Name
Chromosomal
Location
Repeat Motif
ISFH format
GenBank
Accession
Allele in
GenBank
Allele
Range
Number of
Alleles Seen
*
CSF1PO
5q33.3-34
TAGA
X14720
12
6-16
15
FGA
4q28
CTTT
M64982
21
15-51.2
69
TH01
11p15.5
TCAT
D00269
9
3-14
20
TPOX
2p23-pter
GAAT
M68651
11
6-13
10
VWA
12p12-pter
[TCTG][TCTA]
M25858
18
10-24
28
D3S1358
3p
[TCTG][TCTA]
NT_005997
18
9-20
20
D5S818
5q21-31
AGAT
G08446
11
7-16
10
D7S820
7q11.21-22
GATA
G08616
12
6-15
22
D8S1179
8
[TCTA][TCTG]
G08710
12
8-19
13
D13S317
13q22-31
TATC
G09017
13
5-15
14
D16S539
16q24-qter
GATA
G07925
11
5-15
10
D18S51
18q21.3
AGAA
L18333
13
7-27
43
D21S11
21q21
Complex
[TCTA][TCTG]
AP000433
29
24-38
70
* Butler, Forensic DNA Typing, Appendix 1
Short Tandem Repeat (STR) Markers
TCCCAAGCTCTTCCTCTTCCCTAGATCAATACAGACAGAAGACA
GGTGGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA
TAGATATCATTGAAAGACAAAACAGAGATGGATGATAGATACATG
CTTACAGATGCACAC
= 12 GATA repeats (“12” is all that is reported)
The number of consecutive repeat
units can vary between people
7 repeats
8 repeats
9 repeats
10 repeats
11 repeats
12 repeats
13 repeats
Target region
(short tandem repeat)
Short Tandem Repeats (STRs)
Fluorescent
dye label
AATG
AATG
AATG
7 repeats
8 repeats
The repeat region is variable between samples while the
flanking regions where PCR primers bind are constant
Homozygote = both alleles are the same length.
Heterozygote = alleles differ and can be resolved from one another.
Primer positions define PCR product size
Commercial STR Kits
Kit Contents:
Allelic Ladders for Genotyping
PCR Component Mix
Primer Mix
Positive Control DNA Sample
Cost to User: $15-30 per
DNA sample tested.
Currently 2 Suppliers: Applied Biosystems and Promega Corporation
Commercially Available STR Kits
Name
TH01, TPOX, CSF1PO
monoplexes
AmpFlSTR Blue
Source
Promega
Release
Date
STR Loci Included
Feb 1993
TH01, TPOX, CSF1PO
Oct 1996
D3S1358, VWA, FGA
*Power of
Discrimination
1:410
Jan 1997
Amelogenin, TH01, TPOX, CSF1PO
1:410
CTTv
Applied
Biosystems
Applied
Biosystems
Promega
Jan 1997
CSF1PO, TPOX, TH01, VWA (vWF)
FFFL
Promega
Jan 1997
F13A1, FES/FPS, F13B, LPL
GammaSTR
Promega
Jan 1997
D16S539, D13S317, D7S820, D5S818
Promega
Jan 1997
CSF1PO, TPOX, TH01, VWA, D16S539, D13S317,
D7S820, D5S818
1:6600
1:1500
1:1.8x104
1:1.2x108
Applied
Biosystems
Applied
Biosystems
Applied
Biosystems
Applied
Biosystems
May 1997
D3S1358, VWA, FGA, Amelogenin, TH01, TPOX,
CSF1PO, D5S818, D13S317, D7S820
1:3.6x109
Dec 1997
D3S1358, VWA, FGA, Amelogenin, D8S1179,
D21S11, D18S51, D5S818, D13S317, D7S820
1:9.6x1010
May 1998
D3S1358, D16S539, Amelogenin, TH01, TPOX,
CSF1PO, D7S820
1:8.4x105
Feb 1999
D3S1358, VWA, D16S539, D2S1338, Amelogenin,
D8S1179, D21S11, D18S51, D19S433, TH01, FGA
1:3.3x1012
PowerPlex 2.1
Promega
Jun 1999
D3S1358, TH01, D21S11, D18S51, VWA, D8S1179,
TPOX, FGA, Penta E
1:8.5x1010
PowerPlex 16
Promega
May 2000
CSF1PO, FGA, TPOX, TH01, VWA, D3S1358,
D5S818, D7S820, D8S1179, D13S317, D16S539,
D18S51, D21S11, Penta D, Penta E, amelogenin
1:1.8x1017
AmpFlSTR Identifiler
Applied
Biosystems
May 2001
CSF1PO, FGA, TPOX, TH01, VWA, D3S1358,
D5S818, D7S820, D8S1179, D13S317, D16S539,
D18S51, D21S11, D19S433, D2S1338, amelogenin
1:2.1x1017
AmpFlSTR Green I
PowerPlex
(version 1.1 and 1.2 later)
AmpFlSTR Profiler
AmpFlSTR Profiler
Plus
AmpFlSTR COfiler
AmpFlSTR SGM Plus
*Caucasian population (rounded to 2 significant figures)
1:5000
AmpFlSTR®
Identifiler™
D8S1179
6FAM
(blue)
D3S1358
D7S820
D21S11
TH01
D13S317
D16S539
VIC
(green)
TPOX
D19S433
D18S51
VWA
NED
(yellow)
AMEL
D5S818
FGA
PET
(red)
GS500 LIZ size standard
LIZ
(orange)
CSF1PO
D2S1338
Applied Biosystems- Identifiler Allelic Ladders
D8S1179
D7S820
CSF1PO
D21S11
D3S1358
TH01
D13S317
D16S539
D2S1338
D19S433
VWA
TPOX
D18S51
FGA
AMEL
D5S818
STR genotyping is performed by comparison of sample data to allelic ladders.
Promega Corporation- PowerPlex 16
PowerPlex® 16 Ladders
D3S1358
TH01
D5S818
AMEL
VWA
D21S11
D13S317 D7S820
D8S1179
Penta E
D18S51
D16S539
TPOX
Penta D
CSF1PO
FGA
Why STRs are Preferred
Genetic Markers
•
•
•
•
•
•
•
Rapid processing.
Abundant throughout the genome.
Highly variable within populations.
Small size range allows multiplex development.
Discrete alleles allow digital record of data.
Allelic ladders simplify interpretation.
PCR based which allows use of small amounts
of DNA.
• Small product size compatible with degraded
DNA.
Microsatellite Mutations
• Polymerase slippage
• Unequal crossing-over
during meiosis
Paternity Testing with Codis STRs
Separating the Men
from the Sample
Why the Y Chromosome?
• Applications
– 98% of violent crime by men.
– Genealogical purposes.
– Evolutionary studies.
• Advantages to Y Identity
Testing
– Male component isolated
without differential extraction.
– Paternal lineages.
Haplogroups produced by Y SNP genotyping
M42
M96
M89
M9
M45
Underhill et al. (2000) Nature Genetics 26: 358-361
Haplogroups and geographic origins of all
individuals in the Y Chromosome
Consortium collection (2002)
Francesc Calafell et al. Genome Res. 2002; 12: 219-221
Y-Chromosomal STRs
• 59,000,000 base pairs (only chromosome
22 is smaller).
• 161 genes.
• 95% is NRY (nonrecombining Y).
• 5% of it at the tips (telomeric) recombines.
• 44 Y-STR loci have been identified.
• SWGDAM (Scientific Working Group on
DNA Analysis) endorses the use of 11 loci.
Map of Y Chromosome STR Markers
p
q
Nucleic Acids Res. 28(2), e8 (2000)
Selection of Core Y-STR Loci
Selection of
U.S. Core Loci:
DYS19,
DYS385 a/b,
DYS389I/II,
DYS390,
DYS391,
DYS392,
DYS393,
DYS438,
DYS439
J.M. Butler, Forensic DNA
Typing, Table 8.1
Marker Name
DYS19
DYS385
DYS388
DYS389 I
DYS389 II
DYS390
DYS391
DYS392
DYS393
YCAIII
DYS434
DYS435
DYS436
DYS437
DYS438
DYS439
Y-GATA-A4
Y-GATA-A7.1
Y-GATA-A7.2
Y-GATA-A8
Y-GATA-A10
Y-GATA-C4
Y-GATA-H4
Y Chromosome STR Markers
GenBank
Accession
X77751
Z93950
G09695
G09600
G09600
G09611
G09613
G09867
G09601
AC006370
AC002992
AC002992
AC005820
AC002992
AC002531
AC002992
G42670
G42675
G42671
G42672
G42674
G42673
G42676
Repeat Motif
TAGA
GAAA
ATT
(TCTG) (TCTA)
(TCTG) (TCTA)
(TCTA) (TCTG)
TCTA
TAT
AGAT
CA
ATCT
TGGA
GTT
TCTA
TTTTC
AGAT
AGAT
ATAG
TAGA
TCTA
TATC
TATC
TAGA
Allele
Range
8-16
10-22
12-17
I: 7-13
II:23-31
18-27
8-13
7-16
9-15
19-25
8-11
9-13
10-15
8-11
6-12
9-14
11-14
7-12
8-12
8-14
11-14
11-16
10-13
PCR Product
Sizes
178-210 bp
252-300 bp
128-143 bp
239-263 bp
353-385 bp
191-227 bp
275-295 bp
236-263 bp
108-132 bp
192-204 bp
110-122 bp
210-228 bp
128-143 bp
186-202 bp
203-233 bp
238-258 bp
242-254 bp
161-181 bp
174-190 bp
219-244 bp
160-172 bp
251-271 bp
362-370 bp
Reference
Roewer 1992
Schneider 1998
Kayser 1997
Most
Kayser
1997
Kayser 1997
Commonly
Kayser 1997
Used
Kayser
1997
Kayser 1997
Markers
Kayser 1997
Kayser 1997
Ayub 2000
Ayub 2000
Ayub 2000
Ayub 2000
Ayub 2000
Ayub 2000
White 1999
White 1999
White 1999
White 1999
White 1999
White 1999
White 1999
Promega PowerPlex® Y Allelic Ladders
DYS391
DYS438
DYS393
DYS389I
DYS439
DYS437
DYS389II
DYS19
DYS390
DYS392
DYS385 a/b
U.S. Core Loci + DYS437
Single amplification; ladders contain 103 alleles
Yfiler Allelic Ladders
U.S. Core
Loci + DYS437,
DYS448, DYS456,
DYS458, DYS635,
GATA H4
Reliagene- Y-Plex 6, Y-Plex 12
Genotyper Results with Reliagene Y Plex 6 Kit
on 5 male candidate samples for SRM 2395
Megaplex- 21 Y-STR Loci. Hanson
and Ballantyne 2004.
Historical Investigation of Jefferson-Hemings DNA
Thomas Jefferson II
Field Jefferson
Peter Jefferson
Genetic Genealogy Companies
President
Thomas Jefferson
?
Eston Hemings
Thomas Woodson
Same Y
Haplotype
Jefferson
Y Haplotype
Jefferson
Y Haplotype
Different Y Haplotype
SOURCE: Foster et al. (1998) Nature 396:27-28
Figure 9.10, J.M. Butler (2005) Forensic DNA Typing, 2nd Edition © 2005 Elsevier Academic Press
Modern Use of Y-STR Testing
Captured December 13, 2003
Matching Y-STR
Haplotype Used to
Confirm Identity
(along with allele
sharing from
autosomal STRs) Uday and Qusay Hussein
Is this man really
Sadaam Hussein?
Butler, J.M. (2005) Forensic DNA Typing, 2nd Edition, Box 23.1, p. 534
Killed July 22,
2003