1. Bioq. Raúl Horacio Lucero
Jefe de Area Biología Molecular
Instituto de Medicina Regional
2. Exámenes generales: Diagnóstico de especie.
datos fisonómicos, sexo, Datación de los restos.
peso, talla, cabello, color Exámenes generales.
de ojos y piel, marcas.
Elementos extrínsecos.
Registro de voz.
Caracteres patológicos,
Trazado caligráfico. naturales o traumáticos.
Huellas dactilares. Identidad radiográfica y
Huellas genéticas. dental.
Métodos bioquímicos.
3. Grupos sanguíneos: ABO, Minisatélites: sondeos de
RH, MNS, Duffy, Lewis. locus múltiple y locus
Proteínas plasmáticas: único.
haptoglobina, α1- Microsatélites: métodos de
antitripsina, transferrina. PCR.
Enzimas eritrocitarias: Variantes de secuencia:
fosfatasa ácida HLA-DQα, Polymarker,
eritrocitaria, adenilato genoma mitocondrial.
kinasa, PGM, ADA.
HLA: Antígenos de
histocompatibilidad.
4. Existen regiones
codificantes -que
contienen la información
para la síntesis proteica-, y
regiones no codificantes.
Dentro de las no
codificantes existen
regiones polimórficas.
Existen alrededor de 3 x
106 sitios polimóficos en
nuestro genoma.
5. Sitio de adhesión de Sitio de adhesión de
los primers los primers
Alelo 1
Alelo 2
Unidad de Repetición
7. Herramienta
indispensable para la
investigación forense.
Gran número de STRs
disponibles.
Alta sensibilidad.
Evaluación manual o
automatizada.
8.
9.
10. Analizando el Caso.
Material Indubitado
de la Víctima.
Material Subungueal
Tomado de la Víctima
Tejido Dactilar de
la Víctima. Match Match Match
Sangre del
Sospechoso1.
Sangre del
Sospechoso 2
11.
12. 2006:
www.dna.gov
DNA is an important part of the
criminal justice system
Justice for All Act ($1B 2006
over 5 years)
Identifiler 5-dye kit
and ABI 3100
UK National Database 2002 2004 Y-STRs
launched (April 10, CODIS loci
1995) defined PowerPlex® 16 (16
Gill et al. (1985) Forensic loci in single amp)
application of DNA 'fingerprints‘. 1998 2000
Nature 318:577-9FSS Quadruplex STR typing with CE is
fairly routine
1994 1996 First commercial
First STRs
fluorescent STR mtDNA
developed
multiplexes
1990 1992 Capillary electrophoresis of
STRs first described
1985 PCR developed DQA1 & PM
(dot blot) Multiplex STRs
RFLP
13. http://www.fbi.gov/hq/lab/codis/index1.htm
Combined DNA Index System (CODIS)
Launched in October 1998 and now links all 50 states
Used for linking serial crimes and unsolved cases with repeat offenders
Convicted offender and forensic case samples along with a missing persons
index
Requires 13 core STR markers
>27,000 investigations aided nationwide as of Sept 2005
Contains more than 2.8 million DNA profiles
14. Small product sizes are generally compatible with
degraded DNA and PCR enables recovery of information
from small amounts of material
Multiplex amplification with fluorescence detection
enables high power of discrimination in a single test
Commercially available in an easy to use kit format
Uniform set of core STR loci provide capability for
national and international sharing of criminal DNA
profiles
15. An accordion-like DNA sequence that occurs between genes
TCCCAAGCTCTTCCTCTTCCCTAGATCAATACAGACAGAAGACAGGTGGATAGA
TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATATCATTGAAAGA
CAAAACAGAGATGGATGATAGATACATGCTTACAGATGCACAC
= 12 GATA repeats (“12” is all that is reported)
7 repeats The number of consecutive repeat units
8 repeats can vary between people
9 repeats
10 repeats
11 repeats
The FBI has selected 13
12 repeats core STR loci that must be
13 repeats run in all DNA tests in
order to provide a
Target region common currency with
(short tandem repeat)
DNA profiles
16. The polymerase chain reaction (PCR) is used to amplify
STR regions and label the amplicons with fluorescent
dyes using locus-specific primers
8 repeats
Locus 1
10 repeats
8 repeats
Locus 2
9 repeats
Scanned Gel
Image Capillary Electropherogram
17. YCAII
~45%
Requires size based DNA separation to
resolve different alleles from one another
High stutter Dinucleotide (CA)(CA)(CA)(CA)
Trinucleotide (GCC)(GCC)(GCC)
Tetranucleotide (AATG)(AATG)(AATG)
Pentanucleotide (AGAAA)(AGAAA)
Low stutter
Hexanucleotide (AGTACA)(AGTACA)
DYS448
Short tandem repeat (STR) = microsatellite =
<2%
simple sequence repeat (SSR)
18. Category Example Repeat 13 CODIS Loci
Structure
Simple repeats – contain (GATA)(GATA)(GATA) TPOX, CSF1PO,
units of identical length and D5S818, D13S317,
sequence D16S539
Simple repeats with (GATA)(GAT-)(GATA) TH01, D18S51, D7S820
non-consensus alleles
(e.g., TH01 9.3)
Compound repeats – (GATA)(GATA)(GACA) VWA, FGA, D3S1358,
comprise two or more D8S1179
adjacent simple repeats
Complex repeats – (GATA)(GACA)(CA)(CATA) D21S11
contain several repeat
blocks of variable unit length
These categories were first described by Urquhart et al. (1994) Int. J. Legal Med. 107:13-20
19. The efforts of the Human Genome Project have increased
knowledge regarding the human genome, and hence there are
many more STR loci available now than there were 10 years ago
when the 13 CODIS core loci were selected.
More than 20,000 tetranucleotide STR loci have been
characterized in the human genome (Collins et al. An exhaustive DNA
micro-satellite map of the human genome using high performance computing. Genomics
2003;82:10-19)
There may be more than a million STR loci present depending on
how they are counted (Ellegren H. Microsatellites: simple sequences with complex
evolution. Nature Rev Genet 2004;5:435-445).
STR sequences account for approximately 3% of the total human
genome (Lander et al. Initial sequencing and analysis of the human genome. Nature
2001;409:860-921).
Butler, J.M. (2006) Genetics and genomics of core STR loci used in human identity testing. J. Forensic Sci., in press.
20. Compatible primers are the
key to successful multiplex
PCR
STR kits are commercially
available
15 or more STR loci can be
simultaneously amplified
Challenges to Multiplexing
primer design to find compatible
primers (no program exists)
reaction optimization is highly
empirical often taking months
Advantages of Multiplex PCR
–Increases information obtained per unit time (increases power of discrimination)
–Reduces labor to obtain results
–Reduces template required (smaller sample consumed)
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
34.
35.
36.
37. Most are rape cases (>2 out of 3)
Looking for match between evidence
and suspect
Must compare victim’s DNA profile
Challenges
•Mixtures must be resolved
•DNA is often degraded
•Inhibitors to PCR are often present
38. Forensic cases -- matching suspect with
evidence
Paternity testing -- identifying father
Historical investigations
Missing persons investigations
Mass disasters -- putting pieces back together
Military DNA “dog tag”
Convicted felon DNA databases
39. Steps in DNA Sample Processing
Sample Obtained from
Crime Scene or Paternity
Investigation
Biology
DNA
DNA DNA
DNA PCR Amplification
PCR Amplification
Extraction
Extraction Quantitation
Quantitation of Multiple STR markers
of Multiple STR markers
Technology
Separation and Detection of Sample Genotype
PCR Products Determination
(STR Alleles)
Genetics
Comparison of Sample
Comparison of Sample Generation of Case
Generation of Case
Genotype to Other
Genotype to Other Report with Probability
Report with Probability
Sample Results
Sample Results of Random Match
of Random Match
If match occurs, comparison
If match occurs, comparison
of DNA profile to population
of DNA profile to population
databases
databases
41. 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
42. Multiplex PCR
Over 10 Markers Can Be
Copied at Once
Sensitivities to levels less
than 1 ng of DNA
Ability to Handle Mixtures
and Degraded Samples
Different Fluorescent Dyes
Used to Distinguish STR
Alleles with Overlapping Size
Ranges
43. AmpFlSTR® Profiler Plus™
Kit available from PE Biosystems (Foster City, CA)
100 bp 200 bp 300 bp 400 bp
Size Separation
D3 vWA FGA 5-FAM (blue)
Color Separation
A D8 D21 D18 JOE (green)
D5 D13 D7 NED (yellow)
ROX (red)
GS500-internal lane standard
9 STRs amplified along with sex-typing marker amelogenin in a single PCR reaction
44. ABI Prism 310 Genetic Analyzer
capillary
Syringe with polymer
solution
Injection
electrode
Outlet Autosampler tray
buffer
Inlet
buffer
45. Close-up of ABI Prism 310 Sample Loading Area
Electrode
Capillary
Sample Vials
Autosampler Tray
See Technology section for more information on CE
46. Human Identity Testing with Multiplex STRs
AmpFlSTR® SGM Plus™ kit
DNA Size (base pairs)
D3
amelogenin D8 TH01
D19 VWA D21 D16
D18
Two different individuals
D2
FGA
probability of a random match: ~1
in 3 trillion Results obtained in less than 5 hours
with a spot of blood the size of a pinhead
amelogenin D3
D19
D8 VWA D16
D21 D18 D2
FGA
TH01
Simultaneous Analysis of 10 STRs and Gender ID
47. STR genotyping is performed by comparison of
sample data to allelic ladders
Microvariant
allele
48. 45
40
TH01 Marker
35
30
25 Caucasians (N=427)
Frequency
20 Blacks (N=414)
15 Hispanics (N=414)
10
5 *Proc. Int. Sym. Hum. ID
(Promega) 1997, p. 34
0
6 7 8 9 9.3 10
Number of repeats
50. Applications
forensic investigations (98% of violent crime by men)
genealogical purposes
evolutionar y studies
Advantages to Human Identity Testing
male component isolated without differential extraction
paternal lineages
Needs
population studies to evaluate diversity of haplotypes
robust assay for accurate characterization of Y markers
51. Y Chromosome Structure
SRY ~60 Mb total DNA sequence (only
chromosome 22 is smaller)
p AMEL
~2.5 Mb on tips recombine with X
(pseudoautosomal regions)
q 35-36 Mb euchromatin 9.5 Mb
sequenced (27%)
heterochromatin
Genetic variation at
Genetic variation at
multiple points along the Y
multiple points along the Y
chromosome is combined
chromosome is combined
to form a Y haplotype for a
to form a Y haplotype for a
Nucleic Acids Res. 28(2), e8 (2000) sample
sample
52. STRs (microsatellites)
DYS19, DYS385, etc.
mostly tetranucleotide repeats
Bi-allelic markers (unique event polymorphisms--UEP)
SNPs (single nucleotide polymorphisms)
Y Alu polymorphism (YAP) or other insertions/deletions (“indels”)
Minisatellite
MSY1 (DYF155S1) composed of 48-114 copies of a 25 bp repeat
unit with 5 sequence variant repeat types
typed by MVR-PCR (minisatellite variant repeat)
53. Map of Y Chromosome STR Markers
p
q
Nucleic Acids Res. 28(2), e8 (2000)
57. Autosomal STRs provide a higher power of
discrimination and are the preferred method
whenever possible
Due to capabilities for male-specific
amplification, Y-chromosome STRs (Y-STRs) can be
useful in extreme female-male mixtures (e.g., when
differential extraction is not possible such as fingernail
scrapings)
Due to high copy number , mitochondrial DNA
(mtDNA) may be the only source of surviving DNA in
highly degraded specimens or low quantity samples such
as hair shafts
59. Advantages Disadvantages
Extend possible reference Lower power of discrimination due
samples beyond a single to no genetic shuffling with
generation (benefits missing recombination
persons cases and genetic
genealogy) Family members have
indistinguishable haplotypes unless
Family members have mutations have occurred
indistinguishable haplotypes
unless mutations have occurred
61. All sources of DNA are extracted when biological evidence from a crime
scene is processed to isolate the DNA present.
Thus, non-human DNA such as bacterial, fungal, plant, or animal
material may also be present in the total DNA recovered from the
sample along with the relevant human DNA of interest.
For this reason, the DNA Advisory Board (DAB) Standard 9.3
requires human-specific DNA quantitation so that appropriate
levels of human DNA can be included in the subsequent PCR
amplification.
Multiplex STR typing works best with a fairly narrow range
of human DNA – typically 0.5 to 2.0 ng of input DNA works best with
commercial STR kits.
62. 1. Molecular Weight of a DNA Basepair = 618g/mol A =:
313 g/mol; T: 304 g/mol; A-T base pairs = 617 g/mol
G = 329 g/mol; C: 289 g/mol; G-C base pairs = 618 g/mol
2. Molecular Weight of DNA = 1.85 x1012 g/mol
There are 3 billion base pairs in a haploid cell ~3 x 109 bp
(~3 x 109 bp) x (618 g/mol/bp) = 1.85 x 1012 g/mol
3. Quantity of DNA in a Haploid Cell = 3 picograms
1 mole = 6.02 x 1023 molecules
(1.85 x 1012 g/mol) x (1 mole/6.02 x 1023 molecules)
= 3.08 x 10-12 g = 3.08 picograms (pg)
A diploid human cell contains ~6 pg genomic DNA
4. One ng of DNA contains the DNA from 167
diploid cells
1 ng genomic DNA (1000 pg)/6pg/cell = ~333 copies of each locus
(2 per 167 diploid genomes)
63. We generally shoot for 0.5-2 ng
DNA Size (bp)
-A DNA Size (bp)
Relative Fluorescence (RFUs)
+A
100 pg
10 ng template
(overloaded)
template
D3S1358
5 pg
2 ng template
(suggested level)
template
64. What is rtPCR or qPCR?
How does it work?
How does it compare to traditional
methods of Human DNA quantitation?
What techniques are available?
What systems are available?
65. RtPCR is a very recently developed technique
Developed by Higuchi in 1993
Used a modified thermal cycler with a UV detector and a CCD
camera
Ethidium bromide was used as intercalating reporter As [dsDNA]
increased fluorescence increased
First paper on qPCR:
Higuchi, R.; Fockler, C.; Dollinger, G.; Watson, R. “Kinetic PCR
analysis: real-time monitoring of DNA amplification reactions”
Biotechnology (N Y). 1993 Sep;11(9):1026-30
Warning: RT-PCR also means reverse transcriptase PCR
which is used when working with RNA
66. During the exponential expansion of the PCR
the amount of product produced is
proportional to the amount of template. Here
Exponential PCR we show the total amount of product
following 32 cycles.
1.00E+10
9.00E+09
8.00E+09
7.00E+09
ng product
6.00E+09
5.00E+09 2ng template
4.00E+09
3.00E+09
1ng template
2.00E+09 0.5ng template
1.00E+09
0.00E+00
0 5 10 15 20 25 30 35
# Cycles
67. To use PCR as a quantitative technique, the reaction must be
clearly defined
In fact there are several stages to a PCR reaction
Baseline stage
Exponential stage plateau
Plateau stage
exponential
baseline
68. PCR product can not double forever
Limited by
Amount of primer
Taq polymerase activity
Reannealing of product strands
Reach plateau
No more increase in product
End point detection
Run for fixed # cycles and then quantify on agarose
gels
69. Even if same amount of template, different tubes will reach different PCR plateaus
25
Equal template in all tubes
20
PCR product
15
10
5
0
0 10 20 30 40
Cycle
Karen Carleton
Hubbard Center for Genome Studies and Department of
Zoology
70. Different wells reach plateau at different cycle numbers. When you look
changes what you see.
16
14
12
PCR product
10
8
6
4
2
0
0 10 20 30 40
Cycle
Karen Carleton
Hubbard Center for Genome Studies and Department of
Zoology
71. Use data when still in exponential phase
PCR product proportional to initial template
Need to look at PCR product each cycle
Use fluorescent detection, where fluorescence is
proportional to PCR product
Use real time PCR machine which records
fluorescence for each well at each cycle
Karen Carleton
Hubbard Center for Genome Studies and Department of
Zoology
72. Ec is a function of:
• Hybridization
efficiency
• Quantity of
reactants/target
DNA
• Temperature
http://www.med.sc.edu:85/pcr/realtime-home.htm
73. Quantitation of DNA is a based on the number of cycles required
to reach a threshold intensity, Ct.
The greater the amount of starting DNA, the sooner this
threshold value is reached.
Ct
http://www.med.sc.edu:85/pcr/realtime-home.htm
74. The log of DNA template concentration vs Ct is
plotted using a series of stds yielding a
calibration curve
The unknown is then run and the number of
cycles required to reach threshold, Ct is
compared to the calibration curve.
75. Development of a standard curve
5.0 ng
1.3 ng
0.31 ng 0.0 ng
0.078 ng (reagent blank)
Ct
78. Fluorescent intercalating dye - SYBR Green
Fluorescence increases with concentration of
dsDNA
Taqman probes
Fluorescence increases as quenched probe is
digested
Molecular beacons
Fluorescence increases as quenched probe
hybridizes to template
79. Easy
Fluorescence only with dsDNA
Use with existing PCR primers
Generic,
Detects all double stranded products,
including primer dimers
However, can be very specific with
proper primer design
Singleplexed
Multiple probes cannot be used
dsDNA Intercalation
http://www.probes.com/handbook/figures/1557.html
80. Consist of ssDNA with an internal
complementary sequence that keeps reporter
and quencher dyes close → No fluorescence
Reporter
Molecular beacon
Quencher
Following denaturation, beacon anneals to
template, separating both dyes and yielding
fluorescence proportional to PCR product
concentration
81. Improved specificity and multiplexing
Non-specific amplification will not produce a signal
Can multiplex several probes (quantify nuclear, Y, int std.)
Can be tricky to design
Loop portion – binds to DNA template
Stem portion – must be complementary to other stem
Probe must denature from template below 72º so Taq polymerase
does not chew it up during extension step
Tanneal< Tm < Text
Above Tm loop structure reforms and probe leaves template
82. Probe also binds to PCR product during
extension but is always quenched
5’-3’ exonuclease activity of Taq polymerase
digests probe and frees reporter dye from
quencher
Free dye accumulates with PCR product
R Q
Taq
Taq
83.
84. Constituye el punto crítico para la resolución de
una causa judicial.
Cada Servicio de Investigación Forense deberá
establecer claros protocolos para la
manipulación, transporte y conservación de las
evidencias.
Cualquier manipulación inadecuada permitirá a
la defensa invalidar los resultados del análisis.
86. Fue históricamente la fuente de ADN más
común y eficiente.
Los criterios de conservación han cambiado,
simplificándose: pequeñas cantidades a
temperatura ambiente, en papeles de filtro,
bastan para un estudio completo si el
Laboratorio cuenta con equipamiento de última
generación.
87. Soportes
adsorbentes.
Conservación a
temperatura
ambiente.
Largo tiempo de
conservación.
Permite generar un
banco de muestras.
89. Sangre de sospechoso/ s.
Evidencias: hisopados, prendas,
pelos, uñas, etc.
Sangre de la víctima.
90. Material cadavérico fresco: congelado -20C.
Material cadavérico descompuesto: en mezcla de sales
(hasta 2 meses), congelado si el periodo es mayor.
Material Cadavérico esqueletizado: conservar a
temperatura ambiente, en sobres limpios, luego de
lavados.
Se debe evitar en todos los casos el empleo de
fijadores con formol.
91. 2. Protección de la muestra
2.1 Contaminación por material biológico humano
Contaminación anterior o previa
Se debe a la aparición de la material biológico en el lugar donde
luego aparecerán los indicios.
INEVITABLE
Contaminación coetánea o paralela
El material genético de un indicio se mezcla con ADN de otro origen
en el momento de los hechos
INEVITABLE, VALORABLE y UTIL
Contaminación posterior
Debido al depósito de material genético de diversos orígenes en el
indicio con posterioridad al momento de los hechos
EVITABLE
92. TOMA DE MUESTRAS DE REFERENCIA
1. Personas vivas
• Siempre con consentimiento informado
• Debe existir un documento firmado con la autorización expresa para realizar el
análisis
En PERSONAS TRANSFUNDIDAS evitar la toma de sangre, podría detectarse
• Punción venosa (5 ml con EDTA)
SANGRE
el ADN procedente de la sangre transfundida al menos en un corto periodo de
tiempo después a la transfusión • Punción dactilar (gotas depositadas en
papel secante y se dejan secar a TA)
CEL EPITELIALES BUCALES • 2 Hisopos de ambos carrillos
(importante dejarlos secar antes de
enfundar para evitar la proliferación
bacteriana)
PELOS CON BULBO • 10-15 pelos con bulbo
93. TOMA DE MUESTRAS DE REFERENCIA
2. Cadáveres en buen estado de conservación
SANGRE post-mortem 1 ml (anticoagulante tipo EDTA)
MUSCULO ESQUELETICO Aprox 1 gr. Se almacena en un recipiente de
plástico y tapón de rosca.
PIEZAS DENTALES 2 (molares). Dejar en reserva con el fin de
evitar la exhumación.
3. Cadáveres en avanzado estado de putrefacción o esqueletizados
HUESO LARGO Fémur, húmero…
PIEZAS DENTALES 2 (molares). No dañados externamente ni
sometidos a endodoncias.
94. TOMA DE MUESTRAS DE REFERENCIA
4. Cadáveres carbonizados
• Cuando la carbonización no es total es posible analizar MÚSCULO ESQUELÉTICO
de zonas profundas.
• Cuando la carbonización es total recomendable contactar con el laboratorio
5. Otras muestras de referencia de personas fallecidas
• En hospitales (muestras de sangre, biopsias en parafina, preparaciones histológicas…
No utilizar tejidos fijados en formol.
• Ámbito familiar (peines, maquinillas de afeitar, saliva en sellos o sobres…)
95.
96.
97.
98.
99.
100.
101.
102.
103. FIN
Más información sobre análisis de ADN:
• Laboratorio: www.adn.ac
• Sociedad Latinoamericana de
Genética Forense: www.slagf.org
• Tesis doctoral:
www.secretpaternity.com
Editor's Notes
Figure 2.3 The human genome contained in every cell consists of 23 pairs of chromosomes and a small circular genome known as mitochondrial DNA. Chromosomes 1-22 are numbered according to their relative size and occur in single copy pairs within a cell’s nucleus with one copy being inherited from one’s mother and the other copy coming from one’s father. Sex-chromosomes are either X,Y for males or X,X for females. Mitochondrial DNA is inherited only from one’s mother and is located in the mitochondria with hundreds of copies per cell. Together the nuclear DNA material amounts to over 3 billion base pairs (bp) while mitochondrial DNA is only about 16,569 bp in length.
Figure 9.1 Illustration of inheritance patterns from recombining autosomal genetic markers and the lineage markers from the Y-chromosome and mitochondrial DNA.
Figure 9.10 Ancestry of Thomas Jefferson and Eston Hemings male lines. The shaded boxes represent the samples tested by Foster et al. (1998) in their Jefferson Y chromosome study. A male descendant of Eston Hemings, son of Thomas Jefferson’s slave Sally Hemings, was found to have a Y chromosome haplotype that matched male descendants of Field Jefferson, President Thomas Jefferson’s uncle. A male descendant of Thomas Woodson, claimed by some to be descended from Jefferson, had a different Y haplotype and therefore could not have been a Jefferson.