11 DNA Profiling, Forensics, and Other Applications Brief Chapter Outline I. Satellite DNA: A....
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11 DNA Profiling, Forensics, and Other Applications Brief Chapter Outline I. Satellite DNA: A. Repetitive DNA B. Microsatellites C. Minisatellites D. Macrosatellites
11 DNA Profiling, Forensics, and Other Applications Brief
Chapter Outline I. Satellite DNA: A. Repetitive DNA B.
Microsatellites C. Minisatellites D. Macrosatellites II.Population
Genetics and Alleles III.Multilocus Minisatellite VNTR IV.
Single-Locus VNTR for STR V. Restriction Fragment Length
Polymorphisms VI. Methods of DNA Profiling VII.Technical
Considerations: 1. DNA digestion2. Gel electrophoresis3. Probe
selection VIII. Polymerase Chain Reaction IX. Digital DNA Typing X.
Population Comparisons XI. Admissibility of Scientific Evidence in
a Court of Law:A. Frye StandardB. Daubert Standard XII. Databases
A. Cause for Concern? What About Privacy? XIII. Other Methods of
Profiling DNA and Their Applications A.Random Amplification of
Polymorphic DNA B.Amplified Fragment Length Polymorphism
C.Single-Strand Conformation Polymorphism D. Single Nucleotide
Polymorphism E. Mitochondrial DNA and the Y Chromosome: 1.
Mitochondrial Eve2. Y Chromosomal Adam XIV. Forensic Archaeology A.
Biotech Revolution: DNA Profiling and Human Remains
Slide 2
I.Introduction and History of DNA Profiling. A. Since the late
1960s, protein polymorphisms such as the ABO blood groups and MHC
antigens have been used to determine genetic differences among
individuals. B. Because protein tests have limited variability, DNA
testing was developed in 1985 by Alec Jeffreys in England. Testing
helped to solve an immigration dispute in late 1985. C. Jeffreys
testing system was used to solve rape and murder cases in 1986, and
in 1987 DNA fingerprinting was admitted as evidence in both the UK
and the United States. D. The US Office of Technology Assessment
(OTA) determined that DNA fingerprinting was a scientifically valid
way of determining individuality. E. In 1992, the US National
Research Council confirmed the scientific validity of DNA testing
and issued guidelines for its use. DNA evidence is now admissible
in court. F. Many commercial laboratories provide DNA
fingerprinting services for forensic and parentage analysis, such
as Orchid Cellmark.
Slide 3
II. Satellite DNA. A. Repetitive DNA. 1. In two major classes:
a) Tandemly repetitive sequences of satellite DNA (about 10% of the
genome). b) Interspersed repetitive DNA makes up 520% of the
genome. They are scattered throughout the genome and are further
subdivided: (1) SINES (short interspersed elements) are sequences
of fewer than 500 bp. (2) LINES (long interspersed elements) are
sequences of 500 bp or more. 2. Tandemly repeated DNA comprise long
macrosatellite near the centromeres and shorter minro- and
mini-satellite DNA scattered within the the genome. Only found in
eukaryotic organisms, without a known biological function. 3.
Variable Number of Tandem Repeats (VNTRs) (Figure 11.1). a) Made of
a short sequence, or motif, called a core sequence, which is
repeated many times in a row. b) Inherited from the parents. c)
Core sequences range from two to six bp to over 300 bp long. d) The
number of times the core sequence is repeated is variable. e) A
VNTR refers to a single location with different alleles,
characterized by differences in the number of times the core
sequence is repeated. f) Can have hypervariable loci where a locus
may has many different alleles varying in the number of repeats. g)
Jeffreys was able to use DNA probes for VNTRs by using Southern
blotting to yield a DNA fingerprint. h) Can generate by restriction
enzyme digestion or PCR. 4. Sattelite DNA is found only in
eukaryotes. Suggested biological function of sattelite DNA include
providing sequences necessary for the pairing of homologous
chromosomes during meiosis and site of recombination.
Slide 4
Slide 5
B.Microsatellites. 1.Also called simple tandemly repeated
sequences or short tandem repeats (STRs). 2.Very short, with a
repeated sequence of about 2-5 bp. 3.Most common repeated motif is
(CA)n-(GT)n, with n meaning the number of times the sequence is
repeated. 4.The total length of the repeat is less than one kb
(usually 70-200 bp). STR are randomly distributed throughout the
genome. The variation in length between alleles of the same locus
is due to replication slippage. 5.Because of their hypervariability
(multiple alleles/locus), STRs are more valuable than RFLPs which
usually have two alleles/locus. 6.Often several loci are examined
simultaneously by PCR (multiplexing) to generate a fingerprint. 7.
The FBI uses a set of thirteen well-characterized STR loci for DNA
profiling.
Slide 6
C. Minisatellites. 1. Located near the ends of chromosomes (the
telomeres) and vary due to recombination of alleles. 2. Share a
core sequence of about 20 bp units, although the rate of mutation
can be very high. A minisatellite core unite can be repeated up to
a total length of one to 30 kb. 3. The number of alleles can also
be very high, which means that it is hypervariable (greater than
the microsattelites). 4. Loci may number in the thousands, and the
sequences are used to detect length polymorphisms scattered
throughout the genome (called multilocus profiles).
Slide 7
D.Macrosatellites. 1. Located near the centromeres and
telomeres. 2. Megabases in length, and need a special type of
electrophoresis called pulsed-field gel electrophoresis. 3. Length
makes them subject to breakage, so they are not used in forensic
analysis especially that collected samples may already be somewhat
degraded.
Slide 8
III.Population Genetics and Alleles. A.Because humans are
diploid organisms, each individual has two alleles per locus.
B.Individuals could be: 1. Homozygoustwo copies of the same overall
length, even though the DNA sequence may be different. 2.
Heterozygoustwo copies of different overall length. C. Many alleles
exist in a population with the maximum number of alleles being two
times the number of people in the population. D. Some DNA regions
can be hypervariable (usually used in forensic analysis), while
others are not as variable. E. Allelic polymorphisms in a
population are maintained by genetic drift or natural
selection.
Slide 9
IV.Multilocus Minisatellite VNTR (Figure 11.2). A. Supported by
genetic and population data, and the data provided by the probes
are reliable and are used in paternity (Figure 11.3) and
immigration cases (Figure 11.4). B. More difficult to interpret
than single-locus patterns for several reasons: 1. The large number
of bonds usually generated. 2. Incomplete cutting of the DNA. 3.
DNA degradation. 4. Low DNA recovery. 5. Identification problems
with mixed DNA samples from more than one individual. C.DNA
fingerprinting has still been successful in forensic cases and
evaluating the genetic diversity of plants and animals. D.Usually
detected using Southern blot hybridization.
Slide 10
Slide 11
Slide 12
Slide 13
V.Single-Locus VNTR for STR. A.Generate only one DNA fragment
(homozygous) or two fragments (heterozygous). B.If more than one
location is used, the more informative the analysis (Figure 11.5).
C.Is technically less difficult because it eliminates the
possibility of co-migration of alleles, and it is less likely to
produce artifacts (Figure 11.6). D.The method of choice today is
using PCR, by using at least four or five single-locus primer sets
in separate PCR reactions or in the same reaction (called
multiplexing). E.Some potential problems with multiplexing that
need to be overcome: 1. Primers from one locus can sometimes
complex with those of other loci. 2. One locus may not amplify as
well as another locus. 3. The optimization of PCR conditions can
present a challengeannealing temperature of primers and primer
concentrations must be determined and a uniform annealing
temperature may be difficult to determine. 4. If the problems are
not resolved, the absence of a specific STR allele may not actually
represent the individuals genotype. An alternative may be to
recover the DNA from one reaction, and use it in another reaction
(called sequential multiplex amplification). F. Can determine the
frequency of alleles at different loci, as well as the frequency
for combinations of alleles (Table 11.1).
Slide 14
Slide 15
Slide 16
Slide 17
G. The FBI has selected thirteen tetrameric STR loci to make up
the core of the Combined DNA Index System (CODIS). Having this
system has the following benefits: 1. The adoption of this system
by forensic DNA analysts, allowing standardization of methods. 2.
STR alleles are now readily available using commercially available
kits. 3. STR alleles have been well characterized and act according
to known principles of population genetics. 4.Laboratories
worldwide are contributing data to the database so that the STR
allele frequency in many different human populations can be
determined. 5. The data are digital (see later discussion on
digital DNA typing) and therefore ideal for computer databases. 6.
The frequency for each of the thirteen loci can be combined to
calculate the frequency of an individual profile.
Slide 18
H.STR-based DNA typing is the method of choice because: 1. STR
analysis is much less labor intensive than RFLP analysis. 2. DNA
profiles from badly degraded DNA can be obtained. 3. Very small
amounts of DNA are requiredless than 0.20 ng of target DNA can be
used, although 0.5-1.0 ng of DNA is optimal. 4. Small amounts of
contaminants will not yield nonspecific PCR products. 5. Mixed DNA
samples from other people can be resolved. 6. Automated fluorescent
detection of amplified STR fragments can be conducted using DNA
sequencers.
Slide 19
VI. Restriction Fragment Length Polymorphisms (RFLPs). A.
Alleles can differ in sequence by a single base, which can alter
where a restriction enzyme cuts a DNA sequence. This can cause a
difference in restriction enzyme patterns, which can be generated
in two ways: 1. Agarose gel electrophoresis, followed by DNA
hybridization with a probe. 2. PCR amplification of a DNA fragment,
followed by restriction digestion of the PCR product, and agarose
electrophoresis. B. DNA sequence polymorphisms are common in
animals and can be used as inherited markers (Figures 11.17, 11.8a
and 11.8b), which allows for paternity and maternity testing. C.
Can also be used for disease detection, such as sickle cell anemia.
D. More than 100 genes have been mapped using RFLPs, and are
beneficial when alleles are linked to mutated genes that can encode
genetic diseases, because the locations of these genes can be made
(Figure 11.9). E. Individuals can be screened for RFLPs that are
linked to a disease-causing gene.
Slide 20
Slide 21
Slide 22
Slide 23
Slide 24
VII. Methods of DNA Profiling. A. Methods used in DNA
fingerprint analysis include: 1. Southern blot hybridization which
includes restriction enzyme digestion, gel electrophoresi, and
finally autoradiography. 2. PCR. B. The goal of DNA profiling is to
exclude suspects or to determine a possibility of a match between
samples collected from a suspect.
Slide 25
VIII. Technical Considerations. A. Why make technical
considerations? 1. If methods are not followed closely, then DNA
profiles may yield incorrect results. 2. The following
considerations must be made to maintain consistency: a) Preserve
the integrity of DNA. b) Completely digest the DNA with restriction
enzymes. c) Standardize hybridization methods. d) Select
appropriate probes that are stably inherited. 3. Errors may occur
from: a)Contamination of the sample. b)DNA degradation. c)
Difficulties in interpreting the bands on the x-ray film. Artifacts
(for example, extra bands, missing bands, band shifting) might
provide false information. d) Statistical misinterpretation of a
match.
Slide 26
B. DNA. 1. Need to make the following considerations to have
high-quality DNA: a) Tissue samples need to be collected and stored
on ice. b) DNA should be extracted as soon as possible. c) Samples
may be contaminated by bacterial DNA or DNA from other people. d)
Sometimes DNA might be fragmented if it comes from places such as
mummies, fossilized plants, or frozen humans. 2. DNA Digestion. a)
Incomplete digestion of DNA can create inaccurate DNA profiles. b)
DNA may be methylated and will not allow the enzyme to cut it. c)
Enzymes may cut in incorrect spots if there are less than optimal
enzyme conditions. 3. Gel Electrophoresis. a) Using the correct gel
matrix, such as polyacrylamide for very small DNA fragments like
STR fragments. b) The correct percentage of agarose or
polyacrylamide is needed to more optimally separate specific pieces
of DNA. c) The correct voltage is neededhigh voltages do not
separate large pieces well, and low voltages do not separate small
pieces well. d) Thinner gels allow better separation of DNA pieces.
e) DNA may diffuse out of the gel if the gel is submerged too
deeply in the gel running buffer. f) DNA samples loaded in the
middle wells migrate more quickly than samples loaded at the edges
of the gel. 4. Probe Selection. a) Synthetic oligonucleotide probes
are used to cover all sequence variants. b) DNA should also be
hybridized with a bacterial probe (usually a bacterial ribosomal
RNA gene) to detect bacterial sequences.
Slide 27
IX. Polymerase Chain Reaction. A. PCR is easy to conduct,
results are obtained quickly, and very small amounts of DNA from as
little as a single cell can be used. B. Even degraded DNA can be
analyzed with PCR, however cross-contamination is a potential
problem because contaminating DNA can be amplified. C. Usually PCR
products are transferred to a membrane and hybridized with a
labeled probe or with the PCR product by the process of dot blot
hybridization. D. Ideal marker allele for efficient amplification
should have between 100 and 500 bp, so that the pieces can be
amplified from even degraded DNA. E. All samples should be analyzed
with electrophoresis and hybridization. F. Commercial biotechnology
companies market forensic kits that use things such as probe strips
that allow for subtyping of samples and comparison of results.
Slide 28
X.Digital DNA Typing. A. Also called repeat coding, this is
when the variation within one location is measured, and not the
number of repeat units in specific locations. B. The locus is
amplified by PCR and then cut with a restriction enzyme. The enzyme
may cut the DNA or it may not cut the DNA. C. If the DNA is cut or
not (or both), a number is assigned to the repeat, and since
several loci are used, a numerical readout called a barcode is
generated. D. The barcode is used to compare samples with others,
eliminating the need for electrophoresis of each sample because the
DNA pieces do not need to be sized.
Slide 29
XI.Population Comparisons. A. Two major challenges in forensic
analysis are: 1. Calculate probability of coincidental matches by
comparing with a reference population. 2. Find the criteria for
determining what constitutes a relevant reference population. B.
Individual DNA polymorphisms must be used in the context of
population data in order to determine the probability that a match
can occur by chance alone: 1. The individuals data must be compared
to an ethnic group relevant to the individual. 2. Identical
patterns between two individuals or an individual and a sample must
be established. 3. The probability that a DNA banding pattern is
present in another person should be extremely low. 4. Answer the
question What is the probability that a DNA match is random? This
question requires thorough and careful study of the population. 5.
Need to assume that the probes for VNTR loci separate independently
and are not linked, although this requires the sampling of a large
population, which may not be possible in small ethnic groups. Many
laboratories (as well as CODIS) are establishing local population
databases.
Slide 30
XII. Admissibility of Scientific Evidence in a Court of Law. A.
About DNA evidence and how it is submitted in courts: 1. Trial
courts make preliminary determinations of admissibility of evidence
through pretrial hearings where the judge evaluates all evidence.
2. Expert witnesses testify with their opinions on the evidence. 3.
Laws based on the Federal Rules of Evidence, which were signed into
law in 1975. Rule 702 governs the use of scientific evidence and
requires that all scientific testimony be relevant, reliable, and
grounded in scientific methodology. 4. States set the standards by
which DNA evidence is allowed, with the two major standards being
the Frye and Daubert standards. 5. Parties in a case may have to
submit to a Frye or Daubert hearing in order to show that a
scientific principle is well-established and can be used as
evidence. This hearing is usually requested by the defense team to
see if there is any potential weakness in the scientific methods.
6. Rejection of DNA evidence is usually based on factors such as
methods used to collect DNA and the possible contamination of
samples.
Slide 31
B.Frye Standard. 1. Sometimes referred to as the
general-acceptance rule, limits acceptable scientific evidence to
evidence which has been generated by methods that are reliable,
well-established, accepted by the scientific community, and
supported by scientific principles. 2. A Frye test is used to
prevent the presentation of invalid opinions based on invalid
scientific procedures to a jury. 3. Witnesses who present
scientific data must be experts in the field and possess the
academic and professional credentials that allow them to understand
the scientific principles used to generate the evidence. 4. Proof
of reliability of a method must also be established, and a manual
called Technical Working Group on DNA Methods Analysis has been
published and used by many commercial laboratories.
Slide 32
C. Daubert Standard. 1. Evolved from a 1993 decision involving
a claim that the antinausea drug Benectin caused birth defects. The
Supreme Court rejected the Frye standard in this case. 2. In the
Daubert case, Rule 702 took precedence over the Frye standard. 3.
The Daubert standard established six questions that needed to be
answered when considering the evidence: a) Is the hypothesis
presented by the scientific expert testable? b) Has the theory or
method been subjected to peer review and publication? c) What is
the known or potential error rate of the method? d) What are the
experts qualifications and stature in the scientific community? e)
Does the method rely on the special skills and equipment of one
expert or can it be replicated by other experts elsewhere? f) Can
the method and the results be explained in such a way that the
court and the jury can understand and evaluate the evidence? 4.
Scientific knowledge must be produced using the scientific method
and supported by peer review, forcing the experts testimony to be
subject to scientific validation
Slide 33
XIII. Databases. A. How databases are made and used. 1.
Information provided to data banks comes from forensic collections,
tissue samples, blood samples, neonatal screenings, and members of
the armed forces. 2. Examples of DNA databases include CODIS, the
Department of Defense, and the state of Virginia. 3. May be very
useful, but may also infringe on our privacy. B. Cause for Concern?
What About Privacy? 1. Genetic information can be stored in a
database and could be subject to misuse. 2. Specific regulations
need to be in place where donors must be told exactly what data are
stored and must consent to the use of their biological samples. 3.
Employers and insurers must not base any decision on genetic
information.
Slide 34
XIV.Other Methods of Profiling DNA and Their Applications. A.
Random Amplification of Polymorphic DNA (Figure 11.10). 1. Used to
detect variability or polymorphisms in PCR priming sites. 2. Uses
between eight and ten-nucleotide primers, and will generate DNA
fragments of different sizes and cause differing patterns. Patterns
will not be the same for every member of a population. 3. Some
features of RAPD include: a) RAPD methods are simple and can be
performed in a short time. b) Because they are polymorphic, they
can be used as genetic markers. c) They are dominant, and do not
distinguish between homozygous and heterozygous allele states. d)
RAPDs closely linked to a particular gene can be used by animal and
plant breeders to ascertain whether they have transferred the
desired trait. e) Useful for determining genetic variability within
and between populations of bacteria, plants, or animals.
Slide 35
Slide 36
B. Amplified Fragment Length Polymorphism (Figure 11.11). 1.
Used in a variety of fields, from forensic analysis to plant and
animal breeding. 2. Essentially a PCR-amplified RFLP, it assesses
the entire genome instead of just specific locations. It is an
effective tool to use in population genetics studies. 3. Abundant,
randomly distributed, and inherited in a Mendelian fashion. 4. The
method is as follows: a) Genomic DNA is digested to completion with
the enzymes MseI and EcoRI. Combinations of DNA pieces will be
generated: those cut with only MseI, those only cut with EcoRI, and
those cut with both enzymes. b) The ends of the resulting DAN
fragments are ligated to specific 25-30 bp adaptor sequences that
act as priming sites for select primers. c) Preselective PCR is
performed, using primers that have extra nucleotides (one to three)
on their 3 end. Only a small amount of the fragments cut with both
enzymes will be amplified. d) A second PCR, called selective PCR,
is performed using the PCR products from the previous step as a
template. The primer that anneals to the EcoRI adaptor sequence is
labeled with fluorescent or radioactive nucleotides. e) The PCR
products are analyzed by capillary gel or agarose gel
electrophoresis. 5. 100-200 bands are generated, and only a small
number will be polymorphic.
Slide 37
Slide 38
C. Single-Strand Conformation Polymorphism. 1. Single-strand
DNA can change mobility based on its nucleotide sequence. 2.
Asymmetric PCR is done where one primer is in higher amount than
the other. 3. When the low-amount primer is used up, the PCR
reaction continues, generating single-stranded pieces of DNA. 4.
Pieces are separated with native gel electrophoresis (does not
denature DNA). 5. Features include: a) The mobility of
single-strand DNA depends on intramolecular base pairing. This base
pairing can form loops, stems, and other secondary structures,
altering their mobility. b) The exact sequence and location of the
polymorphism can be unknown, and only the mobilities are important
and reflective of the DNA polymorphism. c) Most SSCP methods
analyze single DNA loci of individuals. d) Useful for detecting
individual genetic variation in populations, detecting mutations in
genomic DNA, and serving as molecular markers.
Slide 39
D.Single Nucleotide Polymorphism. 1. Most are nucleotide
substitutions, and are useful to detect mutations in genes that
might be related to disease development. 2. Many new methods have
been developed involving hybridization of allele-specific probes
that fluoresce when they bind to the target sequence. 3. Can be
applied to comparing genotypic variation to phenotypic variation,
ecological research, pharmacogenomics, and the expansion of SNP
databases by data mining.
Slide 40
E. Mitochondrial DNA and the Y Chromosome. 1. Mitochondrial
Eve. a) Mitochondrial DNA studies have shown that: (1) Recent
ancestors of modern humans originated in Africa, and therefore, had
a recent African origin. (2)Modern humans appeared in one founding
population. (3) Our closest ancestors evolved approximately 171,500
years ago. It is believed that all modern humans arose from a few
females at about this time, and all different mitochondrial
sequences coalesced into one. (4) Anatomically modern humans
migrated to other parts of the world to replace other hominids. b)
Mitochondria have a genome of about 16,500 bp, containing 27 genes.
c) There are advantages to using mitochondrial DNA: (1)
Mitochondrial DNA undergoes mutations at a higher rate than nuclear
DNA. Differences between closely related individuals can be
resolved. (2) Mitochondria are inherited only from the maternal
line so that a direct genetic line can be traced without the need
to separate two different lineages (father and mother). (3)
Mitochondrial DNA does not undergo recombination, so there are not
combined male- female lineages to decipher.
Slide 41
2. Y Chromosomal Adam. a) A record of paternal inheritance and
it is believed that all men can be traced back to one ancestral
male who lived between 35,000 and 90,000 years ago. b) Believed to
have originated in Africa, along with mitochondrial Eve. c)
Y-chromosome profiling shows that males moved south from Africa
into Australia and Eurasia. d) Other applications of Y-chromosome
studies include: (1) The evolutionary history of the Lemba, a South
African Bantu-speaking population of possible Jewish ancestry. (2)
Finding that islands of Jewish priests called the Cohanim have been
maintained in populations of Eastern European Jews.
Slide 42
XV. Forensic Archaeology. A. The use of forensic science to
examine and make conclusions about archaeological discoveries. B.
They are also used to solve old crimes. C. Can even use very small
amounts of DNA that may be damaged (such as a mummy). D. Examples
of forensic archaeology include: 1. Identification of individuals.
2. Studying human and animal evolution. 3. Tracing the migration of
humans and animals, including extinct groups. 4. Tracing origins
and relationships of different ethnic groups around the world. 5.
Determining family relationships of ancient remains, such as the
pharaohs of Egypt.
Slide 43
E. Biotech Revolution: DNA Profiling and Human Remains. 1. Two
of the most famous cases dealing with ancient human remains are: a)
Romanov family: (1) Nine skeletons were discovered in Ekaterinburg,
Russia, in 1991. (2) Tests on remains included STR testing,
mitochondrial DNA, and sex chromosome testing. (3) Found the czar,
his wife, and three of his children among the nine. b) Otzi, the
Ice Man discovered in the Alps in 1991: (1) Believed that he died
about 5200 years ago. (2) Found that he probably died of a violent
fight. (3) Found the blood of four other people on his knife, coat,
and arrow.