Title: Joey Fong Slides:212
1SNP and Microsatellites (STR) in DNA
Raymond Fung (Slides24-32 )
Joey Fong (Slides2-12 )
Tara Gonzalez (Slides13-23)
2Group Responsibilities
- Joey Fong- Introduction Slides What led
scientists to this new scientific discovery or
technique? Short definition as to what SNP and
Microsatellites are How scientists tested their
work the outcome of their research. - Tara Gonzalez- Put together the powerpoint
Middle Slides Explanation of the science (SNP
STR) How it works How it applies to crime scene
and forensic science. (Real Life Stories and
examples) - Raymond Fung- Conclusion SlidesWhat are the
advantages/disadvantages of this new
discovery/technique as it relates to crime lab
investigations the advantages and disadvantages
of this new discovery/techniqe as it relates to
courtroom proceedings questions raised by this
discover/technique (new questions, new cases
brought up.)
- NOTE CITATIONS On almost all of the slides a lot
of sources were used and the full citation
couldnt fit on the slides. Instead the number of
the citation (found in the bilbliography) is
noted in this format ( number, number etc.)
3What Are They?
- Single-nucleotide polymorphism SNP is a DNA
sequence occurring when a single nucleotide
(A,T,C, or G) in the genome differs between
members of a species. Almost all common SNPs have
only two alleles
- "SNPs Variations on a Theme." National Center
for Biotechnology Information. Web. 09 Nov. 2009.
lthttp//www.ncbi.nlm.nih.gov/About/primer/snps.htm
lgt. - "Microsatellite Marker Method - Genomics Course."
Biology _at_ Davidson. Web. 09 Nov. 2009.
lthttp//www.bio.davidson.edu/COURSES/genomics/meth
od/microsatellite.htmlgt.
4- SNP." Web. 09 Nov. 2009. lthttp//cmbi.bjmu.edu.cn/
cmbidata/snp/significance/pharmacy.htmgt.
5What Are They?
- Microsatellites are repetitive stretches of short
sequences of DNA used as genetic markers to track
inheritance in families. Also known as Short
Tandem Repeat (STR)
- "Microsatellite Marker Method - Genomics Course."
Biology _at_ Davidson. Web. 09 Nov. 2009.
lthttp//www.bio.davidson.edu/COURSES/genomics/meth
od/microsatellite.htmlgt.
6"Microsatellite Marker Method - Genomics Course."
Biology _at_ Davidson. Web. 09 Nov. 2009.
lthttp//www.bio.davidson.edu/COURSES/genomics/meth
od/microsatellite.htmlgt.
7Significance?
- SNPs can be used in forensic science is to
determine whether an illness is genetic or not. - SNPs also have a special role in drug discovery
strengthen and individuals response to
pharmaceutical agents
- "SNPs Variations on a Theme." National Center
for Biotechnology Information. Web. 09 Nov. 2009.
lthttp//www.ncbi.nlm.nih.gov/About/primer/snps.htm
lgt
8SNP
- SNPs are not responsible for a disease state. In
fact, SNPs are makers for pinpointing a disease
in a human genome. - This is because certain diseases are usually
located near a gene associated with that certain
diseases.
"SNPs Variations on a Theme." National Center
for Biotechnology Information. Web. 09 Nov. 2009.
lthttp//www.ncbi.nlm.nih.gov/About/primer/snps.htm
lgt.
9Significance of Microsatellites
- Microsatellites can be enlarged for
identification. Only a small strand of DNA is
needed to be enlarged
- "SNPs Variations on a Theme." National Center
for Biotechnology Information. Web. 09 Nov. 2009.
lthttp//www.ncbi.nlm.nih.gov/About/primer/snps.htm
lgt.
10Limitations
- Microsatellites - As the genetic distance
increases, the percentage of loci that can be
successfully amplified to view decreases
"SNPs Variations on a Theme." National Center
for Biotechnology Information. Web. 09 Nov. 2009.
lthttp//www.ncbi.nlm.nih.gov/About/primer/snps.htm
lgt.
11Limitations
- SNP Finding single nucleotide changes in the
human genome can be very difficult - However, in the last 20 years biomedical
researchers have developed a many techniques to
make it easier
- "SNPs Variations on a Theme." National Center
for Biotechnology Information. Web. 09 Nov. 2009.
lthttp//www.ncbi.nlm.nih.gov/About/primer/snps.htm
lgt
12Applications
- SNPs can be used to determine whether a victim
died from a disease by looking at the human
genome map and seeing if a disease or diseases
is/are present - Microsatellites can be used for identification of
a suspect or criminal.
- "SNPs Variations on a Theme." National Center
for Biotechnology Information. Web. 09 Nov. 2009.
lthttp//www.ncbi.nlm.nih.gov/About/primer/sns.html
gt. - "Microsatellite Marker Method - Genomics Course."
Biology _at_ Davidson. Web. 09 Nov. 2009.
lthttp//www.bio.davidson.edu/COURSES/genomics/meth
od/microsatellite.htmlgt.
13The Science OF SNP and Microsatellites
- HOW DOES DNA TYPING WORK?
- Only .01 of DNA differs from one person to the
next - this consists of 3 million bases
- DNA can be generated from blood, bone hair or
body tissues/products - Once at the crime scene the evidence must be
collected, the DNA extracted and than the DNA is
analyzed for the presence of DNA Region markers - Scientists find these markers by delegating
probes or small pieces of DNA that will seek out
and bind to a complementary DNA sequence. - A series of probes bound to a DNA creates a
unique pattern for each individual - These DNA profiles are compared to determine
where the suspects DNA profile matches the
profile found at the crime scene - Range that indicates certainty 5-13
( 17,16,9)
14The Science OF SNP and Microsatellites
- DNA polymorphisms are variations in the
nucleotide sequence of DNA - Used as genetic markers especially along
particular chromosomal regions - Ie. Signposts along a road
- Gene markers help display the sequence of repeDNA
polymorphisms are variations in the nucleotide
sequence of DNA - Used as genetic markers especially along
particular chromosomal regions - Ie. Signposts along a road
( 17,16,8,9 )
15Microsatellites
- Microsatellite Analysis
- Microsatellite Analysis is more well known as STR
Analysis or Short Tandem Repeat - The most important fact is its high mutation
rate of 10-2 and 10-5 per gamete so they vary
greatly in copy number between individuals - The analysis starts with the the IDing of regions
of non-coding DNA containing short repeats - Microsatellites can be
- Simple- Uninterrupted array of homologous repeat
motifs - Compound- repeat motif changes- two or more
adjacent simple repeats - Complex-array is interrupted or contains several
repeats of variable unit length - STR-Short Tandem Repeat is known to be the most
successful and commonly used DNA profiling
procedure - STRs are locations, also called LOCIS, on the
chromosome that contain short sequence elements
that repeat themselves throughout the DNA - They are found throughout the human genome which
is why they are so useful - The repeating sequences consist of 3-7 bases
- the entire strand is less than 450 bases long
- 2-5bp in length
( 17,16, 15, 8)
16Microsatellites
- Because they are so small they are less likely to
degrade - so the DNA evidence can be collected from bodies
or stains that have undergone a large amount of
decomposition - TH01 is a common used STR which contains the
repeating sequence A-A-T-G - There are four bases for DNA (A- Adenine, C-
Cytosine, G- Guanine and T- Thymine) - Seven TH01 has been identified in the human
genome these variants contain 5-11 repeats of
the pattern A-A-T-G - When used in a forensic setting the TH01 would be
extracted - a copy of STR would be taken out, copied and
amplified and seperated on an electrophoretic gel
- Observe the distance the STR has moved on the
plate and determine the amount of A-A-T-G repeats
on the STR - Every has two STR types for TH01 (in this case)
one each inherited from each parent
( 17,16,8,15)
17Microsatellites
- STR analysis is useful when the core repeats is
defined and the sequences of bases of repeats are
known - Probability of Identity is also checked
- the probability that two individuals have the
same set of STRS - product of the frequency of occurrence in the
population - Greater number of STRS smaller frequency
- Whats so good about STR analysis?
- hundreds of different types of STRs are found in
genes - The more STRs one can characterize the less
likely it is anyone has those STRS - Concept of multiplexing- a process used to
extract and amplify a combination of STRs. - One system used is the STR Blue kit
- provides materials for the amplified and
detection of three STRS (triplexing) - commonly used because STRS dont overlap and can
be clearly seen - In order to be inputted into CODIS 13 STRs must
be identified
( 17,16,8,15)
18SNP
- SNP- Single Nucleotide polymorphisms- regions of
the genome in which two strains are different by
a single base pair - Most genetic variation between individuals
- SNPS are loci where there is a difference in the
individual base that exists at a certain point on
a genome - Most common type of repeated genetic elements
- Occur about every 1000bp in unrelated individuals
- Variations identified through SNP Analysis
usually deal with - diversity in the population, disease responses,
individual responses to medicine, individuality
etc. - Variations are noted in the untranslated ares of
the genome - that occurs in the 5 and 3 regions
- This is within the introns where variations can
occur without having a huge impact on the DNAs
function - these are points that people in the population
have. One person may have a A-T pair another will
have a G-C Pair - More than 90 of human genes have at least one
SNP
- SNPs can be categorized as
- Bi-, tri- or tetra-alleleic
- Depends on the base that exists at the SNP
Position - it can vary between two, three or four types
- Bi- SNPS though are really the only ones detected
and eventually analyzed
( 17,16,15,11,14)
19What are the results used for?
- HOW ARE THE RESULTS OF THE DNA ANALYSIS USED?
- The scientific procedure used for the DNA
Analysis must be - Robust- able to produce a result
- Sensitive- able to produce a result from a small
amount of evidence - Highly discriminating- able to provide a unique
result that can individualize the evidence - Accurate- involve as little error as possible
- Identifying Victims in major catastrophes 9/11
- Many Victims were unidentified and only left
behind bone and tissue fragments - At the time there was no place to analyze so much
DNA so panel members were snt out to produce
forms and kits needed to enable the medical
examiner to collect DNA - All DNA samples were collected and recorded into
a database - There was around 20,000 pieces of human remains
from the World Trade Center - In 2005 though the search ended because a lot of
the evidence was too small or too damaged to be
accurately identified - Only 1585 of the 2792 who died were identified
- Further identifications though have been underway
since 2007 and the discovery of a new methodology
of DNA extraction
- SNP and Microsatellite analysis have been applied
to various crime scenes and situations
( 17,16)
20What are the results used for?
- MISSING PEOPLE Disappeared Children in Argentina
- People known as the dissapeared were kidnapped
and murdered in Argentina during the 1970s - A lot of them were pregnant women whose children
were taken from them at birth and raised by the
kidnappers - Grandparents of the children have been looking
for them for years - Professor Mary-Claire King has been running DNA
tests on the DNA evidence found in hopes of
reuniting the grandparents with the grandchildren
they never had the opportunity to meet.
( 17,16)
21What are the results used for?
- THE DNA SHOAH PROJECT
- Database for individuals who lost family members
during the Holocaust - May also serve to reunite families separated
during the war - Identify victims who were buried anonymously
22What are the results used for?
- Super Bowl XXXIV Footballs and 2000 Summer
Olympic Games - The NFL uses DNA technology to help keep track of
all of their footballs - to keep a record of them, to insure authenticity
and to prevent sports merchandise fraud - The footballs are marked with a permanent
invisible strand of artificial DNA - the DNA strand is verifiable through the use of a
laser and DNA comparisons - For the 2000 Olympic Games a section of human
genetic code was taken from several Australian
Athletes (the Olympics took place in Sydney that
year) to mark all official goods
( 17,16)
23What are the results used for?
- Son of Louis XVI and Marie Antionette
- Scientists solved one of the so called Greatest
mysteries of all European history by using DNA
tests to prove - Who was the son of the executed French King Louis
XVI - That Marie-Antoinette died in prison as a child
- To prove the son scientists removed the presumed
heart of the child king from his tomb and matched
it with the DNA samples from his family (both
living and dead) - ie. used Maria Antionettes locks of hair
24DNA evidence
- Most significant advance in criminal
investigation since fingerprinting has been DNA
evidence - Analysis on saliva, blood, semen, skin tissue,
hair are all reliable evidence to link criminals
to crimes - In the past 10 years, DNA evidence has been more
widely accepted and used by police, prosecutors,
and courts in the U.S - DNA evidence is the only method able to be used
to exonerate suspects who were wrongly accused,
and also to rule out certain suspects who are not
related to the crime (6)
25First use of DNA evidence
- The first reported use of DNA evidence was in a
non criminal case where a mother-son relationship
was shown through DNA testing - The boy was refused entry to the United Kingdom
because he was lacking proof that he was the son
of his mother who had the right of settlement in
the United Kingdom - In the end, DNA evidence proved that there was a
high probability of the mother-son relationship
and the boy was allowed to enter the U.K (6)
26Cases Related
- In a 1987 case in England, Robert Melias became
the first person convicted of a crime (rape) on
the basis of DNA evidence - In one of the first uses of DNA in a criminal
case in the United States was in November 1987 at
the Circuit Court in Orange County, Florida. - Tommy Lee Andrews was convicted of rape after
DNA tests matched his DNA from a blood sample
with that of semen traces found in the rape
victim (6)
27Cases Related Cont.
- The multiple murder trials in Virginia of Timothy
Wilson Spencer were the first cases in the United
States where the admission of DNA evidence led to
guilty verdicts resulting in a death penalty. - The Virginia Supreme Court upheld the murder and
rape convictions of Spencer, who had been
convicted on the basis of DNA testing that
matched his DNA with that of semen found in
several victims - All states in the U.S have allowed DNA evidence
in criminal trials except four states Maine,
North Dakota, Rhode Island, Utah (6)
28Importance / Advantages 1
- Both microsatellites and SNPs are useful in
identifying diseases - Microsatellites are useful genetic markers they
serve a role in biomedical diagonosis as markers
for certain disease conditions. - Certain microsatellites are related to certain
medical disorders through genetic relationship.
(3)
29Importance / Advantages 2
- Microsatellites are useful markers in detecting
cancer (1) - SNPs do not cause disease, but they can help
determine the chance that someone will develop a
particular illness such as the Alzheimer's
disease (5) - Microsatellites are more importantly used for
parentage analysis -- relatedness testing in
criminal work may involve investigating paternity
in order to establish rape or incest (3)
30Importance / Advantages 3
- Microsatellites have become a significant marker
in forensic studies because of its high
specificity, it is a very high probability of
finding a match with evidence to the suspect so
it is very useful - Microsatellites have many alleles, which is
highly informative and very useful - Advantages of using microsatellites and SNPs is
that it is efficient for large scale studies
because it is not very expensive (7)
31Importance / Advantages 4
- The main advantages of SNPs are
- They commonly and evenly-distributed in the
genome - Methods of detecting SNPs can be easily
automated. The easiness of this technique is what
makes SNPs "high-throughput" markers. - High-throughput means that large numbers of
markers can be quickly obtained at a very small
cost which is very beneficial (4)
32Disadvantages
- The main disadvantage of SNPs is the small number
of alleles present and their low variability - However, the price to obtain large numbers of
SNPs are fairly cheap amount of data able to be
collected makes up for the low variability per
SNP marker (7)
33Bibliography
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009/09/using-microsatellites-and-snps-as-tools-in-
medical-genetic-diagnostics-and-research.htmlgt.
(16)"Human Genome Project Information." DNA
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Genome/elsi/forensics.shtmlgt. - slide 20"Using Microsatellites and SNPs as Tools
in Medical Genetic Diagnostic and Reasearch." Use
of Microsatellites and SNPs (2003) n. pag. Web.
lthttp//ivythesis.typepad.com/term_paper_topics/20
09/09/using-microsatellites-and-snps-as-tools-in-m
edical-genetic-diagnostics-and-research.htmlgt.
"Human Genome Project Information." DNA
Forensics. 19 june 2009. genomics energy gov. ,
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edical-genetic-diagnostics-and-research.htmlgt.
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over." PBS. N.p., n.d. Web. 9 Nov. 2009.
lthttp//www.pbs.org/wgbh/pages/frontline/shows/cas
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over." PBS. N.p., n.d. Web. 9 Nov. 2009.
lthttp//www.pbs.org/wgbh/pages/frontline/shows/cas
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over." PBS. N.p., n.d. Web. 9 Nov. 2009.
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ources/Human_Genome/faq/snps.shtmlgt. - slide 30Mohlke, Karen. "Studying Genetic
Variation II Laboratory Techniques." Web. 9 Nov
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uralResearch/DIRCalendar/CurrentTopicsinGenomeAnal
ysis2006/CourseHandouts/CTGA2006Lec11Grey.pdfgt. - slide 31"Panzea FAQs." Panzea Home. N.p., n.d.
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Variation II Laboratory Techniques." Web. 9 Nov
2009. lthttp//www.genome.gov/Pages/Research/Intram
uralResearch/DIRCalendar/CurrentTopicsinGenomeAnal
ysis2006/CourseHandouts/CTGA2006Lec11Grey.pdfgt.