Applications of DNA Typing
PAY PARTICULAR ATTENTION TO THE ON-LINE READINGS.
08/14/12
I. Human Identity Testing
II. Testing for Hereditary and Infectious Disease
III. Tissue Culture
IV. Anthropology
V. Nonhuman Identification and Studies
VI. Industry & Environment
VII. Miscellaneous
Use the Internet Reading
Instructions and Study
Questions supplements for
the correct online links.
I. Human Identity Testing
A. Forensic
1. Sexual Assault. Over 2/3 of forensic DNA testing involves sexual
assaults. These tests compare semen DNA from the victim or
environment with a suspects' DNA. The victim’s cells also may be
obtained from the alleged rapist. A resulting fetus also can be tested.
-The first use in Illinois was the case of Gary Dotson. Dotson had been
convicted in a 1977 rape, for which he spent 6 years in jail. The woman
recanted her story in 1985 and Governor James Thompson granted
clemency, but the conviction remained on his record. PCR tests excluded
Dotson in 1989.
-In one Illinois case, a sexual assault was alleged to have occurred in a
hospital utility room. Semen evidence was collected from the floor and
from the victim. A suspect was identified from the victim's description.
He was identified by the victim in a line-up. The suspect was also tied to
the assault by other circumstances. DNA testing demonstrated that the
samples were not from the suspect.
2. Murder or battery. Compare crime scene tissue (blood, skin, hair
follicles, etc.) DNA with suspect’s DNA
-Using PCR, samples can be obtained from a single hair, cigarette butts,
sealed envelope flaps, and stamps.
3. Convicted Felon and Forensic Databases: CODIS.
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“The FBI Laboratory's Combined DNA Index* System (CODIS) blends forensic science and
computer technology into an effective tool for solving violent crimes. CODIS enables federal,
state, and local crime labs to exchange and compare DNA profiles electronically, thereby
linking crimes to each other and to convicted offenders.
CODIS began as a pilot project in 1990 serving 14 state and local laboratories. The DNA
Identification Act of 1994 formalized the FBI's authority to establish a national DNA index for
law enforcement purposes. In October 1998, the FBI's National DNA Index System became
operational. CODIS is implemented as a distributed database** with three levels - local, state,
and national. The National DNA Index System is the highest level in CODIS, and enables the
laboratories participating in the CODIS Program to exchange and compare DNA profiles on a
national level. All DNA profiles originate at the local level then flow to the state and national
levels. This allows laboratories within states to exchange DNA profiles according to their
specific legislative or legal requirements.”
-CODIS Mission Statement and Background http://www.fbi.gov/hq/lab/codis/program.htm
CODIS uses a gender identification locus, and greater than four RFLP markers and/or 13
core STR loci.
Guilt and Innocence
When forensic scientists provide a report and testimony about the frequency
estimates, their job is done. The decision as to what constitutes “reasonable
doubt”, the judgment of guilt or innocence reached by the court, may take these
estimates into account, but they must be placed into the circumstances
surrounding the crime and the intent, motive, means, and opportunity available to
the defendant.
Parentage tests are easier since these cases are found in civil court. In contrast
with criminal cases where the higher standard of “beyond a reasonable doubt” is
needed to convict, civil cases, including paternity suits, are determined by a
“preponderance of evidence”. Since most DNA parentage tests conclude the
alleged father was several thousand times more likely to be the father than a
random male, this is considered conclusive proof.
*
DNA Index: A large computer system containing more than one DNA database.
Surveys of DNA profiles from specific populations.
**
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B. Establishing paternity and other family relationships
1) Not just the father…. In one example, DNA testing was used in a criminal
paternity case. The DNA testing revealed that the suspect could have fathered the
child, but the minor mother was not the mother. The DNA profiles of the child
and the alleged minor mother suggested that a sister of the minor could be the
actual mother.
2) Estate settlements
C. Immigration
D. Missing persons and unidentified bodies
-In an Illinois case of an abducted woman, blood was found in a suspect's trunk.
DNA from the parents of the victim determined that the blood was that of the
missing woman. The woman's remains were later found buried in the suspect's
parent's yard.
-In an Illinois case, DNA typing determined that a head was not related to a
headless body.
E. Military ‘Dog Tag’
F. Mass Disasters
G. Historical Investigations:
-The Romanov’s. (online readings)
In 1989, a burial site in Russia uncovered
several bodies. Two years later, 9
skeletons were excavated. Forensic
analysis of the bones, clothing, and other
material from the grave strongly suggested
that the skeletons were those of the former
Russian Czar Nicholas Romanov II, killed
by a firing squad of Bolshevik soldiers.
The evidence, however, was inconclusive.
DNA analysis (of living relatives and the
exhumed body of Nicholas' brother)
provided evidence that the skeleton was
that of the former Czar.
-Thomas Jefferson and Sally Hemings (online readings)
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-Family GenealogyUse Mitochondrial DNA (determines kinship on the mother’s side
or Y chromosome (determines kinshop on the father’s side.
II. Testing for Hereditary and Infectious Disease
A. Genetic disorders:
1. Genetic testing leading to a diagnosis of a genetic disorder can be
accomplished in various ways.
A genetic test is the analysis of entire human chromosomes (cytogenetic
testing), specific areas of the DNA, or indirectly- through proteins or certain
metabolites.
DNA testing: For example, a probe that is complementary to the sequence of
N-bases in the defective gene can be used. If the probe bonds to the person's
DNA, then they contain the defective allele.
2. Types of hereditary disorder testing.
-Screening vs. Testing: Screening involves testing many people
regardless of their specific family background. Testing refers to a specific
individual, usually due to a known family history of the disorder.
-Diagnostic Testing: Testing after symptoms appear
-Predictive Testing: Testing before symptoms appear
-Carrier Testing: Testing a parent before the birth of a child to determine
if the parent “carries” the abnormal allele and, therefore, can pass it on to a
child.
-Preimplantation Testing: Testing an embryo after in vitro fertilization,
before implantation
-Newborn Screening: Testing a newborn
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3. Hundreds of tests have been developed for genetic disorders.
Some examples:
-Breast cancer (BRCA 1, chromosome 17; BRCA 2, chromosome 13)
-Cystic fibrosis (chromosome 7)
-Huntington disease (chromosome 4)
-Mmuscular dystrophy (X chromosome)
Many times, a variety of mutations in a gene cause the disorder. In this
case, other family members may have to be tested in order to pinpoint the
specific mutation.
4. Genetic counseling
Genetic counselors inform patients about genetic conditions, provide
patient education and couseling, and educate other health professionals
about genetics.
5. Epidemiology: The study of the determinants and distribution of
disease, and the application of this study to control health problems. All
diseases are studied by epidemiologists, including infectious and genetic
diseases, toxins, cancer, drug additions, and mental illness.
B. Infectious Disease
Bacteria, viruses and other microorganisms can be detected with DNA tests.
Example: HIV.
In the early stages, HIV can be difficult to diagnose because antibodies
may not be detected, the virus hides inside host cells, and the virus may be
found in relatively small numbers.
PCR can be used to copy few copies of HIV genetic material billions of
times so that it can be detected with probes that are complementary to HIV
DNA.
III. Tissue Culture:
DNA typing is coming into wider use for tissue typing for transplants. Six coding genes
on chromosome six are used for tissue typing.
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IV. Anthropology: The science of the origins and the physical, social, and cultural
development and behavior of human beings.
A. One use of DNA testing is to compare DNA between individuals, populations,
or species. The more DNA the individuals, populations, or species have in
common, the more closely related they are.
The assumption here is that the number of nucleotide (ATCG) differences
increase as the time increases from their last common ancestor. In other words,
two individuals that are closely related (brothers) will have more nucleotides in
common than individuals not as closely related (cousins).
B. Mitochondrial DNA Analysis
“Mitochondrial DNA (mtDNA) typing is increasingly used in human identity
testing when biological evidence may be degraded or when quantities of the
samples in question are limited. Mitochondrial DNA is found in all cells, but it is
most useful when nuclear DNA is scarce, such as with hairs, bones, and teeth.
Since human cells contain several hundred copies of mtDNA, substantially more
template DNA is available for amplification than nuclear DNA.” In humans,
mtDNA is inherited strictly from the mother.
What does the mitochondria do inside of the cell?
C. Neanderthals and Modern Humans
See online readings.
D. Ancient Lifestyles
Example: DNA samples, if available, from the stomachs of ancient people shed
light on their eating habits and, thus, their culture. The presence of parasites also
may shed light on the habits and health of ancient people.
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V. Nonhuman Identification and Studies
A. Cow thieves
-Aug. 3, 1994: 2 men and women drinking at a party
-They decide to go hunting but couldn't find any wild hogs or deer.
However, they did find some cows on the Deseret Ranches. So they shot
and butchered it.
- The next day, at a party, one of men began to sell the meat for $1 per
pound. An informant told a deputy with the Sheriff's Dept., agriculture,
marine, and aviation unit. The deputy found out that a butchered cow had
been reported. The crimes are felonies, theft of a farm animal and armed
trespassing, with a maximum sentence of five years per charge.
- A Sheriff's Sergeant obtained some of the sold meat from a third party.
-Since the Deseret Ranches routinely have calves' DNA tested to prove
parentage, a comparison of the DNA fingerprint of the butchered meat and
a calf's was made. The results indicated a 99% chance that the calf was
the offspring of the butchered cow.
-Without DNA testing, the only way to find the guilty party previously
was usually to retrieve the bullet and hope to find a gun that matched.
- In order to do the DNA testing, a meat sample is not required. Blood
from the back of a truck, skin, hair from the animal or saliva can be used.
B. The American Kennel Club uses DNA genotyping to verify the parentage of
AKC dogs and litters. http://www.akc.org/dna/index.cfm (FYI only, no study
questions).
C. Ancient Samples: DNA in fossils can be compared to DNA of living organisms
so that the extinct organism can be classified in the correct group. For example,
30 million year old bee & termite DNA preserved in amber have been studied
along with the 14,000 year-old bones of saber-toothed cats preserved in tar pits.
D. Dog do-do
1. (1996) The English village of Bruntingthorpe is considered the use of
DNA testing to alleviate a sidewalk menace, dog poop.
-A DNA database could have been developed from a few hairs on each
dog's head. Sidewalk specimens would then be compared to the known
database profiles.
2. (2004) A suburb near Melbourne, Australia also considered performing
a DNA analysis when a owner denied that her pet left the specimen,
despite an officer witnessing the episode.
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VI. Industry & Environment
-Quality control of agricultural products with specific genetic traits.
-Determine pedigrees for seed or livestock breeds.
-Detect bacteria and other organisms that may pollute air, water, soil, and food.
-Illegal poaching.
-Authenticate consumables such as caviar and wine
-DNA banks for endangered species
Declining grizzly bear population
VII. Miscellaneous
A. Identifying Genetic Factors in Human Complex Traits.
-Behavioral disorders: Example: violence.
a. Most biological causes of violence are linked to low levels of
serotonin1. Serotonin transmits nerve signals in the brain and is
important in regulating sleep, sexual behavior, appetite, and
impulsiveness.
Studies have repeatedly implicated it in explosive, destructive,
impulsive behavior, including suicide.
Many things can influence serotonin levels: for example, diet (high
levels of the amino acid tryptophan which is used to make
serotonin, can boost serotonin levels) and environmental stress
(some animals studies have shown a decrease in serotonin in
stressful environments). Serotonin levels are 20-30 times higher in
women than men. They are high in newborns, low in adolescents,
then rise again with age. Genetic defects may also result in
abnormal serotonin metabolism
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b. X chromosome defect found in a Dutch family caused serotonin
disturbances. This family had a long history of violence in the
male members of the family.
c. Another Finnish family with a genetic defect contains men who
are violent and suicidal.
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Serotonin has also been linked to obsessive/compulsive disorder and other behaviors:
http://news.bbc.co.uk/1/hi/health/3205239.stm
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B. Some Other Interesting Uses of DNA Forensic Identification
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Kennewick Man
Kennewick Man has been discovered in the Pacific Northwest. His ancient
remains have caused problems because of competing claims for the remains by
Native American groups, public officials, and scientists. Bones found in the
United States that predate the arrival of Europeans to the Americas are by law
considered Native American, but the bones of Kennewick Man show
characteristics different from Native Americans of that time period. DNA testing
will be used to determine if Kennewick Man's DNA is similar to that of other
Native Americans.
Disappeared grandchildren in Argentina
Numerous people (known as "the Disappeared") were kidnapped and murdered in
Argentina in the 1970s. Many were pregnant. Their children were taken at birth,
along with other young kidnapped children, and were raised by their kidnappers.
The grandparents of these children are now looking for them. Read an article
about a DNA researcher who is helping them.
Tomb of the Unknowns
Son of Louis XVI and Marie Antionette
PARIS, Apr 19, 2000 (Reuters) -- Scientists cracked one of the great mysteries of
European history by using DNA tests to prove that the son of executed French
King Louis XVI and Marie-Antoinette died as a child in prison. Royalists have
argued for 205 years over whether Louis-Charles de France perished in 1795 in a
grim Paris prison or managed to escape the clutches of the French Revolution. In
December 1999, the presumed heart of the child king was removed from its
resting place to enable scientists to compare its DNA make-up with samples from
living and dead members of the royal family -- including a lock of his mother
Marie-Antoinette's hair.
African Lemba tribesmen
In southern Africa, a people known as the Lemba heed the call of the shofar. They
have believed for generations that they are Jews, direct descendants of the biblical
patriarchs Abraham, Isaac, and Jacob. However unlikely the Lemba's claims may
seem, modern science is finding a way to test them. The ever-growing
understanding of human genetics is revealing connections between peoples that
have never been seen before.
Super Bowl XXXIV footballs and 2000 Summer Olympic souvenirs
The NFL used DNA technology to tag all of the Super Bowl XXXIV balls,
ensuring their authenticity for years to come and helping to combat the growing
epidemic of sports memorabilia fraud. The footballs were marked with an
invisible, yet permanent, strand of synthetic DNA. The DNA strand is unique and
is verifiable any time in the future using a specially calibrated laser.
A section of human genetic code taken from several unnamed Australian athletes
was added to ink used to mark all official goods — everything from caps to socks
— from the 2000 Summer Olympic Games. The technology is used as a way to
mark artwork or one-of-a-kind sports souvenirs.
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Snowball the Cat
A woman was murdered in Prince Edward Island, Canada. Her estranged husband was
implicated because a snowy white cat hair was found in a jacket near the scene of the crime,
and DNA fragments from the hair matched DNA fragments from Snowball, the cat belonging
to the husband's parents. M. Menotti-Raymond et al., "Pet cat hair implicates murder
suspect," Nature, 386: 774, 1997.
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Angiosperm Witness for the Prosecution
For the first time a murderer has been convicted on DNA evidence obtained from a plant. The case
was described in the PBS TV series, "Scientific American Frontiers." A young woman was
murdered in Phoenix, Arizona, and a pager found at the scene of the crime led the police to a
prime suspect. He admitted picking up the victim, but claimed she had robbed him of his wallet
and pager. The forensic squad examined the suspect's pickup truck and collected pods later
identified as the fruits of the palo verde tree (Cercidium spp.). One detective went back to the
murder scene and found several palo verde trees, one of which showed damage that could have
been caused by a vehicle. The detective's superior officer innocently suggested the possibility of
linking the fruits and the tree by using DNA comparison, not realizing that this had never been
done before. Several researchers were contacted before a geneticist at the University of Arizona in
Tucson agreed to take on the case. Of course, it was crucial to establish evidence that would stand
up in court on whether individual plants (especially the palo verde trees) have unique patterns of
DNA. A preliminary study on samples from different trees at the murder scene and elsewhere
quickly established that each palo verde tree was unique in its DNA pattern. It was then a simple
matter to link the pods from the suspect's truck to the damaged tree at the murder scene and obtain
a conviction. [WNED-TV (PBS - Buffalo, N.Y.), January 19, 1994]
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Applications of DNA Typing
Worksheet
Punnett Square Problems. The diagrams on this page are Punnett Squares, used to
determine all possible offspring genotypes if the genotypes of both parents are known.
The numbers outside the Punnett Squares are the parental alleles that can be present in
the egg or sperm of the parents (one allele per egg or sperm). Each child inherits one
allele of a given locus from each parent. The numbers inside the squares are the
genotypes possible for the resulting children.
Sample Problem
Punnett Square (a) - At the D21S11 locus, the children of Bob Blackett and
wife Anne can have four different genotypes. Son David is 28, 31. Daughter
Katie is 29, 30. Punnett Square (b) - Bob Blackett inherited the 31allele from
his mother, Norma. Therefore, the 29 allele is from Bob’s father.
paternal was not 29, what would be your conclusion?
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If
Bob's
Case 1
If the genotypes of a mother and several children are known, it is often
possible to predict the genotype of the father. In this case, Karen is the
mother with a genotype of 9, 9.3 at the THO1 locus. From the Punnett
Square, determine the paternal alleles of Tiffany, Melissa, and Amanda.
Their father Steve must have what genotype? If the three daughters had
three different paternal alleles, what would be your conclusion?
Case 2
In this example, the genotype of Karen, the mother, is 16, 17 at the
D18S51 locus. The genotypes of the daughters are either 16, 18 or 17, 18.
In each case, Melissa, Tiffany, and Amanda inherited the 18 allele from
their father, Steve. Can we determine the genotype of Steve for certain?
Explain.
Case 3
Is it possible to determine parental genotypes when only the genotypes of
their children are known? Consider the case of Bob Blackett's four first
cousins, Marilyn, Buddy, Dick and Janet. Bob did not have DNA samples for
their parents, Bud and Louise, who are both deceased. In a real forensic
case, Bud and Louise might represent "missing persons". The children’s
genotypes are as follows: 12/13; 12/18; 17/ 18; and 17/ 18. Predict the
genotypes of the parents. Can you determine which genotype goes with
what parent?
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Case 4
A variation on Case 3 is when there are only two genotypes known for the
children, and both parental genotypes must be predicted. Daughters
Marilyn and Janet are 15, 16 at the locus D3S1358. Sons Buddy and Dick
are 18, 18. Predict the parental genotypes that can give this result. Can you
predict which parent has which genotype?
Case 5
Daughter Marilyn is 16/17 at the locus vWA. Children Buddy, Dick, and
Janet are 16/ 18. What are the possible parental genotypes? Is there more
than one interpretation? Explain.
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Some definitions are given below. Write the appropriate word for each of the definitions
below.
a. A chemical in which low levels has been implicated in explosive, destructive,
impulsive behavior and suicide.
b. Performing genetic tests on many individuals without regard to family history.
c. The science of the origins and the physical, social, and cultural development and
behavior of human beings.
d. Organelle with two membranes and a circular chromosome.
e. Performing DNA analysis on a person specifically due to symptoms or family history.
f. The study of the determinants and distribution of disease.
2. Describe mitochondrial inheritance.
3. Can you distinguish between two siblings using mitochondrial DNA? Why or why
not?
a. yes
b. no
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4. Differentiate between the following:
-Diagnostic Testing:
-Predictive Testing:
-Carrier Prenatal Testing:
-Preimplantation Testing:
-Newborn Screening:
5. When has mitochondrial testing been used? Give examples.
6. Give examples of how DNA typing has been used in Anthropology.
7. Give examples of how DNA typing has been used for nonhuman identification and
studies.
8. Give examples of how DNA typing has been used for industry and environment.
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9. List examples of genetic disorders that currently can be tested for using DNA typing.
10. Describe examples of forensic uses of DNA typing.
11. Other than forensic uses, how else may human identity testing be used?
12. How can DNA testing be used to diagnose infectious disease?
Internet Reading Instructions and Questions
Two Readings 1: Read both of the online readings below:
1. http://www.dnai.org/d/index.html (Click on “Recovering the Romanovs” and read
all pages in “The Romanov Family”, The Mystery of Anna Anderson, and
“Science Solves a Mystery”).
2. Analysis of the Romanov Remains
Describe the the types of DNA evidence used to determine that the three girls in the grave
were the daughters of the Tsar and Tsarina?
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Readings 2: Thomas Jefferson and Sally Hemings
1) For the story concerning Thomas Jefferson and Sally Hemings, view all of the videos
on this site: http://www.pbs.org/wgbh/pages/frontline/shows/jefferson/view/
2) http://www.monticello.org/plantation/hemingscontro/hemings-jefferson_contro.html
1. What chromosome was used for DNA testing to determine if Sally Hemings’
descendents were related to Thomas Jefferson?
2. How could they use this chromosome if Thomas Jefferson had no male children?
3. Why isn’t the DNA test absolute proof that Thomas Jefferson, himself, was the father
of Sally Hemings’ youngest son?
Reading 3: Click here to read about DNA testing of the Y chromosome.
1. The Y chromosome contains STRs.
a. True
b. False
2. The Y chromosome has a low mutation rate. Therefore, mutations on the Y chromosome
represent a record of its evolutionary past, and are used to assist genealogists and
archeologists in their research. As long as a mutation does not affect the individual's
ability to reproduce, it may be preserved and handed down to offspring. An exchange of a
single DNA building block (i.e., a nucleotide) with another is called a Single Nucleotide
Polymorphism (SNP), or a point mutation. Different combinations of polymorphisms on
the Y chromosome are known as
.
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Reading 4: Neanderthals and Modern Humans Scroll to the top and read the entire
article.
http://www.talkorigins.org/faqs/homs/mtDNA.html#more
1. Researchers have obtained and tested the DNA of Neanderthals.
a. True
b. False
2. What type of DNA is used to compare Neanderthal DNA to ours?
3. Why is it easier to use mtDNA rather than nuclear DNA in ancient samples?
4. List some reasons why some researchers feel that Neanderthals were NOT the ancestors of modern
humans or the same species?
Reading 5: Neanderthal DNA Sequenced
NeanderthalDNASequenced.doc
How is this study of Neanderthal DNA different from the previous study?
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