1. DNA as Evidence

2. DNA: What is it? DNA = Deoxyribonucleic acid Structure: a long molecule of nucleotides Function: contains genetic information Found: nucleus of all cells NOTE: DNA can also be found in the mitochondria and is called mtDNA. This DNA is more resistant to breakdown, but only shows maternal linkage.

3. Evidence Nuclear DNA can be found in some materials found at a crime scene: mtDNA can be found in DNA must be extracted from such materials to be analyzed --Blood--Semen --Urine--Saliva --Hair follicles (root) --Bone--Hair--Teeth ***DNA extraction Demo***

4. Evidence HOW ARE DNA RESULTS USED IN INVESTIGATION? Identify a perpetrator in a crime Clear persons wrongly accused of a crime Identify fathers in paternity cases Identify unknown victims remains

5. Ways to analyze extracted DNA 1. RFLP (DNA fingerprinting) an entire DNA molecule = too complex to analyze completely Thus, in RFLP use restriction enzymes to cut DNA into fragments. Run fragments in gel electrophoresis Develop on film a column of banding patterns = DNA fingerprint NOTE: RFLP is one of the oldest forensic DNA techniques. However, it requires large sample sizes and does not work well on samples degraded by the environment (dirt, mold). http://maa.cam.ac.uk/assemblingbodies/exhibition/measurement/capacities/143 /

6. RFLP—DNA fingerprint Image from: http://science.howstuffworks.com/dna-profiling1.htm and

7. Ways to analyze extracted DNA 2. STR (short tandem repeats) “Junk DNA” = sequences that do not code for a gene and are unique to individuals Some junk DNA can have repeating sequences (GATA GATA GATA etc).... call them STR The number of these repeats per loci varies among people, thus we can analyze the VNTR or “variable number” tandem repeats per person. Will show as a DNA profile (see picture on next slide) NOTE: STR/VNTR can be done on small samples because can perform PCR (polymerase chain reaction) to amplify the sample. STR is used for CODIS.

8. Image from: http://dnaphenomena.blogspot.com/2011/05/dna-profiling.html DNA profile created by STR analysis

9. Activity to demonstrate the difference between RFLP (DNA fingerprint) and STR (DNA profile) Click on image or go to this link: http://www.dnai.org/d/index.html  students explore the activity individually or in pairs

10. 3. Karyotype =organized picture of chromosomes Useful how? if suspect has a genetic disorder, this is quick way to analyze if evidence sample is a match one way identify if blood sample is human NOTE:(Human karyotype = 23 pairs of chromosomes, or 46 total chromosomes) Ways to analyze extracted DNA

11. Karyotypes a) Human? b) Male or Female? c) Genetic Disorder? 1. Answers: -human -female -no disorder

12. Karyotypes a) Human? b) Male or Female? c) Genetic Disorder? 2. Answer: -Human -Male -Genetic Disorder (Klinefelter Syndrome) Learn about Klinefelter Syndrome

13. Karyotypes a) Human? b) Male or Female? c) Genetic Disorder? 3. Answers: -not human (dog) -male -no disorder

14. CODIS =COmbined DNA Index System It is an FBI database that catalogs DNA analyzed using STR Standard 13 specific STR regions used Odds of 2 people have the same 13-loci DNA profile= 1 in a billion Two parts to CODIS  1. Convicted Offender Index: contains DNA profiles of convicted sex offenders and other violent crimes  2. Forensic Index: contains DNA from the crime scene Information from: http://www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics.shtml Image above and Article about DNA database http://www.nytimes.com/2009/04/19/us/19DNA.html

15. More on DNA...

16. DNA identification can be quite effective if used intelligently. Portions of the DNA sequence that vary the most among humans must be used. Consider the scenario of a crime scene investigation... Assume that type O blood is found at the crime scene. Type O occurs in about 45% of Americans. If investigators type only for ABO, finding that the "suspect" in a crime is type O really doesn't reveal very much. If, in addition to being type O, the suspect is a blond, and blond hair is found at the crime scene, you now have two bits of evidence to suggest who really did it. However, there are a lot of Type O blonds out there. If you find that the crime scene has footprints from a pair of Nike Air Jordans (with a distinctive tread design) and the suspect, in addition to being type O and blond, is also wearing Air Jordans with the same tread design, you are much closer to linking the suspect with the crime scene. In this way, by accumulating bits of linking evidence in a chain, where each bit by itself isn't very strong but the set of all of them together is very strong, you can argue that your suspect really is the right person. With DNA, the same kind of thinking is used; you can look for matches (based on sequence or on numbers of small repeating units of DNA sequence) at many different locations on the person's genome; one or two (even three) aren't enough to be confident that the suspect is the right one, but thirteen sites are used. A match at all thirteen is rare enough that you (or a prosecutor or a jury) can be very confident ("beyond a reasonable doubt") that the right person is accused. http://www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics.shtml Is DNA effective in identifying persons?

17. Because we are the same species, 99.9 percent of human DNA is the same in everyone, thus only 0.1 percent of our DNA is unique ! Each human cell contains three billion DNA base pairs. Our unique DNA, 0.1 percent of 3 billion, amounts to 3 million base pairs. This is more than enough to provide profiles that accurately identify a person. The only exception is identical twins, who share 100% identical DNA. Content from: http://learn.genetics.utah.edu/content/labs/gel/forensics/; Image from:http://ngm.nationalgeographic.com/2012/01/twins/miller-text 13 loci

18. In 1996, the FBI Laboratory established 13 STR loci (locations on chromosomes) for inclusion in a DNA fingerprint in CODIS. These are nationally/internationally recognized as the standard for human ID 13 loci Content and images from: http://www.forensicdnacenter.com/dna-str.html; http://www.dna.gov/dna-databases/codis

19. Each person’s DNA contains two copies of each chromosome and thus of each of the 13 loci, one from each parent. When determining the relationship between two individuals, their genetic profiles are compared to see if they share the same inheritance patterns at a statistically conclusive rate. For example...this sample report from a commercial DNA paternity testing laboratory signifies how relatedness between parents and child is identified on those special markers: This shows partial results—match among five markers The complete test results for this example—match on 16 markers between the child and the tested man to draw a conclusion of whether or not the man is the biological father. http://en.wikipedia.org/wiki/DNA_profiling#DNA_family_relationship_analysis DNA family relationship analysis Such as paternity, maternity, siblingship and other kinships DNA MarkerMotherChildAlleged father D21S1128, 3028, 3129, 31 D7S8209, 1010, 1111, 12 TH0114, 1514, 1615, 16 D13S3177, 87, 98, 9 D19S43314, 16.214, 1515, 17 The report shows the genetic profiles of each tested person. If there are markers shared among the tested individuals, the probability of biological relationship is calculated to determine how likely the tested individuals share the same markers due to a blood relationship (PI—paternity index and Probability of Paternity).

20. Y-STR = Short Tandem Repeats found on the male-specific Y Chromosome. The Y-STRs are inherited through the paternal line with little change through generations. Y-STRs have been used by forensic laboratories to examine sexual assault evidence. In a sexual assault case, evidence such as vaginal swabs will contain both female and male DNA. Since there is no Y-STR in the female evidence, the only contribution of Y-STR can only come from the assailant(s) in a sexual assault case. Y-STR is also used for non-sexual assault cases where mixed samples are collected from evidence. Content from: http://www.forensicdnacenter.com/dna-str.html; Images from: http://www.pearsall-family.org/PearsallDNASurnameProject.htm and http://www.cstl.nist.gov/strbase/ystrpos1.htm

21. Mitochondrial DNA (mtDNA) Unlike nuclear DNA, which is passed from both mother and father to the offspring, mitochondrial DNA (mtDNA) is maternally inherited. Content from: http://www.forensicdnacenter.com/mt-dna.html; Image from: http://www.ivfcenterhawaii.com/content/ivf_treatments/in_vitro_fertilization.html mtDNA is useful because... It is present in high copy number (many mitochondria within a cell, vs. one nucleus) It is not degraded as quickly

22. http://www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics. shtml http://www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics. shtml Learn more about DNA and forensics from the human genome project website

23. Blood Typing If samples of blood are present at a crime scene, blood typing can be done first. This process is quicker and cheaper than DNA fingerprinting. However it is only CLASS evidence so it will only get you so far.

24. WBC RBC Platelet

25. Most common blood type

29. Activities Cafeteria Capers Lab (http://www.nclark.net/Cafeteria_Caper.pdf) Recovering the Romanovs Exploration (http://www.dnai.org/d/index.html)

30. My notes...

31. Is DNA effective in identifying persons? [answer provided by Daniel Drell of the U.S. DOE Human Genome Program] DNA identification can be quite effective if used intelligently. Portions of the DNA sequence that vary the most among humans must be used; also, portions must be large enough to overcome the fact that human mating is not absolutely random. Consider the scenario of a crime scene investigation... Assume that type O blood is found at the crime scene. Type O occurs in about 45% of Americans. If investigators type only for ABO, finding that the "suspect" in a crime is type O really doesn't reveal very much. If, in addition to being type O, the suspect is a blond, and blond hair is found at the crime scene, you now have two bits of evidence to suggest who really did it. However, there are a lot of Type O blonds out there. If you find that the crime scene has footprints from a pair of Nike Air Jordans (with a distinctive tread design) and the suspect, in addition to being type O and blond, is also wearing Air Jordans with the same tread design, you are much closer to linking the suspect with the crime scene. In this way, by accumulating bits of linking evidence in a chain, where each bit by itself isn't very strong but the set of all of them together is very strong, you can argue that your suspect really is the right person. With DNA, the same kind of thinking is used; you can look for matches (based on sequence or on numbers of small repeating units of DNA sequence) at many different locations on the person's genome; one or two (even three) aren't enough to be confident that the suspect is the right one, but thirteen sites are used. A match at all thirteen is rare enough that you (or a prosecutor or a jury) can be very confident ("beyond a reasonable doubt") that the right person is accused. http://www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics.shtml

32. Almost every cell in our bodies contains DNA, the genetic material that programs how cells work. 99.9 percent of human DNA is the same in everyone, meaning that only 0.1 percent of our DNA is unique! Each human cell contains three billion DNA base pairs. Our unique DNA, 0.1 percent of 3 billion, amounts to 3 million base pairs. This is more than enough to provide profiles that accurately identify a person. The only exception is identical twins, who share 100 percent identical DNA. (http://learn.genetics.utah.edu/content/labs/gel/forensics/) Beginning in 1996, the FBI Laboratory launched a nationwide forensic science effort to establish core STR loci for inclusion within the national database known as CODIS (Combined DNA Index System). The 13 CODIS loci are CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51 and D21S11. These loci are nationally and internationally recognized as the standard for human identification. http://www.forensicdnacenter.com/dna-str.html To identify individuals, forensic scientists scan 13 DNA regions, or loci, that vary from person to person and use the data to create a DNA profile of that individual (sometimes called a DNA fingerprint). There is an extremely small chance that another person has the same DNA profile for a particular set of 13 regions 13 loci

33. DNA MarkerMotherChildAlleged father D21S1128, 3028, 3129, 31 D7S8209, 1010, 1111, 12 TH0114, 1514, 1615, 16 D13S3177, 87, 98, 9 D19S43314, 16.214, 1515, 17 DNA family relationship analysis Using PCR technology, DNA analysis is widely applied to determine genetic family relationships such as paternity, maternity, siblingship and other kinships.PCR During conception, the father’s sperm cell and the mother’s egg cell, each containing half the amount of DNA found in other body cells, meet and fuse to form a fertilized egg, called a zygote. The zygote contains a complete set of DNA molecules, a unique combination of DNA from both parents. This zygote divides and multiplies into an embryo and later, a full human being. At each stage of development, all the cells forming the body contain the same DNA—half from the father and half from the mother. This fact allows the relationship testing to use all types of all samples including loose cells from the cheeks collected using buccal swabs, blood or other types of samples. While a lot of DNA contains information for a certain function, there is some called junk DNA, which is currently used for human identification. At some special locations (called loci) in the junk DNA, predictable inheritance patterns were found to be useful in determining biological relationships. These locations contain specific DNA markers that DNA scientists use to identify individuals. In a routine DNA paternity test, the markers used are Short Tandem Repeats (STRs), short pieces of DNA that occur in highly differential repeat patterns among individuals.Short Tandem Repeats Each person’s DNA contains two copies of these markers—one copy inherited from the father and one from the mother. Within a population, the markers at each person’s DNA location could differ in length and sometimes sequence, depending on the markers inherited from the parents. The combination of marker sizes found in each person makes up his/her unique genetic profile. When determining the relationship between two individuals, their genetic profiles are compared to see if they share the same inheritance patterns at a statistically conclusive rate. For example, the following sample report from this commercial DNA paternity testing laboratory Universal Genetics signifies how relatedness between parents and child is identified on those special markers: The partial results indicate that the child and the alleged father’s DNA match among these five markers. The complete test results show this correlation on 16 markers between the child and the tested man to draw a conclusion of whether or not the man is the biological father. Scientifically, each marker is assigned with a Paternity Index (PI), which is a statistical measure of how powerfully a match at a particular marker indicates paternity. The PI of each marker is multiplied with each other to generate the Combined Paternity Index (CPI), which indicates the overall probability of an individual being the biological father of the tested child relative to any random man from the entire population of the same race. The CPI is then converted into a Probability of Paternity showing the degree of relatedness between the alleged father and child. The DNA test report in other family relationship tests, such as grandparentage and siblingship tests, is similar to a paternity test report. Instead of the Combined Paternity Index, a different value, such as a Siblingship Index, is reported. The report shows the genetic profiles of each tested person. If there are markers shared among the tested individuals, the probability of biological relationship is calculated to determine how likely the tested individuals share the same markers due to a blood relationship. http://en.wikipedia.org/wiki/DNA_profiling#DNA_family_relationship_analysis

34. Y-STR Y- STRs are Short Tandem Repeats (STRs, refer to the STR page for more details) found on the male-specific Y Chromosome. The coding genes, mostly found on the short arm of the Y Chromosome, are vital to male sex determination, spermatogenesis and other male related functions. The Y-STRs are polymorphic among unrelated males and are inherited through the paternal line with little change through generations.STR page Y-STRs have been used by forensic laboratories to examine sexual assault evidence. In a sexual assault case, evidence such as vaginal swabs will contain both female and male DNA. Differential extraction is often used to separate the male component from the female component. More often, however, the male and female components cannot be separated completely. As a result, the female component could exist prominently even in the male component after separation. When the "male DNA sample" undergoes the PCR amplification process, the female DNA component is amplified as well, sometimes masking the male DNA, which makes analysis difficult. Masking does not occur when Y-STRs are examined. Since there is no Y-STR in the female evidence, the only contribution of Y-STR can only come from the assailant(s) in a sexual assault case. The male component will be easily detected, since only this part of DNA will be amplified. The Y-STR system is especially helpful when there are more than one assailant. The mixed pattern in the evidence can help to identify those males responsible for the assault. Y-STR is also used for non-sexual assault cases where mixed samples are collected from evidence. Sometimes, regular STR will cause the masking effect if there is a very small quantity of male DNA in the mixed sample. Performing Y-STR testing can help to identify all males who have contributed to the evidence. http://www.forensicdnacenter.com/dna-str.html

35. mtDNA Mitochondrial DNA (mtDNA) Unlike nuclear DNA, which is passed from both mother and father to the offspring, mitochondrial DNA (mtDNA) is maternally inherited. At fertilization, the mtDNA, contained in the tail end of the spermatozoa, is never allowed to enter the ovum, deleting the male mtDNA information from the offspring's genome. Mitochondrial DNA is useful for forensic purposes because of two properties. First, part of the mitochondrial genome is highly polymorphic, making it useful for human identification. The two most variable regions known as HV1 and HV2 are usually amplified and sequenced to compare the difference between the evidence and reference samples. Secondly, although mtDNA comprises less than 1% of the total DNA within a cell, its genes exist in high amounts. Because mtDNA is present in high copy number, it is very useful when analyzing degraded samples or samples that lack nuclear DNA. One example is hair, which is a common item of evidence, especially when there is little or no root present to test. The examination of mtDNA in evidence such as bone and teeth, which may contain degraded DNA, can produce a satisfactory profile because of the high copy number of mitochondrial sequences. Mitochondrial DNA testing was performed in a number of high-profile cases such as the Boston Strangler, the Green River murders, and the Laci Peterson homicide. It is also used for historically important cases like the Romanovs and the unknown soldier from the Vietnam war. http://www.forensicdnacenter.com/mt-dna.html