DNA in Forensic Science

DNA in Forensic Science Quiz Crafted by-  

Dr. Ruchi Sharma

Forensic Examiner/Reporting Officer (DNA)

Forensic Science Laboratory

Rohini, Delhi.

Introduction to DNA in Forensic Science with a Case Study 

His name Colin Pitchfork might not be as recognizable as Charles Manson or Jeffrey Dahmer. But for those in the forensic science community, it’s a name that holds weight. Pitchfork was the first murderer to be caught using DNA analysis. When 15-year-old Dawn Ashworth was raped and murdered in Leicestershire, England, in late July 1986, Alec Jeffreys was a genetics professor at the nearby University of Leicester. A few years earlier, he had discovered that patterns in some regions of a person’s DNA could be used to distinguish one individual from another. So far, Jeffreys had put his DNA pattern recognition technique to work in paternity and immigration cases, but now the police wanted him to help solve Ashworth’s murder as well as a similar one that happened in 1983. The police already had a suspect, Richard Buckland, who had even confessed to Ashworth’s murder. When Jeffreys analyzed DNA samples from the 1983 and 1986 crime scenes and from Buckland, he found matching DNA from both crime scenes—but the recovered DNA didn’t match Buckland’s genetic code.

In an attempt to find the real culprit—the one whose DNA had been left behind—the police undertook a genetic dragnet. They obtained blood and saliva samples from more than 4,000 men in the Leicestershire area between the ages of 17 and 34 and had Jeffreys analyze the DNA. They didn’t find a match until a man was overheard saying he’d been paid to pose as someone else and provide false samples. The person trying to evade the DNA dragnet was Colin Pitchfork. When Pitchfork’s DNA was analyzed, it matched the crime scene samples. Pitchfork was arrested on Sept. 19, 1987, and convicted and sentenced to life in prison the following January.

Although DNA evidence alone is not enough to secure a conviction today, DNA profiling has become the gold standard in forensic science since that first case 30 years ago. Despite being dogged by sample processing delays because of forensic lab backlogs, the technique has gotten progressively faster and more sensitive: Today, investigators can retrieve DNA profiles from skin cells left behind when a criminal merely touches a surface. This improved sensitivity combined with new data analysis approaches has made it possible for investigators to identify and distinguish multiple individuals from the DNA in a mixed sample. And it’s made possible efforts that are under way to develop user-friendly instruments that can run and analyze samples in less than two hours.

Characterization, or ''typing," of blood, semen, and other body fluids has been used for forensic purposes for more than 50 years. It began with blood groups, such as those of the ABO system, and later was extended to serum proteins and red-cell enzymes and in some forensic applications, particularly paternity testing, to human leukocyte antigens (HLA) , which are associated with tissue types. The genetically determined person-to-person variation revealed by such typing was used mainly to include or exclude suspects, that is, to determine whether a person showed a combination of genetically determined characteristics consistent with having been the source of an evidence sample in a criminal case or having been the father of a child in a paternity case. Except when HLA testing was used, the chance that a randomly chosen person would be excluded by the tests was about 98%; that left a 2% chance that the test would "include" an innocent person.

In the last decade, methods have become available for deoxyribonucleic acid (DNA) typing, that is, for showing distinguishing differences in the genetic material itself. Advances in DNA technology in the 1970s paved the way for the detection of variation (polymorphism) in specific DNA sequences and shifted the study of human variation from the protein products of DNA to DNA itself. By analyzing a sufficient number of regions of DNA that show much person-to-person variability, one can reduce the probability of a chance match (inclusion) of two persons to an extremely low level. Indeed, the probability can, in principle, be made so low that DNA typing becomes not simply a method for exclusion or inclusion, but a means of absolute identification.

Here is the List of Questions with Answers along with explanation

Que 1. In which year was the Human Genome Project completed?

a) 1999                                   

b) 2000                                   

c) 2002                       

d) 2003

Answer: (d) 2003

Explanation: The Human Genome Project (HGP) was one of the great feats of exploration in history. Rather than an outward exploration of the planet or the cosmos, the HGP was an inward voyage of discovery led by an international team of researchers looking to sequence and map all of the genes together known as the genome of members of our species, Homo sapiens. Beginning on October 1, 1990 and completed in April 2003, the HGP gave us the ability, for the first time, to read nature's complete genetic blueprint for building a human being.

Que 2. Base pairs found in single copy of human genome are

a) 3 billion                  

b) 1 billion                  

c) 4 billion                  

d) 3 million

Answer: (a) 3 billion

Explanation: The bases are adenine (A), thymine (T), guanine (G) and cytosine (C). Bases on opposite strands pair specifically; an A always pairs with a T, and a C always with a G. The human genome contains approximately 3 billion of these base pairs, which reside in the 23 pairs of chromosomes within the nucleus of all our cells

Que 3. Phenol chloroform extraction is also known as

a) Inorganic extraction     

b) Organic extraction

c) Chelex extraction      

d) Differential extraction

Answer: ( b) Organic extraction

Explanation: phenol–chloroform extraction also called as Organic extraction uses sodium dodecylsulfate (SDS) and proteinase K for the enzymatic digestion of proteins and nonnucleic acid cellular components. A mixture of phenol:chloroform:isoamyl alcohol (25:24:1) is then added to promote the partitioning of lipids and cellular debris into the organic phase, leaving isolated DNA in the aqueous phase. Following centrifugation, the aqueous phase containing the purified DNA can be transferred to a clean tube for analysis. DNA can also be recovered and concentrated from the aqueous phase by ethanol precipitation or through the use of a centrifugal filter unit which allows for additional purification and concentration of the DNA in the samples. Organic extraction recovers double-stranded DNA and was required for early RFLP methods. 

Que 4. Which of the following are PCR inhibitors?

a) Heme                      

b) Indigo dye             

c) Melanin from hair          

d) All of the above

Answer: (d) All of the above

Explanation: Common sample types known to contain inhibitors include blood, fabrics, tissues and soil. Other important sources of inhibitors are the materials and reagents that come into contact with samples during processing or DNA purification. These include excess KCl, NaCl and other salts, ionic detergents such as sodium deoxycholate, sarkosyl and SDS, ethanol and isopropanol, phenol  and others. In bellow figure it is shown that Heam, Indigo dye and melanin all are PCR inhibitor.

Que 5. What is the other name of ‘molecular xeroxing’?

a) PCR                                   

b) RT-PCR                 

c) Electrophoresis       

d) RFLP

Answer: (a) PCR

Explanation: The polymerase chain reaction (PCR) is Sometimes called as "molecular photocopying, or molecular xeroxing" is a fast and inexpensive technique used to "amplify" - copy - small segments of DNA

Que 6. Markers for human identification (STRs) are found in which region of DNA?

a) Coding                   

b) Noncoding             

c) Exons                     

4) HLA DQA1

Answer: (b) Noncoding

Explanation: Short tandem repeats (STRs), also known as microsatellites or simple sequence repeats, are short tandem repeated DNA sequences that involve a repetitive unit of 1-6 bp, forming series with lengths of up to 100 nucleotides (nt). STRs are widely found in prokaryotes and eukaryotes, including humans. They appear scattered more or less evenly throughout the human genome, accounting for about 3% of the entire genome. However, their distribution within chromosomes is not quite uniform—they appear less frequently in sub-telomeric regions. Most STRs are found in the noncoding regions, while only about 8% locate in the coding regions 

Que 7. One turn of DNA spiral has how many nucleotides?

a) 10                           

b) 12                           

c) 14                           

d) 15

Answer: (a) 10

Explanation: The variation of energy with the twist of the base pairs about the helix axis shows the straight DNA free in solution is most stable with about 10 1/2 base pairs per turn rather than 10 as observed in the solid state, whereas superhelical DNA in chromatin is most stable with about 10 base pairs per turn

Que 8. Who described the double helical structure of DNA?

a) Kary Mullis            

b) Alec Jeffery                       

c) Watson & Crick     

d) A. Kornberg

Answer: (c) Watson & Crick

Explanation: The double helix is a description of the molecular shape of a double-stranded DNA molecule. In 1953, Francis Crick and James Watson first described the molecular structure of DNA, which they called a "double helix,"

Que 9. Applications of Y chromosome typing in forensic science is

a) Can be done when male is azoospermic

b) Verification of amelogenin Y deficient males

c) In gang rape cases

d) all of the above

Answer: (d) all of the above

Explanation: The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, One of the limiting factors for clarifying rape crimes is the lack of spermatozoa collected fromvaginal material, which makes the identification of genetic material from the perpetrator difficult. This difficulty is even greater in cases of azoospermic individuals where the loss of viable sperm in the semen is related to the individual’s constitution or due to elective surgery; vasectomy. The Y-chromosome short tandem repeat (STR) typing has become an important tool in forensic analysis, first because of the ease of amplification of male DNA from a mixed sample when one of the donors is a male, and the other a female, even when the concentration of female DNA is much higher than that of the male and second, because it bypasses the need for carrying out the differential extraction of sperm and nonsperm material. In cases where multiple males are con- tributors, for example gang rape, the number of donors can be estimated because of the haploid nature of Y-STRs. Also this technique can be used in cases of Y deficient made by amelogenin typing.

Que 10. If a wife carrier for haemophilia marries a normal man what percentage of children will be haemophilic?

a) 100%                                  

b) 75%                        

c) 50%                        

d) 25%

Answer: (d) 25%

Explanation: Haemophilia is a X-linked recessive disorder. One copy of the affected gene in males in each cell is sufficient to cause the disorder (XhY). Females with two copies of the affected gene show the disorder (XhXh). Females heterozygous (XhX) for this trait be normal but serve as a carrier of the disease. According to the question, the female is carrier for colour blindness (XhX) and father is normal (XY).  Hence, 25% of the of all children will have haemophilia. 

Que 11. What is the natural function of restriction enzymes?

a) Protecting bacteria by cleaving the DNA of infecting viruses.

b) Protecting bacteria by cleaving their own DNA

c) Protecting bacteria by methylating their own DNA

d) Protecting bacteria by methylating the DNA of infecting viruses.

Answer: (a) Protecting bacteria by cleaving the DNA of infecting viruses.

Explanation: Restriction enzyme, also called restriction endonuclease, a protein produced by bacteria that cleaves DNA at specific sites along the molecule. In the bacterial cell, restriction enzymes cleave foreign DNA, thus eliminating infecting organisms.

Que 12. Which of the following is not a suggested precaution when taking samples of DNA at a crime scene?

a) Wear gloves & change them often.

b) Avoid touching any area where DNA evidence may exist.

c) Air-dry evidence before packaging evidence

d) Use plastic bags

Answer: (d) Use plastic bags

Explanation: It may be impossible to completely eliminate crime scene contamination. And Crime Scene Officers are not the only ones to blame. When first responders arrive at a scene, their responsibility is to the victim(s) and not the preservation of evidence. There's simply no way to account for all the possibilities.

But precautions can and should be taken. The National Criminal Justice Reference Service (NCJRS) outlines the following tips for preventing evidence contamination:

1. Wear gloves and change them often

2. Use disposable instruments or clean them thoroughly before and after handling each sample

3. Avoid touching the area where DNA may exist

4. Avoid talking, sneezing, and coughing over evidence

5. Avoid touching your face, nose, and mouth when collecting and packaging evidence

6. Air-dry evidence thoroughly before packaging

7. Put evidence into new paper bags or envelopes, not into plastic bags, and don't use staples"

Crime Scene Officers should also use different tools—tweezers, fingerprint brushes and powders, swabs—at every scene. Hence D is the correct option. 

Que 13. The tracking dye in agarose gel electrophoresis of DNA is

a) Bromophenol blue         

b) Ethidium bromide         

c) Giemsa                   

d) Commassie blue

Answer: (a) Bromophenol blue       

Explanation: The tracking dyes are xylene cyanol FF (4 kB) and bromphenol blue (300 bp) or orange G (50 bp) in a 50% glycerol solution. Adding tracking dye to the sample will increase its density so it falls into the well of the gel and provides a visible marker to monitor the progress of electrophoresis.

Que 14. Which of the following is not a component of PCR reaction mix?

a) Template DNA             

b) Primers                         

c) dNTPs                         

d) LIZ

Answer: (d) LIZ

Explanation: Following are the component of PCR typing.

DNA template- the sample DNA that contains the target sequence. At the beginning of the reaction, high temperature is applied to the original double-stranded DNA molecule to separate the strands from each other.

DNA polymerase- a type of enzyme that synthesizes new strands of DNA complementary to the target sequence. The first and most commonly used of these enzymes isTaqDNA polymerase (fromThermis aquaticus), whereasPfuDNA polymerase (fromPyrococcus furiosus) is used widely because of its higher fidelity when copying DNA. Although these enzymes are subtly different, they both have two capabilities that make them suitable for PCR: 1) they can generate new strands of DNA using a DNA template and primers, and 2) they are heat resistant.

Primers- short pieces of single-stranded DNA that are complementary to the target sequence. The polymerase begins synthesizing new DNA from the end of the primer.

Nucleotides (dNTPs or deoxynucleotide triphosphates)- single units of the bases A, T, G, and C, which are essentially "building blocks" for new DNA strands.

Que 15. Replication of chromosomes occurs during which phase of cell cycle?

a) S phase                   

b) Metaphase              

c) Telophase               

d) Anaphase

Answer: (a) S phase

Explanation: Fortunately, our cells have defense mechanisms to shield us from these damaging events. In the eukaryotic cell cycle, chromosome duplication occurs during "S phase" (the phase of DNA synthesis) and chromosome segregation occurs during "M phase" (the mitosis phase)