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Quiz: Forensic DNA Profiling

Test your understanding of DNA structure, STRs, PCR amplification, electropherogram interpretation, and random match probability with these questions.

1. What makes Short Tandem Repeats (STRs) particularly well-suited for forensic DNA profiling compared to other regions of the genome?

  1. STRs are found only in criminals' DNA, making them uniquely diagnostic for criminal investigations
  2. STRs are highly polymorphic (many alleles exist), short enough to amplify from degraded DNA, and PCR amplification is well-standardized globally
  3. STRs are located on mitochondrial DNA, giving them the high copy number needed for trace evidence analysis
  4. STRs encode proteins that can be matched to tissue type, allowing both identity and body part identification
Show Answer

The correct answer is B. STRs are ideal forensic markers for three reasons: (1) they are highly polymorphic — many different allele sizes (repeat counts) exist in the population, giving statistical power; (2) they are short (100–400 base pairs) — small enough to be amplified even from degraded DNA; and (3) PCR amplification of STRs is reliable and globally standardized, allowing profiles to be compared across jurisdictions. STRs are found in all human DNA and are located primarily in non-coding regions of nuclear chromosomes.

Concept Tested: Short Tandem Repeats (STRs)

2. During PCR amplification, DNA denaturation occurs at approximately 94–96°C. What happens to the DNA molecule at this temperature?

  1. The DNA molecule is degraded into individual nucleotides, which are then reassembled by DNA polymerase
  2. Hydrogen bonds between complementary base pairs break, causing the double helix to separate into two single strands
  3. The primers bind to the target region of the DNA, marking the sites where new strand synthesis will begin
  4. Taq polymerase begins synthesizing new DNA strands using the existing strands as templates
Show Answer

The correct answer is B. Denaturation in PCR occurs at approximately 94–96°C — high enough to break the hydrogen bonds between complementary base pairs (A-T and G-C), causing the double-stranded DNA helix to "melt" open into two separate single strands. Each single strand then serves as a template for new strand synthesis. The DNA is not degraded — the covalent bonds within each strand remain intact. Taq polymerase is heat-stable specifically because it must withstand this high denaturation temperature.

Concept Tested: DNA Denaturation

3. In capillary electrophoresis, smaller DNA fragments migrate faster than larger ones. What is the practical result of this size-based separation?

  1. Smaller fragments are selectively destroyed, leaving only large allele sizes on the electropherogram
  2. DNA fragments are separated by size, so alleles from different STR loci with different repeat counts appear at different positions on the electropherogram
  3. Fragments are separated by electrical charge, allowing positively charged alleles to be distinguished from negatively charged ones
  4. Smaller fragments travel to the negative electrode and larger fragments to the positive electrode, creating two separate electropherograms
Show Answer

The correct answer is B. In capillary electrophoresis, all DNA fragments carry negative charges and migrate toward the positive electrode, but smaller fragments move faster through the gel matrix than larger ones. This separates STR alleles — which differ by the number of repeat units (and therefore by size) — into distinct peaks at different positions on the x-axis of the electropherogram. The horizontal position of each peak identifies the allele size (in base pairs), and the fluorescent dye color distinguishes which STR locus the peak belongs to.

Concept Tested: Capillary Electrophoresis

4. A forensic analyst reads an electropherogram and sees a single peak at a CODIS locus. What does a single peak at a given locus most likely indicate?

  1. The sample is contaminated, because all individuals should show two different peaks at every locus
  2. The PCR amplification failed for that locus, so only one allele was successfully amplified
  3. The individual is homozygous at that locus — they inherited the same number of STR repeats from both parents
  4. The sample is from a female, because women only inherit one allele at each autosomal locus
Show Answer

The correct answer is C. A single peak at a CODIS locus indicates homozygosity — the individual inherited the same allele size (same number of STR repeats) from both parents. Both alleles are the same size, so they migrate to the same position and appear as one peak. A heterozygous individual has two different allele sizes and shows two peaks. Single peaks can also result from PCR or amplification failures (allelic dropout), which analysts must distinguish from true homozygosity using quality control procedures.

Concept Tested: Homozygous vs Heterozygous

5. Mitochondrial DNA (mtDNA) is particularly useful for analyzing hair shafts without a root. What property of mtDNA explains this advantage?

  1. mtDNA is located in the cell nucleus, where it is better protected from environmental degradation than nuclear DNA
  2. mtDNA has a high copy number — each cell contains hundreds to thousands of mitochondria — providing abundant template even in cells with minimal nuclear DNA
  3. mtDNA is double-stranded like nuclear DNA but uses a different base pairing system that is more resistant to degradation
  4. mtDNA carries the complete human genome, making it a reliable backup when nuclear DNA is unavailable
Show Answer

The correct answer is B. Mitochondrial DNA is present in the cytoplasm of cells in hundreds to thousands of copies per cell (one copy per mitochondrion, many mitochondria per cell). In contrast, nuclear DNA is present in only two copies per nucleated cell. Hair shafts without roots contain very few or no nucleated cells, but still contain mitochondria. The high copy number of mtDNA means enough template remains even in extremely degraded, old, or cell-poor samples. The tradeoff is that mtDNA cannot uniquely identify an individual — only maternal lineage.

Concept Tested: Mitochondrial DNA

6. Y-STR analysis is especially valuable in sexual assault cases involving mixed biological samples. Why?

  1. Y-STRs are amplified with higher efficiency than autosomal STRs, giving better results from small samples
  2. Y-STR analysis detects only male-derived DNA, allowing a male contributor's profile to be obtained from a mixture that contains far more female DNA
  3. Y-STRs are present in sperm cells only, so they confirm the presence of semen without requiring a PSA test
  4. Y-STR profiles can uniquely identify a male individual, providing stronger evidence than autosomal STRs
Show Answer

The correct answer is B. In sexual assault cases, the biological sample often contains a mixture dominated by the victim's DNA (female) with a small proportion of the male contributor's DNA. Y-STR analysis targets STR loci on the Y chromosome — which is present only in males. This allows the male contributor's Y-STR profile to be obtained even when autosomal STR analysis fails or produces an uninterpretable mixture. The limitation is that Y-STRs cannot uniquely identify an individual — all patrilineally related males share the same Y-STR haplotype.

Concept Tested: Y-STR Analysis

7. The product rule is used to calculate the random match probability (RMP) from a multi-locus DNA profile. What statistical assumption allows the genotype frequencies at each locus to be multiplied together?

  1. All STR loci are located on the same chromosome, so their inheritance is perfectly correlated
  2. The CODIS loci are on different chromosomes or sufficiently far apart, so they segregate independently and their frequencies can be multiplied
  3. Population databases have proven that STR allele frequencies are identical across all human ethnic groups
  4. The product rule applies because PCR amplification produces equal numbers of copies from every allele at every locus
Show Answer

The correct answer is B. The product rule requires statistical independence between loci. The CODIS STR loci were selected specifically because they are located on different chromosomes (or sufficiently far apart on the same chromosome) that they segregate independently during meiosis. Because the allele frequency at one locus is not correlated with the allele frequency at another, the probability of matching at multiple loci can be calculated by multiplying the individual locus frequencies — yielding the combined random match probability.

Concept Tested: Product Rule in Statistics

8. A crime scene DNA profile matches a suspect at three loci with genotype frequencies of 0.10, 0.05, and 0.08. What is the random match probability?

  1. 1 in 23 — the three frequencies are added together and then inverted
  2. 1 in 2,500 — the product 0.10 × 0.05 × 0.08 = 0.0004, which is approximately 1 in 2,500
  3. 1 in 250 — the product is 0.004 at three loci when standard population corrections are applied
  4. 1 in 25,000 — the product rule uses the square root of each frequency for heterozygous loci
Show Answer

The correct answer is B. Applying the product rule: 0.10 × 0.05 × 0.08 = 0.0004 = 1 in 2,500. This means that approximately 1 in every 2,500 unrelated individuals in the reference population would be expected to share this same three-locus profile by chance. Note that this calculation covers only 3 of 20 CODIS loci — a complete 20-locus profile would yield an RMP in the range of 1 in quintillions, making accidental matches essentially impossible.

Concept Tested: Random Match Probability

9. CODIS uses 20 core STR loci plus the amelogenin marker. What does the amelogenin marker determine?

  1. The approximate age of the DNA donor by measuring telomere length at the amelogenin locus
  2. The ethnic background of the DNA donor based on population-specific allele frequencies
  3. The biological sex of the DNA donor — XX = female, XY = male — based on the sex chromosome-specific amplification product sizes
  4. Whether the DNA sample has been degraded, since amelogenin is the most stable STR locus in the CODIS panel
Show Answer

The correct answer is C. The amelogenin marker is amplified from sequences on both the X and Y chromosomes, but the X-chromosome version produces a slightly different size product than the Y-chromosome version. Females (XX) show only the X-type peak; males (XY) show both X and Y peaks. This provides biological sex determination from a DNA sample, which is a useful supplementary piece of information in forensic cases. Amelogenin does not determine age, ethnicity, or DNA quality.

Concept Tested: CODIS Loci

10. After PCR amplification in the annealing step (approximately 55–65°C), what happens, and why is primer design critical to the specificity of DNA profiling?

  1. DNA polymerase binds to the template and begins synthesizing new DNA strands without directional guidance
  2. Primers bind to their complementary sequences flanking the target STR locus; locus-specific primer sequences ensure only the desired region is amplified
  3. The temperature causes all non-target DNA sequences to denature while leaving the STR loci intact
  4. Fluorescent dyes are incorporated into the new DNA strands, marking each amplified fragment for detection
Show Answer

The correct answer is B. During annealing, the temperature drops to 55–65°C so that short primer sequences can bind to their complementary sequences on the single-stranded template DNA. Primers are designed to be complementary only to the sequences flanking a specific STR locus — one primer on each strand. This specificity means DNA polymerase in the extension step will only copy the target region. In forensic multiplex PCR kits, primers for all 20 CODIS loci are included simultaneously, and the specific primer sequences ensure each locus is amplified independently and correctly.

Concept Tested: DNA Annealing