DNA Forensics – Episode #001

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Episode Summary

Reginald discusses the development of DNA forensics with Dr. Steven Strangelove and statisical lawyer Eleanor Lestrade. They discuss the different types of DNA analysis (VNTR, STR, and RLFP), DNA augmentation via PCR, and gel electrophoresis for DNA visualization. They then dig into the gritty matters of the CODIS system and privacy concerns as well. To top of the show, Reginald uses his newfound knowledge to solve a murder case at UBC-Okanagan.

UBC-Okanagan Image
UBC0-Okanagan: Picturesque setting of a grisly laboratory murder investigated on this week’s show. Photo copyright UBC.

Supporting Information

Additional graphics and supporting information as discussed in the show are here to support your understanding of this subject matter.

Figure 1: Image of gel electrophoresis in 1% agarose solution resulting from Cyber Green dye fluorescing under UV viewer.  Samples were treated using RFLP analysis of blood samples found in UBC-Okanagan murder scene.  From left to right, wells are Crime Scene DNA, suspect 4 (Fiona Jensen), Suspect 3 (Brian Mulroney), Suspect 2 (Ludwig Bennison), Suspect 1 (Janessa Wright), and the last well is the DNA ladder. The DNA fingerprint of the crime scene and Suspect C match, while all other samples are very different indicating that Suspect C committed the crime.</p class=”figure-table”>

Figure 2: Image of gel electrophoresis result in 3% agarose gel of DNA visualized using Cyber Green dye fluorescing under UV light taken with an exposure of 0.600s.  From left to right, bands are TH01 DNA Ladder, Crime Scene STR-PCR, Suspect 1 (Janessa Wright) STR-PCR, Suspect 2 (Ludwig Bennison) STR-PCR, Suspect 3 (Brian Mulroney) STR-PCR, Suspect 4 (Fiona Jensen) STR-PCR, DNA Analyst 1 VNTR-PCR, DNA Analyst 2 VNTR-PCR, VNTR-PCR Positive Control, and lastly the EdvoQuick DNA ladder.  Based on the above image, the VNTR analyst samples failed to be processed properly, while the positive control functioned properly suggesting that the DNA sampling method for VNTR was poor. The crime scene VNTR-PCR matches with Suspect 3, Brian Mulroney, suggesting that he committed the murder.  All other VNTR-PCR samples are vastly different from the crime scene DNA, suggesting their innocence in the murder.</p class=”figure-table”>

From the image of gel electrophoresis in 1% agarose gel solution (Figure 1), Restriction Fragment Length Polymorphism (denoted as RFLP) analysis was used to identify fragmentation pattern of DNA. The DNA ladder used for RFLP analysis in the lab was digested phage λ DNA, which yielded 6 fragments when cut with restriction enzyme (RE) HindIII. Table 1 represents the distance traveled by the DNA fragments from the wells of the gel, as well as the corresponding band sizes. From this data, Figure 3 was used to demonstrate the relationship between band size and the DNA fragmentation pattern. The equation displayed was used to calculate fragment size, which allows us to compare the crime scene and suspect DNA profiles to find the murderer.

Table 1: The DNA fragments visualized by gel electrophoresis. The corresponding band sizes (in base pairs) were retrieved from D’Souza & Plunkett, 2019.</p class=”figure-table”>

Distance traveled on gel (mm)

Band Size (in base pairs)

9

23130

12

9416

13.5

6557

20

4361

21

2322

32.5

2027

Figure 3: Represents the relationship of distance traveled on gel by DNA fragments and their corresponding band size in base pairs. The equation derived from the exponential trendline is used to calculate fragment size of the bands, which was used to compare crime scene and suspect profiles. The murderer identified in the case study was suspect 3, Brian Mulroney.</p class=”figure-table”>

The fragment sizes of the suspects compared to the crime scene DNA is shown in Table 2. It was found to be that Suspect 3 and the crime scene profile matched, and therefore Brian Mulroney was identified as the murderer of this case.

Table 2: The fragmentation sizes of the fragmentation patterns of crime scene, suspect 1, suspect 2, suspect 3 and suspect 4 DNA profiles. The comparison of these fragmentation sizes allows us to identify suspect 3 as the murderer when compared to the crime scene data.</p class=”figure-table”>

Crime Scene

Suspect 1

Suspect 2

Suspect 3

Suspect 4

Fragmentation Size (BP)

5786

4775

1743

4775

3941

2012

7717

6369

5514

3941

2684

5786

4775

1743

4551

2215

1131

Short Tandem Repeats denoted as STR, represents the number of repeats inherited you’re your mom and dad. It is known that different STR values at one locus indicates the parents had a different number of repeats at the locus, and the same values tells us the parents has the same number of repeats on the locus. In the lab a simulation TH01 allele ladder was used for STR analysis, where the bands represent alleles with certain number of repeats. This analysis looks at the TH01 locus of the suspects and crime scene DNA profiles. Table 3 illustrates the TH01 genotypes of the suspects 1-4 compared to the crime scene DNA.

Table 3: The STR analysis of the TH01 locus in suspects and crime scene DNA. The comparison of allele repeats allowed us to further identify suspect 3 as a match for the crime scene DNA collected.</p class=”figure-table”>

Crime Scene

Suspect 1

Suspect 2

Suspect 3

Suspect 4

TH01 genotype

5,8 genotype

5,9 genotype

4,7 genotype

5,8 genotype

4,9 genotype

In the lab, Variable Number Tandem Repeats (VNTR) analysis was used on our check cells by amplifying the D1S80 locus via Polymerase Chain Reaction (PCR). Referring to Figure 2, the right most lane, the EdvoQuick DNA ladder was used to conduct VNTR analysis.

Figure 4: Represents the relationship of distance travelled on gel by DNA fragments and their corresponding band size in base pairs. The equations derived from the exponential trendlines is used to calculate fragment size of the bands. The orange trendline equation represents the Edvoquick DNA ladder used to compare crime scene data in VNTR analysis. The blue trendline equation represents the Edvoquick DNA ladder used to compare sample students in VNTR analysis. Data results were retrieved from D’Souza & Plunkett, 2019.

The first sample student (AF) and sample student 2 (AA) data was retrieved from Sample VNTR results from the UBC Okanagan Bioc 393 Canvas website (D’Souza & Plunkett, 2019). The measurements of band sizes of sample students were used to identify fragmentation size, genotype at the D1S80 locus, and allelic frequency. This data was compared to the crime scene DNA profile, shown in Table 4.

Table 4: The sample students (AF) and second sample student (AA) are analyzed via VNTR on the D1S80 locus. This data allowed us to find the D1S80 locus genotype. The fragmentation size, and therefore genotype differ between the student samples and the crime scene genotype. Allele Frequency of the students and crime scene is also displayed.

Sample

Distance travelled on gel (mm)

Fragmentation Size (BP)

Genotype at D1S80 (number of repeats)

Allele Frequency

AF

24

421

17

0.0143

AA

23.5

441

19

0.0049

CS

35

44.5

636

384

30

15

0.0283

0.0015

The Random Match Probability test denoted as RMP calculates the probability of a genetic match by chance. Below, you can find the RMP calculation of the TH01 loci and the D1S80 loci of the crime scene DNA allelic frequencies. The heterozygote and homozygote equations were retrieved from the Crime Scene Investigation Pre-lab on UBC Okanagan Bioc 393 canvas website (D’Souza & Plunkett, 2019). These equations are derived from the Hardy-Weinberg equilibrium equation. Table 5 summarizes the crime scene values.

Table 5: A summary of the crime scene values used to calculate RMP.

CRIME SCENE DATA

Loci

Genotype

Allele Frequencies

TH01

5,8

0.019, 0.1255

D1S80

15

0.0015

Heterozygote locus RMP formula: 2pq. Retrieved from the Crime Scene Investigation Pre-lab on UBC Okanagan Bioc 393 canvas website (D’Souza & Plunkett, 2019).

2pq=2(0.019×0.1255)x(0.0015)=7.2E(-6)

Who Did It?

Based on the above results, and as discussed in the podcast, the murderer was Brian Mulroney.

Hearing Impaired Listeners

For all those who are hearing impaired, a written transcript of the podcast is available here.

References

Issan, Y., Avlas, O., & Daniel, O. (2018). Investigation of different ways in which the CODIS 7.0 may be used in mass disaster identification. Journal of Forensic Sciences, doi:10.1111/1556-4029.13915

Plunkett, R., D’Souza, B., Biochemistry 393 Lab Manual Labs 7 and 8 CSI. Kelowna, BC: UBC-Okanagan.

Walsh, P. S., Metzger, D. A., & Higuchi, R. (1991, April 1). Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques, 10(4), 506-513. Retrieved from https://europepmc.org/abstract/med/1867860

Acknowledgements:

The podcast makers would like to acknowledge the assistance of Alexander Corbett, Dylan Nemes, and Gurprett Saini in data collection.