DNA Profiling

What do you think of when you hear the three letters DNA? Do you think of genetics, labs, or perhaps something else? Well, you probably think of something at least remotely scientific because you have probably previously learned that DNA carries the genetic information of living beings. DNA is the basis of how our genes are transferred from generation to generation. Since DNA makes up almost all living organisms, we can use DNA to create genetically modified organisms, study diseases, profile humans, and even figure out lineages. Keep reading to get more clues about how researchers and forensic scientists use DNA profiling to make the world better!

DNA profiling definition

DNA profiling can also be referred to as DNA fingerprinting, and Alec Jeffries, a geneticist at the University of Leicester in 1984, first invented it.

We can identify individuals or samples using DNA because even though most of the genome is identical in different humans (~99.9%), there are some key differences.

The human genome includes the coding regions and non-coding regions of DNA.

The parts of DNA that vary in humans are called genetic markers; since their locations are known, we can use them to identify individuals. The different types of genetic markers in humans are:

• Short tandem repeats (STRs)

• Single Nucleotide Polymorphisms (SNPs)

• Restriction fragment length polymorphisms (RFLPs)

There are a bunch of different STRs throughout the genome. Different STRs have different repeating units in different locations shown below:

Figure 1: Two Different STRs are shown. Daniela Lin, Study Smarter Originals.

In Figure 1, examples of two different STRs are shown. The first one, STR-1, is made up of GAC and has two repeats. The second one, STR-2, has two repeats but is made up of CAG.

To understand DNA profiling, let’s focus on just one STR illustrated in Figure 3. Humans all have short tandem repeats; it's the length or the number of nucleotides that varies between all of us.

Figure 2: Humans with varied STRs shown. Daniela Lin, Study Smarter Originals.

Figure 2 shows that the number of repeats between the same STRs (STR-1 GAC) differs from person to person. Person 1 has six base pairs or two repeats, person 2 has three repeats or nine base pairs, and finally, person 3 has four repeats or twelve base pairs in the same place in the genome.

STRs still take a long time to map, but you only have to map at specific genome points. It’s good for DNA profiling, as explained above.

In this example, four different humans’ nucleotide sequence at one point in their genome is shown below:

1. GACGACCTA

2. GACGACCAA

3. GACGACCGA

4. GACGACCCA

In the example shown above, the letters highlighted in red are SNPs because each human has a different nucleotide at that spot.

SNPs are more common than STRs because the probability of finding one different nucleotide at different points is higher than finding different numbers of repeats. As a result, SNPs also allow us to get a more complete genetic view.

The bad thing about SNPs is that you need to map the entire genome, making it take longer than STRs. Next-generation sequencing, a type of efficient sequencing technology, has made it more accessible.

SNPs are better than STRs at comparing genes between populations and making family trees.

The last part of this section explains what restriction fragment length polymorphisms (RFLPs) are.

Don’t worry about knowing what gel electrophoresis is or exactly how RFLP works; we will compare it to the method used to profile DNA today in the next section.

This method is no longer used for DNA profiling because other techniques we will discuss next are faster and cheaper. This is because RFLPs involves all the steps described above and need to build a probe or a single-stranded sequence of DNA or RNA used to search for complementary sequences.

We need to use probes for RFLPs because many indiscernible fragments can be made when restriction enzymes snip genomes.

DNA profiling steps

Now that we understand what DNA profiling is and why it works. We can now learn how we create them.

1. We need to collect a DNA sample:

• We can obtain this from any substance with cells (e.g., blood, saliva, hair, fingernails, etc.)

2. We need to extract the DNA from the sample collected:

• First, we must break open the cells by adding chemicals like alcohol or detergents.

• Next, we must separate DNA from other cell components like lipids or proteins.

3. We need to amplify the STR fragments:

• We use PCR or Polymerase Chain Reaction to amplify 13 STR regions.

We amplify STRs by using DNA primers that only bind to the DNA on each region of the STR, as shown in Figure 3. The primers allow DNA polymerase to bind and make copies. After a while, we end up with a ton of copies!

Figure 3: DNA polymerase and primers enable PCR to work. Daniela Lin, Study Smarter Originals.

4. We use gel electrophoresis to determine the length of STRs:

• STR fragments can be separated by gel electrophoresis because smaller fragments move through the gel faster than larger ones.

• The number of bands and where they are in the gel electrophoresis make our DNA profile.

• We need to compare our results to a DNA ladder or a mix of DNA fragments whose size we know, as shown in Figure 4.

Figure 4: Gel electrophoresis illustrated. Daniela Lin, Study Smarter Originals.

The longer STR fragments stay nearer to the negative part than shorter STR fragments because the longer DNA fragments have to push through the agarose gel more. The DNA moves from the negative to the positive end because it's negatively charged due to the presence of phosphate groups.

Another type of electrophoresis we use in DNA profiling is called capillary electrophoresis. Like gel electrophoresis, capillary electrophoresis features the same first three steps.

1. Collect DNA sample(s).

2. Extract DNA sample(s).

3. Amplify STR fragments.

When we amplify primers, we do the exact procedure explained above with gel electrophoresis, except our primers are fluorescent.

4. This step is different as we determine the length of STRs using capillary electrophoresis:

• We use a laser and detector to make an electropherogram or a plot of our DNA profile.

• The number of peaks and where they are located on the graph create our DNA profile. Like gel electrophoresis, we also use a DNA ladder to determine the size and length of an STR, as illustrated in Figure 5.

Figure 5: Capillary electrophoresis shown. Daniela Lin, Study Smarter Originals.

Similarly to gel electrophoresis, the longer STR fragments stay nearer to the negative part (anode) than shorter STR fragments because the longer DNA fragments have to push through the capillary tube more. The DNA moves from the negative to the positive (cathode) end because it is negatively charged due to the presence of phosphate groups.

DNA profiling examples

Cons of DNA profiling

After understanding all the wonders DNA profiling can do, we should also consider some cons of DNA profiling.

1. DNA samples are delicate and can be ruined quickl by contamination, so we can no longer test them.

2. We need a lot of samples for the test to be accurate. For example, we need 13 STRs to test with PCR.

3. Improper procedures and handling could lead to inaccurate results. For instance, we need to ensure that the gel, buffer, and current are all okay when we perform gel electrophoresis.

4. User needs to interpret the results correctly for the test to be valid.

5. DNA samples can be easily gathered, meaning we could have a lot of data that means nothing. For example, if the crime scene has copious amounts of DNA, then forensic scientists must compare every single one to rule out suspects.

Risks of DNA profiling

This section will discuss the ethical issues or risks of building DNA profiles.

1. Privacy and data protection:

• DNA databases and banks can be subject to hacking which can lead to new ways for scammers to commit identity theft.

• DNA databases can be stored indefinitely and don't guarantee anonymity which could be used not only by the federal government but also by sites like 23andMe, depending on who the database belongs to.

2. DNA evidence doesn’t always tell the correct story:

• What we mean by this is sometimes crime scenes could be so overly contaminated that DNA will tell us that so and the so person was here, but it won’t tell you if that’s the person you’re looking for. Maybe the DNA was there at the wrong place and time.

• There’s also human error and bias that could influence DNA evidence. For instance, researchers have shown that forensic scientists can arrive at wildly different results with the same DNA mixtures.

• Due to the United States history and potential human error, racial bias can be a potential risk with DNA profiling.

Although there are potential cons and risks to DNA profiling, there are also a lot of positives. DNA profiling has rightfully freed many innocent people because as long as the procedures are followed, DNA is accurate. DNA profiling has also been used for adopted individuals to find their biological relatives, identify genetic diseases, etc. Overall, DNA profiling can be a great advent depending on how we as a society use it.