The following is an interview with Dr. Monte Miller, Ph.D of conducted via email:

What are some major challenges to DNA research?

“DNA research and forensic DNA research can be very different. I will address forensic DNA research. I think the major challenge is time. It takes quite a bit of work to run the DNA and analyze the results. And the costs prohibit labs from just hiring more people. As the justice community finds that DNA can help solve all types of crimes they are increasingly taking more samples so that even when more money is thrown at the problem the crime labs still get further behind.”

Who generally funds research?

“Either the government or someone who will make money, like drug companies or business that can make money on inventions. Also some hospitals and medical schools.”

Which US agencies are involved with regulating technology and research in this field?

“US research in biomedical sciences is almost always carried out by NIH, the National Institute of Health. As far as regulation, the rules of what is acceptable to CODIS and these kinds of things are ultimately regulated by the FBI.”

How exactly does CODIS work? How are DNA fingerprints shared among investigators?

“CODIS (combined DNA index system) has several levels, national, state and local. The national is used to hunt for crimes committed by the same person, or to connect a person to other crimes, just like fingerprints. The state keeps their own, some of these profiles are not eligible for the national. Local databases are kept by the labs. Combined together, they are CODIS. They are not really shared with investigators. New profiles, or people arrested, are entered, and each one that is entered is checked against what is already in the database to see if there are matches, again, like fingerprints."

In CODIS, are the DNA prints pictures?

“No, the machines produce the profiles and are put together by a machine as sort of a picture for analysts to look at to interpret. But they are entered into CODIS and refered [sic] to by analysts by their numbers and Locus. For example at the Locus TPOX my DNA profile is an 8,11.”

What do you mean by number? I know locus means location, but what's TPOX?

"TPOX is the name for a locus. They all have names. Most of the names consist of numbers and letters telling us where in the genome it is found.

The number assigned is actually the number of repeats seen. For example GATC-GATC-GATC-GATC-GATC is a tetrameric repeat of 5. Tetra means four, so a four base pair repeated five times. Most of forensic tests look for specific known tetrameric repeats, and are simply named after the number of repeats. So if you look at the area we call TPOX (locus) then it could repeat from 1-20 times. What you usually see is 6-13 repeats and humans almost always have an 8, 10, or an 11."

What conditions must be met before DNA is entered into CODIS?

“There are several criteria. It has to be a good enough sample to be unique, or close to it, so if it matches it is a good match and likely to be helpful. Unknown evidence samples are entered and they try to match them to other crimes. There is also a part of CODIS for missing persons and their relatives. There is another part of it for samples of people that they know where they came from, like people in jail or accused of some crimes. They try to match the known people to other crimes, or people accused of one crime to other crimes. The theory is that 20% of the people commit 85% of the crimes, so if you find a profile, or enter the profile of a bad guy, you may get a match, or you may be able to match up crimes committed by the same person and this helps figure out who did it."

Does it ever leave?

"If you are found not guilty you can ask that your profile be removed, there are specific rules for removal."

Are there any ethical, legal, or social issues when working with forensic sciences?

"Yes, you have people's lives on the line. Almost all of the forensic work has ethical and legal implications. On a brader [sic] scale these become social issues of justice for all of us. The biggest problem that I see almost daily is that some crime labs work for the District Attorney's Offices or the police department, and they answer directly to them. This causes a conflict of interest as the crime lab becomes the tool for the police to put somebody in jail. The good crime labs are independant [sic]. They simply look at the evidence, generate data and facts, report them, and explain them to the court system. When the analysts become biased the  accused cannot get a fair trial."

When comparing DNA, how many sections must match for the two to be considered related?

"If we compare evidence to a person's known DNA is has to be an exact match. Your DNA does not change over time and is the same throughout your body. So a perfect match is required. A close match and we will start to look at your relatives though.

But for parents, you received half of your DNA from each of your parents, so you match 50% with them." 


What machines and tools do you commonly use when working with DNA? What are their specific purposes, and how do they work?

"You can purify your own DNA with common household items, so separating DNA is pretty easy. Evaluating it usually uses a process called electrophoresis. DNA is negatively charged so it moves towards the positive pole if placed in an electric field. These machines are set up many different ways for different purposes, like discovering sizes or sequences."

Where does size differ and why?

"Size differs throughout your genome. It differs due to mutations over millions of years slowly causing genes to drift in size. These differences are what forensic scientists use to determine your DNA fingerprint that is unique to you."

Do sizes differ in actual measurements or in length of sequence?

"A diffrence in the number of bases becomes difference in length, this necessarily becomes a difference in sequence. Think of the bases as legos. If you have a difference in length, there is a difference in sequence and a difference in size. But you can have a difference in sequence with the same number of legos so the same size."

Are you saying that, in example, the gene for eye color in bigger than the gene for hair color, or are you saying that there are different colors for hair because the gene for hair color differs in size?

"Gene bases (lego blocks) are turned into amino acids and eventually long chains of amino acids called proteins. Differences in DNA coding causes different amino acids which causes different activities. Think of them like tools, some tools are like big machines, others are small, all kinds of different sizes. Hair color and eye color are almost certainly different sizes, but the size is not the key thing, just like a tool, the size is directly related to what the gene or tool has to do. So yes they have different sizes and this is determined by the sequence."

When would you use the different kinds of PCR testing?

"STR is the normal forensic testing.

Y-Chromosomal is used when you have a mixture of male-female but the male is low, so it is hard to get an accurate read of the male profile. This test has lower statistics, but tests only ofor [sic] male DNA. Good test to use in sexual assault cases.

Mitochondrial DNA testing is used as a last resort, usually. Mitochondia [sic] are not part of the genomic DNA, they are small organelles that are inherited from your mother and found thoughout a cell in the cytoplasm. They are the source of the electron transport chain and the energy producers of the body. You get very few from your father and these can rarely be found by testing. This test is good for family screening for missing persons or when unknown remains are found. Again the statistics are lower than normal STRs, but it a valuable tool. The other good thing is that you can get mito DNA from hair, when normal genomic DNA is only found in the root, mito is throughout the hair. Also, since mito is a small circular DNA it can be run by PCR when other genomic DNA is degraded. It can also be found in bones and teeth when genomic DNA is gone."

Why do Y-Chromosomal and Mitochondrial testing have lower statistics?

"Y-Chromosomal and Mitochondrial testing is based on taking the sequence of one section, then checking a database for the rarity of that sequence. So they end up looking at and analyzing just one section of DNA.

Forensic Testing, STRs, looks at the frequencies of 32 sections, and does statistical analysis based on the frequecy [sic] that each allele is found in the population. These frequencies are known, so they are able to calculate 30 diffenrent sections. They do not calculate the sex determining genes, X and Y, though they look at them."

What does it mean when DNA is degraded?

"When someone dies, or the cells of the body are detached from it or in some way lose their nourishment, which is derived from the body, the cells begin to break down. A dead body will essentially liquify itself in a few days, this is decomposition. From inside the cell the DNA is slowly chopped up into smaller fragments. Also, when you have something like a blood drop, the DNA is damaged by chemicals, sulight, moisture, and bacteria, among other things. These all serve to chop up the DNA and this will cause the areas that you want to evaluate to be braken [sic] up and you can't copy or read them. This is called degradation, or degraded DNA."

What does it mean when DNA is contaminated? How do you know it happens?

"Contaminated DNA is when two objects come in contact and the DNA from one contaminates the other. When you are processing evidence you must keep each sample of evidence separate so that you know that the DNA on it came from it, and not some other sample you collected. For example, if I am collecting samples from a crime scene I need to wear gloves, or the sample could get contaminated with my DNA.

The other situation, which is not contamination is a mixture. If you and I shake hands firmly, and then I swab your hand, it would have a mixture of my DNA and yours. If one man kills another, and gets the victim's blood on his clothes, you can find a mixture of DNA from both people sometimes from the evidence. This is not contamination but merely a mixture because there is more than one set of DNA on the sample taken.

The difference is that contamination usually means that the source of DNA is a collection or evidence processing mistake, while a mixture is just a sample with more than one set of DNA on it."

Thank you so much for taking the time to answer all of our questions. My partner and I really appreciate it; you've been an immense help to us. 

"You are welcome. Good luck!"



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