What I Need to Know:
When I needed to make my essential question, I started trying to think of problems that matter, issues that would continue to effect me in my future. That brought up questions of what my future would entail. I aim to succeed in a forensics career and one of the biggest problems facing forensics today is the issues that prevail in DNA profiling. If there was a way to improve DNA profiling, then the career I want to go into would be improved. I could continue to improve it throughout my future in the profession. So, in order to research something that would benefit forensic DNA profiling, I asked the Essential Question: How reliably can pharmacogenomics be used to create an accurate and precise genetic profile that I could implement in a forensic setting?
Working in a pharmacogenomics lab for a year was pivotal to solving my essential question. Throughout my time there, I knew that I would need to learn as much as I could about the process and the explanations behind the process as I could. I needed to find the differences between pharmacogenomics testing and forensics DNA profiling. I needed to understand the success and failure rates of each method.
Working in a pharmacogenomics lab for a year was pivotal to solving my essential question. Throughout my time there, I knew that I would need to learn as much as I could about the process and the explanations behind the process as I could. I needed to find the differences between pharmacogenomics testing and forensics DNA profiling. I needed to understand the success and failure rates of each method.
What I Know or Assume:
At the start of this process, I did not know a lot about the DNA profiling nor the pharmacogenomics testing process. I understood the basics of how it would work. DNA would have to be extracted from a sample. The DNA would need to be removed from contaminants. Then, there was a good chance that the DNA would need to be elongated - likely through something such as PCR (polymerase chain reaction). These were all assumptions with the knowledge of how DNA moved through those processes, but beyond that, I had no clue. I hadn't even known what pharmacogenomics was until I started working at Aeon.
The Story of My Search:
DNA Profiling -
SOP 1. Place samples into microcentrifuge tubes. 2. Add Buffer g2, Proteinase K, and cRNA. 3. Mix by vortexing and incubate. 4. Spin tubes and then transfer supernatant and substrate to tube with a basket. 5. Centrifuge. 6. Transfer liquid to a new sample tube. 7. Vortex and centrifuge primer mix. 8. Swirl PCR reaction mix gently. 9. Make a set of positive standards. 10. Prepare a master mix. 11. Vortex master mix then centrifuge. 12. Put master mix in each well. 13. Add samples into wells. 14. Centrifuge. 15. Load plate into machine. 16. Make a standard curve dilution series. 17. Start the machine. 18. Compare results with standard curve dilution series. 19. Set in PCR for certain STR (short tandem repeat) loci. 20. Transcribe values of samples. 21. Load into genetic analyzer. 22. Analyze data. Genes Analyzed CSF1PO, FGA, THO1, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045. Susceptibility to Degradation One of the main problems found in DNA profiling is the degradation that can occur to the DNA in a forensics case. Some crimes are not discovered for long periods of time, or are submitted to harsh climates. Therefore, DNA found at crimes scenes is often degraded to the point of only being able to produce a partial profile instead of an optimal full one. On the other hand, when matching a full DNA profile with a suspect, the odds of the profile matching any other person are often in the "1 in two and a half billion" (Gunasekera, Costas 2010) range. CODIS, a national database for DNA profiles, even claims that it aided 368,464 investigations since it's creation and up to January of this year. |
Pharmacogenomics Testing -
SOP 1. Receive samples. 2. Cut swabs and transfer into each respective well. 3. Pipette Proteinase K and PK Buffer mix into wells. 4. Shake and then incubate. 5. Add Lysis Buffer to plate. 6. Shake and then transfer to a different plate and add isopropanol. 7. Shake and add DNA binding bead mix. 8. Place relevant plates and washes into machine and start. 9. Perform 1/10th dilution. 10. Centrifuge elution plate. 11. Pipette DNA into dilution plate and centrifuge. 12. Pipette reagent mix into 384 well plate. 13. Pipette dilution into 384 well plate. 14. Centrifuge plate. 15. Put 384 plate in PCR and run. 16. Thaw Open Array plates. 17. Centrifuge elution plates. 18. Pipette Open Array master mix into 384 well plate. 19. Pipette DNA into 384 well plate. 20. Pipette nuclease free water where designated. 21. Centrifuge plate and then score covering on 384 well plate. 22. Place materials into another machine and start the program. 23. Seal Open Array plate and fill it with immersion fluid before screwing it closed. 24. Wipe down plate. 25. Put it into another machine and begin test. 26. Analyze data. Genes Analyzed CYP2D6, CYP2C19, CYP3A4, CYP3A5, COMT, MTHFR, F5, F2, CYP2C9, CYP2B6, APOE, S1C1B1, and 4 additional genes. Susceptibility to Degradation At my workplace, a certain concentration of DNA is required to be able to complete the tests. Typically, it is preferable that the DNA is above 5 on the CT, CT Means graph. Three other interns and myself subjected our DNA samples to various tests in order to affect it's stability and ability to be run on the machines. The concentrations were as follows: Dry Mouth - 24.772 and 30.968 Acidity - 26.178 and 26.428 Dried Out - 24.584 and 24.267 Heat - 26.015 and 24.758 Intense Heat - 24.502 Mouthwash - 23.974 and 24.252 -80 Degrees Celsius - 24.247 and 27.131 Salinity - 25.200 and 25.195 Freeze/Thaw Cycle: 27.052 and 24.258 |
Interview
1. How long did it take you to become the department head at Aeon Global Health?
"I started in March 2014 as a laboratory tech in toxicology. The Genetics department started in January 2014 and started to have an increase in samples by March 2014 when I started. I only worked in Tox[icology] for about a week before I got chosen to work in the genetics lab. We only had PGX [pharmacogenomics] at that time. I became the Department Head for PGX in April 2015. So, about a year before I moved up. I have seen it take much longer for other laboratory techs. We then introduced the Women’s Health Department and Hereditary Cancer department. We then made a larger umbrella and included all 3 genetic departments under one lab – “The Genetic Department” – where I managed all 3 as of August 2017.”
2. How unique is each person's pharmacogenomic test results?
"Every test is unique in the fact that everyone’s DNA makeup is completely different. Though we have not compared identical twins that would be a great experiment. We have seen patient results from one family dynamic (mom, dad, and son), where all 3 patients had different results. You could see in the son’s report that it favors both the mom and dad.”
3. Do you prefer to work pharmacogenomics or women's health? Why?
"All of our techs prefer to work with PGX, including myself. That is due to the type of swab we are extracting from. The PGX is a buccal swab (cheek swab) where the Women’s health swab is a vaginal swab and tends to be more viscous. So, it is typical for our male staff to try and get out of participating in that extraction. Personally, I do not mind it as much due to the fact that I have worked with stool samples in the past and nothing beats that!”
4. What college education do you have and how well do you think it prepared you for your job?
"I have a Bachelor of Science Degree concentration in the area of Health Science from Brenau University. Most of our techs have a chemistry, or biology bachelor science degree. I believe any science concentration will prepare you enough to work inside a laboratory. A science degree will give you the basic pipetting, logic, and math skills necessary to function in a lab day to day. I have encountered multiple PhD biologists that are of course more prepared than most, but still lack basic laboratory skills. That is due to their concentration more geared towards a research-based degree or bioinformatics/computer-based degree.”
5. Can you tell what medicines a person is taking through the pharmacogenomics test?
"You cannot tell what type of medications a person is taking through this test. That test would be a Toxicology test which is another department, but still offered in this facility. A PGX test will give a patient’s potential to metabolize such drugs to prevent adverse drug effects. For example, Kali goes to the doctor for her heart condition to be prescribed cardiac medications. Sometimes the medication we are prescribed do not relieve us of our symptoms or can create more problems for us. It could take a doctor months of trial and error and trying out different types of medications before the patient sees any relief. Why go through the process of trying different medications to find out what drug works best for you? You are wasting time, money, and causing potential dangers to your body. There are thousands of people that die from ADE (Adverse Drug Events) a year. When you only have one copy of a gene instead of your normal 2 copies then drugs can sit in your body and build up toxins due to being a slow metabolizer. On the other hand, you can have 3-4 copies of a gene and be a rapid metabolizer where you get no benefits of the drug because it is going right through your system.”
6. Have you been in any other job than this? If so, what was it and how difficult is this job compared to it?
"This is the first job I got right out of college. I have had other jobs before but none of them are as rewarding as this one. The other jobs I had were retail and administrative positions. Those types of jobs are very easy in my eyes but were also necessary to learn as it is the foundation of my current job. I learned customer service, computer and organizational skills that are necessary to have when being a laboratory manager. It is not all about science unfortunately.”
7. If you could suggest one improvement to the pharmacogenomics testing process, what would it be?
"The main improvement I would make to the PGX department would be to bring back a test we used to do called Copy Number Variation on CYP2D6. This gene is responsible for 25% of the pharmaceutical industry. It converts codeine into morphine. So, there are a lot of medications affected by this gene. This gene is known for having multiple copies especially within the Asian demographic. We had to stop testing for it because Medicare would no longer pay it.”
8. Why did you choose to go into this field of science rather than something else?
"To be honest, I did not choose to go into this field. This field chose me. When I graduated with my Science degree, I had no idea which route I would go. I knew that I wanted to do something meaningful and that would make a difference. I did not seek out this position when I entered the work field. I was simply just trying to get my foot in the door in the medical field. I took interest into this field and excelled at it, which is why I am where I am now. You never know where you will end up or the journey life takes you. As long as you know what you want out of your career, you will end up where you want to be.”
9. What qualifications are necessary to obtain a pharmacogenomics job?
"Expertise in good laboratory practices, knowledge of quality control and sequencing assays – good written and verbal communication skills with a strong attention to detail and documentation – excellent interpersonal and employee management skills, BA, BS, MS in Medical Technology/Medical Laboratory Science, Molecular Biology, Genetics, or related life science field with a Supervisors License is required at some laboratories depending on state requirement’s. Certification by ASCP as a Molecular Biologist or equivalent registry as a Medical Technologist or a Medical Laboratory Scientist, Licensure from the Tennessee Department of Health as a Medical Technological Supervisor, Medical Laboratory Scientist, or Special Analyst is required. Requires MT.
"Managers are responsible for following all procedures and protocols pertaining to patient sample processing, pre-analytical, analytical, and post-analytical testing and Laboratory Information Management System, supervising employees, creating shift schedules, participating in employee performance reviews and disciplinary procedures and maintain specimen testing integrity and efficient turn-around times to ensure client and patient satisfaction.”
10. How can I, as a high school student, prepare for a career in pharmacogenomics?
"As a high school student, it will be difficult to prepare for a career in Pharmacogenomics considering you do not get enough practice in the laboratory until college. High school lab time is very limited. The internship is the best way to prepare for PGX when you are in high school. In college, there are many biology and chemistry classes you can take that will prepare you very well for any laboratory job. The key to getting the most out of your classes is paying attention to the laboratory portion and feeling comfortable using the equipment. Pay attention to different extraction techniques and qualification methods in class and that will give you the upper hand.”
1. How long did it take you to become the department head at Aeon Global Health?
"I started in March 2014 as a laboratory tech in toxicology. The Genetics department started in January 2014 and started to have an increase in samples by March 2014 when I started. I only worked in Tox[icology] for about a week before I got chosen to work in the genetics lab. We only had PGX [pharmacogenomics] at that time. I became the Department Head for PGX in April 2015. So, about a year before I moved up. I have seen it take much longer for other laboratory techs. We then introduced the Women’s Health Department and Hereditary Cancer department. We then made a larger umbrella and included all 3 genetic departments under one lab – “The Genetic Department” – where I managed all 3 as of August 2017.”
2. How unique is each person's pharmacogenomic test results?
"Every test is unique in the fact that everyone’s DNA makeup is completely different. Though we have not compared identical twins that would be a great experiment. We have seen patient results from one family dynamic (mom, dad, and son), where all 3 patients had different results. You could see in the son’s report that it favors both the mom and dad.”
3. Do you prefer to work pharmacogenomics or women's health? Why?
"All of our techs prefer to work with PGX, including myself. That is due to the type of swab we are extracting from. The PGX is a buccal swab (cheek swab) where the Women’s health swab is a vaginal swab and tends to be more viscous. So, it is typical for our male staff to try and get out of participating in that extraction. Personally, I do not mind it as much due to the fact that I have worked with stool samples in the past and nothing beats that!”
4. What college education do you have and how well do you think it prepared you for your job?
"I have a Bachelor of Science Degree concentration in the area of Health Science from Brenau University. Most of our techs have a chemistry, or biology bachelor science degree. I believe any science concentration will prepare you enough to work inside a laboratory. A science degree will give you the basic pipetting, logic, and math skills necessary to function in a lab day to day. I have encountered multiple PhD biologists that are of course more prepared than most, but still lack basic laboratory skills. That is due to their concentration more geared towards a research-based degree or bioinformatics/computer-based degree.”
5. Can you tell what medicines a person is taking through the pharmacogenomics test?
"You cannot tell what type of medications a person is taking through this test. That test would be a Toxicology test which is another department, but still offered in this facility. A PGX test will give a patient’s potential to metabolize such drugs to prevent adverse drug effects. For example, Kali goes to the doctor for her heart condition to be prescribed cardiac medications. Sometimes the medication we are prescribed do not relieve us of our symptoms or can create more problems for us. It could take a doctor months of trial and error and trying out different types of medications before the patient sees any relief. Why go through the process of trying different medications to find out what drug works best for you? You are wasting time, money, and causing potential dangers to your body. There are thousands of people that die from ADE (Adverse Drug Events) a year. When you only have one copy of a gene instead of your normal 2 copies then drugs can sit in your body and build up toxins due to being a slow metabolizer. On the other hand, you can have 3-4 copies of a gene and be a rapid metabolizer where you get no benefits of the drug because it is going right through your system.”
6. Have you been in any other job than this? If so, what was it and how difficult is this job compared to it?
"This is the first job I got right out of college. I have had other jobs before but none of them are as rewarding as this one. The other jobs I had were retail and administrative positions. Those types of jobs are very easy in my eyes but were also necessary to learn as it is the foundation of my current job. I learned customer service, computer and organizational skills that are necessary to have when being a laboratory manager. It is not all about science unfortunately.”
7. If you could suggest one improvement to the pharmacogenomics testing process, what would it be?
"The main improvement I would make to the PGX department would be to bring back a test we used to do called Copy Number Variation on CYP2D6. This gene is responsible for 25% of the pharmaceutical industry. It converts codeine into morphine. So, there are a lot of medications affected by this gene. This gene is known for having multiple copies especially within the Asian demographic. We had to stop testing for it because Medicare would no longer pay it.”
8. Why did you choose to go into this field of science rather than something else?
"To be honest, I did not choose to go into this field. This field chose me. When I graduated with my Science degree, I had no idea which route I would go. I knew that I wanted to do something meaningful and that would make a difference. I did not seek out this position when I entered the work field. I was simply just trying to get my foot in the door in the medical field. I took interest into this field and excelled at it, which is why I am where I am now. You never know where you will end up or the journey life takes you. As long as you know what you want out of your career, you will end up where you want to be.”
9. What qualifications are necessary to obtain a pharmacogenomics job?
"Expertise in good laboratory practices, knowledge of quality control and sequencing assays – good written and verbal communication skills with a strong attention to detail and documentation – excellent interpersonal and employee management skills, BA, BS, MS in Medical Technology/Medical Laboratory Science, Molecular Biology, Genetics, or related life science field with a Supervisors License is required at some laboratories depending on state requirement’s. Certification by ASCP as a Molecular Biologist or equivalent registry as a Medical Technologist or a Medical Laboratory Scientist, Licensure from the Tennessee Department of Health as a Medical Technological Supervisor, Medical Laboratory Scientist, or Special Analyst is required. Requires MT.
"Managers are responsible for following all procedures and protocols pertaining to patient sample processing, pre-analytical, analytical, and post-analytical testing and Laboratory Information Management System, supervising employees, creating shift schedules, participating in employee performance reviews and disciplinary procedures and maintain specimen testing integrity and efficient turn-around times to ensure client and patient satisfaction.”
10. How can I, as a high school student, prepare for a career in pharmacogenomics?
"As a high school student, it will be difficult to prepare for a career in Pharmacogenomics considering you do not get enough practice in the laboratory until college. High school lab time is very limited. The internship is the best way to prepare for PGX when you are in high school. In college, there are many biology and chemistry classes you can take that will prepare you very well for any laboratory job. The key to getting the most out of your classes is paying attention to the laboratory portion and feeling comfortable using the equipment. Pay attention to different extraction techniques and qualification methods in class and that will give you the upper hand.”
What I Discovered in the End:
There are several main conclusions that I reached at the end of my search:
1. No overlap of genes tested by pharmacogenomics and forensics.
2. DNA found at crime scenes are often damaged and degraded in some way or another.
3. DNA purposefully treated in an attempt to degrade it (or negatively affect the testing process) did not affect the DNA to the point of making it unusable.
4. DNA profiling should only be used in accordance with other evidence as it is relatively easy to cause false positives with it.
5. Forensics method sometimes cannot differentiate between mixed partial profiles and a single full profile.
6. The actual process of analyzing pharmacogenomic samples and forensic samples are relatively similar.
7. Pharmacogenomics are different for each person, even showing some level of variability in twins, although some tested genes have different variability in different populations.
8. Forensic results are relatively different for each person, but there can be false positives between people due to errors in partial/full profiles and mixed DNA samples.
9. Both come with the same risk of having the tests performed by humans and being subjected to human errors.
10. Forensics has CODIS which lists 20 STR loci that are observed whereas pharmacogenomics loci are determined by what insurances pay for.
In the end, pharmacogenomics could absolutely be used to create an accurate and precise genetic profile - in terms of the DNA sample's metabolic rates for various drugs. Those results are still unique and still would be viable as a unique, recognizable identification for a person. However, it offers no more trustworthiness than the current process of forensic DNA profiling. Pharmacogenomic testing does not differentiate well between multiple sample sources in the same sample and therefore runs into the same problem as forensic DNA profiling.
1. No overlap of genes tested by pharmacogenomics and forensics.
2. DNA found at crime scenes are often damaged and degraded in some way or another.
3. DNA purposefully treated in an attempt to degrade it (or negatively affect the testing process) did not affect the DNA to the point of making it unusable.
4. DNA profiling should only be used in accordance with other evidence as it is relatively easy to cause false positives with it.
5. Forensics method sometimes cannot differentiate between mixed partial profiles and a single full profile.
6. The actual process of analyzing pharmacogenomic samples and forensic samples are relatively similar.
7. Pharmacogenomics are different for each person, even showing some level of variability in twins, although some tested genes have different variability in different populations.
8. Forensic results are relatively different for each person, but there can be false positives between people due to errors in partial/full profiles and mixed DNA samples.
9. Both come with the same risk of having the tests performed by humans and being subjected to human errors.
10. Forensics has CODIS which lists 20 STR loci that are observed whereas pharmacogenomics loci are determined by what insurances pay for.
In the end, pharmacogenomics could absolutely be used to create an accurate and precise genetic profile - in terms of the DNA sample's metabolic rates for various drugs. Those results are still unique and still would be viable as a unique, recognizable identification for a person. However, it offers no more trustworthiness than the current process of forensic DNA profiling. Pharmacogenomic testing does not differentiate well between multiple sample sources in the same sample and therefore runs into the same problem as forensic DNA profiling.