How not to die when working in the lab – Biosafety

What’s your biggest concern for your safety when walking into work each morning? That you’ll get a papercut or burn your tongue on your morning coffee? Maybe if you’re in a higher risk profession (like a contractor) you’re worried about something falling on your head.  As a scientist, may researcher enter the lab every day and have to worry about being infected by what they are researching!

blood tubes

Blood tubes collected for our biobank

Human tissue and blood may contain viruses like HIV or hepatitis that’s just needs entry into your body through a cut or in the mucus membranes of your nose. Or maybe you’re working with viruses like the flu to see how they infect cells. And what of those people who are studying the deadliest diseases like Ebola – how do they study these diseases or work to develop vaccines or treatment drugs without getting Ebola themselves? BIOSAFETY!

Wow. Boring. Right? Well, kind of. I spent this last week taking a refresher course on biosafety and the reading was DULL, but sitting down to think about all of the implications it becomes fascinating.

The thing is, anything that would infect you is likely invisible.  If you’re working with human tissue or blood, you can see the blood but not what might be inside of it (bacteria or a virus) that could infect you.  And if you drop a blood tube on the floor, you can see the pool of blood but not the microscopic aerosolized droplets in the air just waiting to be inhaled. So how does a scientist take care of these hazards not just so they don’t get sick but so they don’t infect the public as well?

Good news is that scientists think about this a lot.  First, depending on what you’re working on depends on how careful you have to be. Compare this to the difference between giving a 4-year-old plastic play-doh scissors versus sharp surgical scissors – they have different risks associated with them and you’d treat the kid using them in different ways.  In the same way, working with things that are not known to infect humans and cause disease (like bacterial cells) don’t need to be handled as carefully as those that cause deadly diseases that are spread through the air (like Ebola).  This is what defines the “risk group” on a scale of 1-4, where 1 is the lowest risk and 4 is the highest. The play doh scissors or bacterial cells would be Risk Group 1 and the sharp surgical scissor or Ebola virus would be Risk Group 4.

This then helps researchers figure out what protective measures need to be taken – also called Biosafety Levels (abbreviated as BSL) 1-4.  For example, level 1 can be done in the laboratory out in the open wearing a lab coat and gloves.  Level 2 requires research to be done in a biosafety cabinet so that anything that spills or is aerosolized is contained.  Level 3 is for agents that cause moderate to severe disease and in this case the experiment needs to be completely contained in a glove box or in a special room with controlled air flow. Level 4 is for agents that cause lethal disease that has no treatment or cure (like Ebola). In this case the BSL-4 is what you may see on TV or movies where researchers are fully enclosed in a “space suit” to prevent any contact between the person and the agent.


In my lab, we regularly work with human tissue and blood and because the tissue or blood may be infected with certain biological agents, they are considered risk group 2. We always wear a lab coat and gloves and work inside a hood.  When moving these tubes from one place to another, we make sure that there are at least two layers of containment – the blood tube is the first layer and this is inside a plastic bag as the second layer. We also get re-trained every year to make sure we remember how to handle spills (just in case).

Now because we’re all morbid creatures, I’m sure you’re wondering what’s happened when this hasn’t worked. Here is an article about the most common infections acquired in the lab and how they were acquired.  For more newsy stories, here is a story about a researcher who contracted plague in the lab. Eek! Definitely reinforces the importance of being careful in the lab.

Institutional Review Board (IRB) – Keeping Research Subjects Safe


I was working over the holiday weekend, but at least I was working in my decorated living room with a fire going (the high in Arizona was only 66 today!!)

Hope you had a fabulous Thanksgiving weekend! Four day weekends are great, and even I took some time off to enjoy the holiday with my husband and the puppies.  And then I got back to work because I have an Institutional Review Board (shortened usually to the acronym IRB) meeting in two weeks and the committee has eight new protocols to review. This likely means very little to you, but the IRB is what ensures that the rights and welfare of humans participating as subjects in a research study are adequately protected. And here’s why that’s important…

In a previous post, I explained clinical research.  Clinical research studies new drugs or devices to determine if they are safe or effective. As you can imagine, at a world-class hospital, we have hundreds of clinical trials. You can check out information about these clinical trials by following the links for the Barrow Neurological Institute, St Joseph’s Hospital and Medical Center and the University of Arizona Cancer Center at Dignity Health.  Physicians and surgeons are studying new treatments for many different cancers, devices like the NovoTFF for glioblastoma, and comparing new drugs or combinations of drugs to current treatments to see if the new regime works better.

Now if a  company wants to test a new drug, they can’t just pick up the phone and ask their physician buddy if they could just use a few of their patients to test some stuff out. But why not?  Honestly, it’s because at one point researchers did some pretty crappy things in the name of science.  Thins like Nazis studying prisoners against their will and in the US and scientists who studied the untreated progression of syphilis in black patients in Tuskegee, Alabama from the 1930s-1970s. In these and other cases, the welfare of the patient (who is called a subject once they are part of a research study) wasn’t considered AT ALL and what the subjects had to endure was truly awful.

To avoid this from happening in the future, in 1974 the government passed the National Research Act, which resulted in the Belmont Report. From this, three ethical principles were developed in the treatment of research subjects:

  • Respect for persons.  This respect includes allowing them to make their own informed decisions about participating in the research.  This also means that the researcher conducting the study needs to be honest and not try to deceive or coerce patients into participating in the study. For example, the researcher can’t tell the patient that the research will be painless and cure their disease if they know it won’t.
  • Beneficence: Basically this ensures that the researchers do no harm to the research participants – for example, like the harm done during WWII or in untreated syphilis patients.
  • Justice:This is to avoid taking advantage of the patient or a vulnerable patient population.  For example, there are special rules to prevent taking advantage of prisoners or children. This principle also tries to make sure that all research participants receive benefit equally.

protocol for IRB reviewThese ethical principles have been developed into processes that are regulated by the Food and Drug Administration (FDA) and Department of Health and Human Services (specifically Office for Human Research Protections). How does the government make sure these regulations are followed?  Any institution that is performing human subject research has to obtain a Federalwide Assurance, which essentially registers the hospital or university with the government and assures the government that the hospital will follow the ethical rules and guidelines to conduct this research.

For each project or clinical trial involving human subjects, the investigator needs to put together a proposal – what we call a protocol.  This protocol includes information about exactly what is going to be done to the subjects, what the risks are, what the alternatives are for treatment, and how the subject’s safety and confidentiality will be safeguarded. This protocol is the sent to the IRB along with LOTS of other documents about how the patient will be informed about the research (in Informed Consent Form), whether or not the investigators have been trained to perform the research, and information about the drug or device being used.

The IRB is responsible at individual institutions for making sure that patients who become subjects in human subjects research are treated with respect, beneficence and justice while also decreasing the potential risks and letting the patient know what these risks are. The IRB reviews each new protocol (which is exactly what I am doing this weekend!) and at the IRB meeting (which is once a month from 7-9AM), the investigators present their protocol.  The IRB members then ask questions to the investigator and discuss the research after the investigators leave the room.  What do we discuss? It’s confidential for individual studies, but we may talk about how the study is being performed and identify possible problems with the study. We may also talk about the informed consent (what the patient reads to learn about the study – more on that in the next post) and if it accurately explains the research and the risks. We then can vote to approve the study, to send the protocol back to the investigator to answer questions or modify the protocol or to reject the study.

After the study has been approved, the IRB is also responsible for monitoring active research projects.  For example, we receive annual reports that let us know how many people have decided to participate in the study. We also monitor “adverse events.” Adverse events (or AEs) are any event that isn’t anticipated.  This can be anything from nausea to a broken leg to a rash to a missed appointment to death (death is considered a serious adverse event). Whenever an AE happens, the IRB is informed so that if it seems like there are too many of one type of AE, we can take measures to avoid them or tell the subject about an additional risk or shut the research project down.

My participation on the IRB is a responsibility I take seriously because I want any patient who comes to the facilities I work at to understand the research that may be made available to them.  And this understanding includes knowing what the research is all about and what risks the research entails. This is why I’m spending my holiday weekend reviewing research protocols for the IRB.

What is Personalized Medicine?

bullseyeA few years ago I was asked to teach a course to adults at the ASU Osher School of Lifelong Learning about the Emerging Era of Personalized Medicine. This was exciting because it would give me the opportunity to help empower these adults to better understand their health, the science behind what make them sick, and what scientists and doctors are doing to cure them.  This was also a challenging course to develop because only a few years ago personalized medicine wasn’t the common buzzword like it is today. In fact, in early 2014, the Personalized Medicine Coalition contracted a research survey that found that 6 in 10 of people surveyed hadn’t heard of the term “personalized medicine” (see all results of the survey here). Despite the public being unaware of this huge advance, in the past few years, scientists and doctors continue to evolve this concept and medicine isn’t just “personalized” but now it can also be described as “precision,” predictive,” “individualized,” “stratified,” “evidence-based,” “genomic” and much, much more.

So what is new about this type of medicine?  Of course since the days of Hippocrates, doctors have provided care to patients that take their “personalized” needs in mind. Based on the patient’s symptoms and their experiences, the doctor provides treatment. But what if two patients have the same symptoms but different underlying diseases?  A fever and a headache could be the flu or malaria. Or two people could have the same disease, like breast cancer, but the underlying genetic changes are different so that the cancer should be treated differently for each patient.

The current concept of personalized/precision medicine uses each person’s individual traits (genetic, proteomic, metabolomic, all the -omics) and harnesses our molecular understanding of disease for the prevention, diagnosis, and treatment of disease.

personalized-med2The ultimate goal of personalized medicine is to improve patient health and disease outcomes. The graph above shows how better understanding the genetic and molecular causes of disease can improve health at all phases of disease progression.

  1. Knowing the risk factors that cause of disease (either environmental, like smoking, or genetic, like the BRCA gene mutation) can help to prevent disease before it starts by eliminating the risk factors or providing additional screening to catch the disease early.
  2. Biomarkers that detect disease before major symptoms can be used to treat the disease early, which usually has a better outcome than treating a disease that has progressed further (think stage 1 versus stage 4 metastatic cancer).
  3. Once a disease has been diagnosed, the molecular understanding of the disease can help determine what treatment the patient should receive (see below for an example).
  4. Biomarkers can also be used to predict whether the disease will progress slowly or quickly or whether or not a selected treatment is working.

For all aspects of personalized medicine, there lies the promise to make an enormous impact both on public health but also on decreasing the cost of healthcare.

breast_cancerLet’s use breast cancer as an example of how personalized medicine plays out in real life, right now. For breast cancer detection, breast self-exams and mammograms are typically used.  With personalized medicine, we now have an understanding of one of the genetic risk factors of breast cancer – mutations in the BRCA genes.  Patients at higher risk for developing breast cancer because of these mutations can be monitored more closely or preventative action can be taken. In the past, breast cancer treatment focused on treated with non-specific chemotherapy and surgery. Although both of these treatments are still of value, now doctors also test for the presence of certain breast cancer genes like Her2.  If Her2 is present in breast cancer cell, the drug Herceptin that specifically targets this Her2 gene can be used to specifically kill those cancer cells. If Her2 isn’t present, this drug isn’t effective, causes negative side effects and wastes time and money when a more effective treatment could be used.  Once breast cancer is diagnosed, a patient would be interested in knowing how quickly their cancer will progress. This used to be primarily based on the stage of the cancer, where stage 4 cancers have spread to other locations in the body so the prognosis isn’t great. Based on molecular markers, scientists have now created panels of biomarkers (Oncotype DX and MammaPrint) that predict breast cancer recurrence after treatment.

These personalized medicine-based tests and drugs are incredible. However, this is a field that both holds considerable promise and requires lots of work to be done.  For every incredible targeted therapy developed, there are patients that are still waiting for the treatment for their disease or the genetic variant of their disease.  In future posts, I’ll talk a lot about both the promise and the pitfalls of personalized medicine.

If you want to learn more about personalized medicine, check out this YouTube video with a cartoon comparing treatment with and without the concept of personalized medicine.

What does it mean when I have genes that increase my “risk” of disease? Like Alzheimer’s?

The last few posts (here and here) have been about people who have carrier mutations.  These people have one recessive gene mutation that they could pass on to their child.  If the child inherits two recessive genes (one from each parent), they will get the disease.  That’s how it works with recessive diseases that are caused by one gene.  About 4,000 diseases are caused by mutations in one gene (either in dominant or recessive genes).  But that leaves all of the other diseases…

Since we’re still talking about genetics, let’s stick to diseases that are caused at least in
part by gene mutations as compared to diseases caused by infection, for example.  There are many diseases that are caused by mutations in multiple genes (the technical word for this is polygenic). In these cases, no one gene can be identified as the single cause of the disease.  The genes that are involved in causing the disease can be on many different chromosomes in many different locations on these chromosomes and only if mutated in combination will someone get the disease.  And these mutations may only cause the disease if exposed to a certain environmental factor (like cigarette smoke).


If this sounds confusing and complicated to you – it is.  Scientists find it confusing and complicated too. It’s much more difficult to pinpoint the exact genes that cause a  disease if there is more than one mutation in more than one gene.  It’s like a puzzle, but you don’t know the number of pieces in advance or what the puzzle looks like.  So if you fit two pieces together (or identify two genes that are mutated), you don’t know if you have completed the puzzle and figured out what is causing a disease or if you need to look deeper.

Scientifically, this is a complicated question, but for the patient who doesn’t care how many genes cause the disease, what does it mean to them? What does this mean for risk?  If a gene is found to be associated with a polygenic disease, mutations in this gene may increase or decrease your risk of that disease.  But unlike genes cause by dominant or recessive genes, no one can say for sure 100% either way if you have a particular gene mutation that you will or won’t get a disease.

A great example of this is Alzheimer’s disease.  Only in early onset Alzheimer’s (0.1% of all cases), one dominant genetic mutation the cause of the disease. However, in 99.9% of Alzheimer’s Disease cases, more than one gene is involved (at least three genes, but probably more).  One gene that is well studied in association with Alzheimer’s Disease risk is the gene apolipoprotein E (ApoE, for short).  There are three different versions of the ApoE gene called ApoE2, ApoE3, and ApoE4 – each representing a different mutation in the ApoE gene.  The E2 version (found with 8.4% frequency in the population) is protective against Alzheimer’s Disease.  The E3 version (found with 77.9% frequency in the population) is essentially neutral (neither causing or protecting from disease).  The E4 version (found with 13.7% frequency in the general population) is the one that causes the problems and and increase the risk from 20% in a person who has zero copies of E4 to 91% risk in a person with two ApoE4 copies.  The more copied of E4 the more likely a person is to get Alzheimer’s disease at a younger age as well. And if you’re wondering, this is ABSOLUTE risk, not relative.

alzheimersAlzheimer’s disease is a particularly tricky example to use because there are few, if any, preventative treatments for the disease.  So even if you know that you have two copies of ApoE4, there isn’t much that you can do.  However, there are other diseases, where certain genes increase risk for a disease (like I described for the BRCA mutations and breast cancer risk).  In this case there are potential preventative treatments, though even after those treatments, the decrease in risk is significant but cannot be eliminated.  Overall, it’s important to understand the complexity of disease and how many factors (including unknown factors) can contribute to disease risk and onset. For scientists, knowing the risk factors can help to detect disease early or develop targeted therapies to treat the disease. For doctors, it helps to predict disease risk and tailor treatment.  And for the patient, it helps to know that diseases are complicated and risk isn’t 0% or 100%.


What does it mean if I’m a “carrier”?

What does it mean when someone “carries” anything?  The definition of “carry”is to hold or support something while moving somewhere.  Often when you carry something it’s heavy, a burden.  When you’re a genetic carrier, it’s much the same.  You’re holding or supporting a recessive gene mutation as you move around in your normal everyday life.  Even though the recessive gene doesn’t affect you, it’s a genetic burden, because you could pass the trait down to your child.

cfLet’s remind ourselves what it means to have a recessive gene (or re-read the original post referencing 50 Shades of Grey).  You have two copies of every chromosome, and on each of these chromosomes is copies of each gene (called alleles – pronounced AL-eels).  These genes can be slightly different.  In some cases they are different enough that one copy doesn’t work as expected or work at all (these are the “recessive” genes we talked about in an earlier post).  Often the functional copy of the gene can compensate for the copy that doesn’t work right.  But in the case where both copies of the gene don’t work correctly, the person can end up with a disease.  The example that we used previously was cystic fibrosis.  A person will have cystic fibrosis only when the have two copies of the mutated CFTR gene.  The same is true for sickle cell anemia, which is caused by having two mutated copies of the hemoglobin gene called HbgS.  If a person only has one copy of HbgS, the other normal hemoglobin can produce enough hemoglobin to function just fine.  However, if there are two copies of HbgS, the HbgS protein structure collapses in cases where the person doesn’t have enough oxygen and this causes the red blood cells to make a sickle shape.
youandpartnercarrierThere are a number of diseases that are caused by having two copied of a mutated recessive gene (many are listed here).  But again, if you only have one copy, you’re just fine – but you carry that gene mutation. If you have children with someone else who is a carrier (meaning that they also have one copy of a recessive gene that would cause disease), then you have a 25% chance of having a child with that disease, because they have 25% chance of getting two copies of the recessive gene.

This isn’t a huge deal – only 25%, right?  Except that you would never know from looking at someone if they are a carrier.  And you wouldn’t know from living with yourself for all these years if you are a carrier.  And some populations or ethnic groups are more likely than others to be carriers for recessive genes for certain diseases. If you look at the chart below, I have listed a few ethnic groups and diseases which they are often genetic carriers.  After the name of the disease, I have listed the likelihood of someone from that ethnic group being a carrier for a recessive gene that would cause that disease. For Caucasians, if you and 28 people are sitting in a room, one person would carry a mutation in one copy of the CFTR gene that would cause cystic fibrosis. It is estimated that at least one in five Eastern European Ashkenazi Jewish individuals is a carrier of one gene that would cause a genetic disorder.

carrierSo what should you do now that you know that you could be a carrier for gene that could cause a disease.  There are options – the first one being doing nothing at all.  You could also look at your family history.  Are there people in your family or your partners family with a recessive genetic disease like Wilson Disease or Tay-Sachs?  If so, you may want to get tested for common recessive genes. On the other hand even without family history, if you are from a particular ethnic group such as Ashkenazi Jew, you may be encouraged to get tested no matter what (see an interesting guidance about this here) before or during pregnancy.  There is also the possibility that you want to be prepared, and before you and your partner get pregnant that both of you are tested for common carriers. Next post, we’ll talk more about what you can do if you are a carrier.





What is risk? Absolute versus Relative

riskMy mom and I were talking this afternoon – we talk every day on my drive home from work (I celebrated the day I got Bluetooth in my car) – about Angelina Jolie.  It was difficult to miss the news this past week about her New York Times opinion piece describing why she decided to remove her ovaries and Fallopian tubes.  There have been a number of interesting articles both praising (here or here or here) or criticizing or clarifying her choice.  That’s not what I want to talk about and it’s not what my mom and I talked about.  What we talked about was risk.  Most stories talking about Angelina Jolie mention that because of the gene mutation she had, there was an 87% risk of her developing breast cancer.  Despite the fact that 87% is awfully specific (and based on limited data from a certain number of women with this mutation that were studied over time), what I want to focus on isn’t the number, but what the number refers to.  In particular, I want to point out that there are different ways of talking about risk – and this is important when reading about any scientific information in the news.

coin_flipLet’s start with a quick definition – risk is the chance that something will happen.  These are usually percentages.  There is a 50% chance when you flip a coin that it will land on heads.  The risk is 50%.  Of course, when applied to the chance of developing a disease, or having a particular treatment outcome, or surviving an accident, the numbers are a lot more difficult to calculate than a coin flip.  But they are also more confusing when describing the risk as well.


rosk_tableI’m sure you’ve read news stories that say something like “Drinking more than 3 caffeinated drinks a day increases your risk of a heart attack by 50%” (this is a completely fictional example!!!) Fifty percent. What a HUGE risk.  Except what they don’t tell you is that without drinking caffeinated drinks, your risk of having a heart attach is only 1%.  So a 50% increase means your risk only increases to 2%.  This is the difference between relative versus absolute risk.  50% is the risk relative to what the actual baseline risk, whereas the absolute risk tells you the actual chance of something happening.

Let’s look at another example.  “This new drug decreases the risk of blindness in diabetic patients by 50% over 5 years”.  This is promising news!  Except, again, the 50% is relative risk – what you want to know is what the chance of a diabetic patient going blind?  If the chance that a diabetic patient goes blind is 60%, then a decrease of 50% is huge. There is only a 30% chance of blindness now.  Ont he other hand, if like the previous example, the actual chance of going blind is 2%, the 50% decrease is less impressive.  This makes the decrease in risk no less important to the patients who take the drug and don’t go blind – but it does affect how you read a news story describing the effect of the drug and whether or not you may want to take an expensive drug.

Now let’s get back to Angelina Jolie. The actual risk for breast cancer in the general population over a lifetime is ~12%.  If you have the mutations in the genes (called BRCA1/BRCA2) that Angelina Jolie has, it increases the risk to 40-80%. This is the absolute increase in the chance of getting breast cancer.  And as you may notice – the risk has a range (based on a number of factors – family history, health history, etc that we’ll get into in another post).

So how can you be a more savvy reader? You can be tipped off to relative risk by phrases like “increased by”, “decreased by”, “more than” or “less than”.  This only tells us the difference compared to baseline, but gives NO indication of what that baseline risk is. Absolute risk, on the other hand, provides the best estimate of what the overall likelihood of something happening will be.