QUEST Community Science Blog Author: Dr. Barry Starr

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Forcing Scientists Into The Public Square

February 1st, 2010 by Dr. Barry Starr

Carl Sagan’s scientific career took a bruising because of his outreach work.

I am convinced that a lot of people’s misconceptions about science could be cleared up with a little outreach from scientists. I’m talking about outreach activities like creating websites that give good, reliable, understandable information, talking to school and adult groups, getting involved in museums, PBS, the Discovery Channel, etc.

Getting scientists to do any of this is the tricky part. They have no immediate incentives to do it and in fact, there are disincentives. But they need to learn that it is in their best interests.

Taxpayers pay most scientists’ salaries through federal grants. An uninformed, suspicious, or actively hostile public obviously will not want to pay for scientific research. So anything that can be done to inform the public about the good work being done will probably loosen the purse strings in Washington at least a bit.

Of course the problem with this argument is that it uses an abstract fear of something in the distant future. Sort of like global warming.

As we’ve learned from that, most people aren’t willing to sacrifice much for far off, future dangers. If gas is cheap, we’ll keep driving big cars. And we certainly won’t sacrifice any current goods for a future that may or may not come to pass.

Same thing with scientists. Outreach is a thankless task that can actually work against the people who do it. Scientists who do a lot of outreach are often perceived as not being serious about true science and they’re dinged for it.

There is also no incentive at Universities to do outreach. As anyone who has been involved in academic science knows, the key to success is to get government grants that help fund the scientist’s research, his or her department and the University. Everything else an academic scientist does takes a backseat to this. And outreach isn’t even in the car.

Outreach takes scientists away from the lab. It is in the lab where results are generated that can be published to get grants to fund more research. Less time on research equals less money.

So to get scientists doing outreach, we need to change the incentives. There either has to be a change at Universities so that outreach is valued. And by valued I mean tenure track positions or long term funding for people to do outreach. Frankly this is pretty unlikely.

The other possibility is to include outreach as part of a scientist’s grant. In other words, to get money for their research, scientists will need to do some outreach.

I am aware of two major funding agencies—the National Science Foundation (NSF) and the National Human Genome Research Institute (NHGRI)*—that mandate outreach for at least some of their grants. These mandates are a critical first step in getting more digestible science out to the public. But to make a major dent, we need the NIH to get involved too. They fund a whole lot more research and so a whole lot more outreach would get done too.

The NSF and NHGRI requirements are definitely causing a lot of scientists to scramble around and try to find outreach projects to fund. (Email me if you have some spare money lying around!) But I don’t know the quality of the outreach that is being done.

Hopefully the people doing outreach are better than the average scientist at talking or writing about science with the public. For the most part, the money would probably best be spent on hiring someone with a scientific background who is good at explaining science. Or in training scientists first in how to effectively communicate science to the public.

All of this points to another major issue—we need to figure out what we want from these outreach opportunities. Is it to provide a good source of information for the public? To enhance understanding of how science works? To teach people how to tell good science from bad? To train the next generation of scientists? To…? No one is really providing leadership on these questions. Let’s hope someone does soon.

*The NHGRI is interested in increasing the numbers of genomic scientists who are under-represented minorities. Definitely worthwhile but not really doing a lot for the public understanding of science.

Here is a great book on the subject: Unscientific America: How Scientific Illiteracy Threatens our Future.




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Posted in KQED | 2 Comments

The Wild, Wild Web

January 18th, 2010 by Dr. Barry Starr

It can be hard to tell which science is good, bad, or ugly on the web.

I have often thought that the percentage of good scientific information on the web must be pretty low. So I decided to test the idea out on a question I was recently working on.

Someone asked me if humans started out with O blood type and then only later developed A and B.  A quick look at PubMed showed that this was not the case.  Most of the recent genetics studies point to A coming first, followed by B about 3.5 million years ago and then, finally, about 1 million years ago, O.

This makes some intuitive sense if we think about what A, B, and O are.  O is a form of A that doesn’t work any more because of a mutation*.  This makes the idea that a broken gene came before a working one pretty unlikely.  Not impossible, just not all that likely.

Now I researched this answer the way I usually do—I headed straight for PubMed to get the hard scientific data.  I can do that because I work for Stanford and so have access to lots of journal articles and I have the scientific background to decipher the geneticsese these reports are written in.

What I also did this time was to try to find the answer without PubMed.  I started out on Yahoo searching for human blood type evolution.  Yikes.

Links 1, 2, and 7 talk about primate A and B blood types.  Gorillas have B and chimpanzees have A and a bit of O.  From this the authors try to conclude that we are somehow a mix of these two…perhaps gorillas and Neanderthals are closely related to each other and so are chimps and Cro Magnon.  In this scenario, humans come from a mix of Cro Magnon and Neanderthals.

This is certainly not the case.  Gorillas do have a blood type similar to B but it isn’t the same as ours at the gene level.  And if current evolutionary history is to be believed, we split from gorillas way before our B blood type was born.  So we did not get our B from gorillas.

Also, chimpanzee O is not the same as our O…it developed well after we split as well.  We even know that Neanderthals have our O blood type and not a chimp’s (and certainly not a gorilla’s!).

Links 3, 5, and 9 use blood type genetics to show that Adam and Eve could have founded the human race.  Links 4, 6, and 8 talk about the blood type diet.  And link 10 connects blood groups to aliens.

Google does a bit better.  You get eight similar links but you also get an NPR piece that does pretty well and a Dawkins forum comments piece that can get you to the answer eventually.  However, you have to wade through a lot of stuff to get there and you only know to home in on the comment with the correct information if you already know the right answer.

Obviously what is popular isn’t always what is right.  (And the prize for stating the obvious goes to Dr. Starr!)  I thought I’d try Wikipedia next.  Wikipedia can have many factual errors but it often gets the overall story line correct.  Unfortunately there isn’t an article on this subject.  There is on one the blood type diet though…

So what is a non-scientist to do?  There don’t seem to be a lot of options.

There are websites like mine at Understanding Genetics that try to give the real scoop on what current science says about various issues.  But they tend to focus on a single topic and don’t often appear at the top of a website search.  (Understanding Genetics is an exception in that it gets enough hits to often be on the first or second page if the query is worded in the right way.)

I am not sure what the answer is to getting better science via the web.  Maybe we need a web based encyclopedia about science written by scientists.

The tricky part will be to get them to do it.  And to have it make sense to anyone but another scientist in that particular field.  And for them to do it impartially.

I’m curious how other people find their science online.  And how they make sure it is reliable.

* This isn’t weird, blue eyes and red hair work the same way.




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Posted in Health, KQED | 5 Comments

Careful What You Choose

January 4th, 2010 by Dr. Barry Starr

When choosing an embryo, a little bit of knowledge is a dangerous thing.

People often think about certain versions of a gene as either good or bad. One that leads to depression is bad while one that protects you from HIV infection is good.

For most genes this is almost certainly too simplistic a view. Many versions of genes can be good or bad depending on your situation.

For example, the delta 32 version of the CCR5 gene can make you more resistant to HIV infection. But it also makes you more susceptible to infection by the West Nile Virus.

Which version is best for you depends on where and how you live. If you’re an IV drug user who lives somewhere up north, then you would probably benefit most from the delta 32 version. But if you are a faithfully monogamous man in Africa or Central America, then you might do better with the more common version of the CCR5 gene.

As I talk about in a recent GeneWatch article, the same is true for the SERT gene and depression. This gene comes in two versions, long and short.

Studies have shown that people who only have the short version are at a higher risk for depression. A deeper look at the data shows that this is only the case if these people had a traumatic childhood. People with two short versions who had a happy childhood are actually more resistant to depression than people with the longer gene versions.

This all matters because we are at the point where you can choose some of your child’s gene versions. And too simplistic a view of genes could cause you to make the wrong choice.

People who undergo in vitro fertilization (IVF) can go through an additional procedure called preimplantation genetic diagnosis (PGD). Basically PGD allows you to look at an embryo’s DNA before it is placed in the womb. This means that when multiple embryos are created, you can choose which one to implant based on its genes.

Fortunately we can’t really change the embryo’s DNA for the foreseeable future so you’re stuck with whatever genes you and your partner can contribute. But as we are able to look at more and more genes with less and less DNA, we are getting very close to a Gattaca-like future where we can choose many of our children’s genes.

And as the two previous examples showed, this won’t be a simple choice! There are undoubtedly hundreds of genes just like these where what effect they have on someone depends on how and where that person lives, how they were raised, etc. It might be best to restrict this sort of thing except for cases where the child might end up with a devastating illness like cystic fibrosis or sickle cell anemia.

In some ways, this sort of thing is already being restricted. For example, when a fertility doctor in L.A. suggested that he might offer parents a chance to choose what eye, hair, and skin color their children might have, the public uproar shut down the service before it even began.

I’m not sure that less politically sensitive gene selection would cause such a furor. It may be that we need some sort of government regulation to protect people from what they don’t know. Or maybe parents need to take a course before selecting which embryo they want…




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Posted in Health, KQED | 8 Comments

Don't Forget about Life Style Choices

December 21st, 2009 by Dr. Barry Starr

For most of us, avoiding these is just as important as the genes we inherit.

As someone who studies genes, I tend to give the environment short shrift. I have to watch out for that because it can cause a blind spot in how I think about biology. And how I live my life.

As readers of this blog might remember, I was recently diagnosed with metabolic syndrome just as I was undergoing DNA testing. This was a wake up call in a couple of different ways.

First off, it confirmed my belief that we can’t get a lot out of genetic testing for complicated diseases right now. I couldn’t look at my DNA and predict that I would end up with high cholesterol, triglycerides and glucose levels. We just don’t know enough yet about our genes to be able to figure this out from any available DNA test.

But I could have guessed this might be a problem from my lifestyle and family history. All four of my grandparents developed Type 2 diabetes which put me at a pretty high risk. Of course I thought I could beat the odds and so lived a life filled with couch sitting, Haagen Dazs, and Double Western Bacon Cheeseburgers (cue Homer Simpson drool). Until my diagnosis.

Then I decided to see if all this talk of diet and exercise actually can have a significant impact on me. Or was I destined to high cholesterol, triglycerides and glucose levels because of the genes I got from my parents.

The doctor told me to lose weight, exercise more and eat better. So I did.

I lost 30 pounds by changing my diet and walking 30 minutes a day. This dropped my body mass index (BMI) from overweight (27.8) to normal (23.5).

I also stopped eating most sweets, and cut my saturated fats down to 15 grams per day. And the effects on my blood work have been amazing.

Here are a few of the stats:



	Desired	9/21/2009	11/16/2009
Total Cholesterol	<200	205(H)	115
Cholesterol/HDL	<5	5.4(H)	2.5
Triglycerides	<150	351(H)	85
Fasting Glucose	70-100	122(H)	104(H)



As you can see, everything is now in the normal range except for glucose which is still a bit worrisome. Now I just need to maintain this regimen which, in America, won’t be easy.

I probably panicked and went overboard anyway. I should have tried to just add exercise and see if that was good enough. If not, then cut back on sweets and saturated fats. I did bad science on myself by changing too many variables at once.

I think what I can conclude is that my set of genes makes me particularly susceptible to my lifestyle choices. Some lucky people are born with genes that let them get away with poor diet and no exercise.

I am not one of those lucky ones. Although perhaps more lucky than those people who make these changes and still have these health issues.




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Posted in Health, KQED | 1 Comment

Beware Helicopter Parents

December 7th, 2009 by Dr. Barry Starr

Current DNA tests could not have predicted that George W. Bush would be our 43rd President of the United States.

Time recently had a great article on helicopter parents. These are the parents who hover around their kids, protecting them from any harm. They are undoubtedly doing this to ensure their kids’ success in life.

I don’t want to get into the plusses and minuses of this parenting style…to each his own. What I do want to do is to warn them away from a new genetic testing company that seems designed to target them.

This testing company, called My Gene Profile, claims to be able to use genetics to help parents figure out where their child’s inborn talents lie. The idea, then, is for parents to point their children towards interests or careers that match up with what the genetic test says.

The talents the company is looking at are not simple ones like tongue rolling or bending your thumb back (neither of which we can yet determine genetically). They claim to be able to tell you if your child will be smart, creative, good at sports, and near as I can tell, five other similarly broad traits.

This is impossible given our current knowledge of genetics. And frankly, I am not sure we’ll ever be able to figure any of this out with a simple genetic test. Most of these traits are more than just the DNA we inherit.

Let’s take IQ as an example. Most of the studies I have seen point to about half of someone’s IQ coming from genes and the other half from the environment. Any test done right now won’t look at how the environment affected a child’s DNA. And they certainly won’t look at how the environment influenced the growth and development of the brain or how it affected synapse connections or about a million other things to do with intelligence and the brain.

Still, 50% from genes is a lot. If we could get a complete readout of how our genes influence our IQ that might be at the very least interesting. But we can’t.

Scientists believe there are at least 100 genes that contribute to IQ. So far they’ve only identified a handful and none of them have been shown to have reproducibly significant effects on IQ.

For example, scientists have found that having certain versions of the CHRM2 gene affects your ability to organize things in a logical way. The effects aren’t huge though. 23andMe (a company that I have tested with) reports that the variations that they look at in this gene can lead to a 6 point swing in IQ. Woopty doo.

If you drill down a bit farther, some scientists claim that you can get much larger differences. For example, at the furthest extremes, people with one set of variations in this gene averaged an IQ of 85 while people with a second set averaged an IQ of 103. Sounds impressive.

Except that a larger follow up study was not able to see the same effect. In this study, scientists weren’t able to find any connection between variations in the CHRM2 gene and IQ. And CHRM2 is by far the best characterized IQ gene.

Most likely the way that genetics contributes to IQ is that each of the 100 or so genes tweaks IQ a bit higher or lower. So to get a complete readout on IQ you’d need to look at all of these genes. This is difficult to do right now since we only know about a few of them.

And to make things even more complicated, the genetic contribution to IQ probably isn’t a simple summing up of these different variations. They don’t exist in a vacuum—these gene variations all interact with each other too.

What this means is that we may never be able to get an accurate prediction about genetic IQ from our genes. There are lots of possible combinations all with different outcomes. In other words, everyone’s IQ genetics may be unique which would make predictions impossible.

The bottom line is that there is not nearly enough data out there to figure out someone’s IQ or intellectual potential. And this goes for athletic ability, creativity and any other similarly complicated trait. We can’t even predict eye color yet very well from our DNA!

So consumers be aware of what a genetic test can and can’t deliver based on what scientists know. Testing for cystic fibrosis, pretty good. Testing for intelligence, not so much.

A final example. Imagine that Einstein’s parents had tested his genes for IQ with a company that looked at four or five IQ genes. And let’s say that he happened to have versions of these genes that lead to a lower IQ. Of course, since it is Einstein his other 95 or 96 or so IQ genes swamp out the effects of these few genes. But the testing company misses this and recommends that he not take an academic career. A little knowledge is a dangerous thing.

*This is common with genetic studies. There is a promising result with a small group that disappears when scientists look at a larger group.




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Posted in Health, KQED | Please Comment

Who Owns My DNA?

November 23rd, 2009 by Dr. Barry Starr

If a DNA testing company gets bought out, what happens to their customers' DNA? Image by Molly Eyres. / CC BY 2.0

One niggling worry I had when I decided to get some genetic testing from 23andMe was what would happen to my DNA if the company failed. By all accounts, 23andMe is a very healthy company* so it was more of a theoretical worry for me. Not so for deCODEme folks…

Like 23andMe, deCODEme looks at hundreds of thousands of different areas of a customer’s DNA in order to predict that customer’s future health and provide information about his or her ancestry and traits. This week deCODEme’s parent company, DeCode Genetics, filed for bankruptcy. Press reports indicate that parts of the company will go up for auction. I am not sure if that includes deCODEme but I am sure all of their customers are sweating it out right now.

The big question now isn’t whether these people will still get good service from deCODEme. Instead it is what the company that buys deCODEme will do with all those customers’ DNA. Will they maintain deCODEme’s previous privacy policies? Or, in the worst case scenario, will they connect DNA to name and sell the combination to the highest bidder?

I have to say that at first I was a little panicky when I started thinking about this. Especially when I started to contemplate what my health insurance company would do to me if they got a hold of my DNA.

Everyone has some genetic problems lurking in their DNA and I am sure that insurance companies would be happy to limit or even drop people’s coverage based on this. The new health care reform bills are supposed to prevent an insurance company from dropping someone based on a pre-existing condition but I am not sure if something like this counts. If it doesn’t, then I would probably end up with a policy that doesn’t cover conditions my DNA says that I am more likely to get. (Very useful insurance!)

If the new bill does consider potential risks from our DNA a pre-existing condition, then this isn’t really that big a worry. Except that I bet the new bills allow the insurance companies to jack up someone’s premiums based on their pre-existing conditions. In which case they’ll charge me so much I’ll have to drop my coverage anyway.

The other possible uses for my DNA that I could think of paled in comparison to this one. For example, I don’t think I’d mind if they sold my DNA to a pharmaceutical company so that the company could make a useful drug. Or to academics so that my DNA could be used to learn something about the human genome. It seems like those are sort of noble purposes for my DNA, kind of like donating it to science.

I couldn’t really think of much else that other companies might do with my DNA. Of course if the health insurance scenario were to happen, that would be plenty bad enough.

* Especially since one of the cofounders, Anne Wojcicki, is married to Sergey Brin, Google cofounder.




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Posted in Health, KQED, Partners | 7 Comments

Trick or Trait

November 9th, 2009 by Dr. Barry Starr

"Mysteries of DNA" image courtesy Mark H. Adams. Full-size version.

As anyone who follows this blog knows, I recently took a 23andMe genetic test and have been blogging about it ever since. Today I thought I would focus on one of the fun parts of the service: traits.

Lots of our traits are at least partly dependent on our genes. So a genetic test should be able to tell me a bit about what I’ll look and even be like in the future. It may even tell me what I can expect for my kids.

Here is what is available on the 23andMe test (click on the image for a larger version):



As you can see, some of this is pretty obvious…I know my eye color for example. It is kind of cool to see my blue eyes written in my DNA but not necessarily that helpful. When I click on eye color, I find out that people with this particular bit of DNA have a 72% chance for blue eyes, a 27% chance for green and a 1% for brown. (Incidentally, this 1% brown is probably a big reason why blue-eyed parents can have a brown-eyed child.)

What would have made this report more interesting for me is what it meant for my kids’ eye color. Does it mean I’ll have blue-eyed kids? This of course depends on my wife’s genes but it would be cool to have the option of including my wife’s data to find out.

Other less obvious traits were very interesting to me. The results say that like most mammals, I should be lactose intolerant. Which I am not—I’m fine drinking milk. So did 23andMe get it wrong?

Probably not. The science is pretty good on this topic. People with a certain difference in their lactase gene almost always lose the ability to make lactase as adults. No lactase means lactose intolerance.

When I dug deeper on the website I got some hand waving about other genetic influences or the environment. A better explanation is that I will probably become lactose intolerant at some point in my adult life—it just hasn’t happened yet.

Losing the ability to make lactase is a gradual thing. It happens to some people early in adulthood and others later on. I am probably one of the “later ons.” Something to look forward to…

One trait that I’ve always been a bit interested in is HIV resistance. Some people are more resistant to infection by HIV (the virus that causes AIDS). If these people do become infected, they tend to develop AIDS symptoms much more slowly as well.

In Europeans at least, this resistance has been tied to a DNA difference called CCR5-delta32. The people who are resistant to infection and who develop AIDS more gradually tend to have two copies of this DNA difference.

This DNA difference has been proposed to have become common in Europeans because it also makes people resistant to either the plague or smallpox. If true, my ancestors must have died like flies from the plague or smallpox because I don’t have the DNA difference.

I also now know about what my DNA tells me about my earwax, how I respond to a certain bitter chemical, and whether I flush from alcohol. These are sort of interesting but not very.

This part of the 23andMe experience is kind of fun though. I really enjoy it when genetic theory matches up with what I can see about me. It sort of validates genetics…




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An Incomplete for 23andMe's Carrier Testing

October 26th, 2009 by Dr. Barry Starr

What can genetic testing tell you?

A while back I took a 23andMe genetic test that looks at over 600,000 different spots on my DNA. The last few blogs I have been going over my genetic test results with an eye on how useful they are. And how well the results are explained.

Last blog I wrote about how current genetic tests aren’t that great at predicting your risk for common, complicated diseases like diabetes or Alzheimer’s. This time I thought I’d focus on what today’s genetic tests can be very good at and whether or not 23andMe does a good job with these.

Current genetic tests are very good at predicting your risk for rare, simple genetic diseases like cystic fibrosis (CF) or Huntington’s disease (HD). And at predicting the chances that your kids will get these diseases too.

Genetic tests for these diseases work because most of them are caused by a single gene gone awry. Testing for a single gene is relatively easy.

For example, most cases of CF happen because of known differences in the CFTR gene. A genetic test can look for these differences and tell you if you and/or your spouse have any of them. If you both do, they can also give you a pretty good idea about the chances that your kids will get them too.

Of course, we don’t know all of the differences in the CFTR gene that can cause CF. And some differences only cause CF some of the time. And there are people with everyday, run-of-the-mill CFTR genes who get CF because of differences in different genes.

Still, as genetic tests go, these are pretty good. If a test comes up with a known CFTR difference that causes CF, then you have a pretty good idea of what your chances for developing CF are. If your spouse gets tested too, then your kids’ chances can be determined as well.

So how does 23andMe do? OK, I guess…

First off, they look at eight of these sorts of diseases under a category called Carrier Status. The diseases they look at are shown in this image:



For me, the first big result is that I am a carrier for a variant that can lead to hemochromatosis. This isn’t surprising since 1 in 8-12 people of Northern European descent in the U.S. are too, but it is definitely something to watch out for. It may be important for my wife to be checked too so we can make sure none of our kids got two copies. (Luckily hemochromatosis is easily treated by giving blood on a regular basis.)

Some of the other results are less illuminating. For example, I do not carry the CF difference they test for (delta F508). This is of course great news. Unfortunately, this variant only accounts for about half of the CF cases out there. Which means I could be a carrier for CF, just not a carrier of the most common variant that they happen to test for.

The same thing goes for most if not all of the other carrier status diseases (sickle cell anemia is an exception). Some like BRCA (breast cancer) are as poorly covered as CF while others like Bloom’s disease cover a larger percentage of cases.

23andMe is pretty upfront about the limitations of their testing once you dig a bit into the results. But still, if they’re going to look at 600,000 different parts of my DNA, you’d think they could add a few more to give me a stronger answer about whether or not I am a CF carrier.




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Posted in Health | 1 Comment

Do These Genes Make Me Look Diabetic?

October 12th, 2009 by Dr. Barry Starr

Could a genetic test have told me I was at a higher risk for developing type 2 diabetes? Image source: aldenchadwickThis sounds contrived but it isn't.  A couple of weeks ago I was diagnosed with metabolic syndrome.  Right when I am in the middle of talking about genetic testing!

Metabolic syndrome isn’t quite as scary as it sounds.  Basically I am on my way to type 2 diabetes.  But if I eat better and get off the couch, I should stave off the disease and get better.

My question, naturally, is whether or not a genetic test could have told me I was at a higher risk for developing type 2 diabetes.  And whether I would have done anything with that result.

As you know if you’ve been following my blog, I took a 23andMe genetic test and have been writing about it since.  The image below shows what the front page of my clinical report looks like (click to enlarge):



According to the DNA checked in this test, I am in the average risk range for type 2 diabetes.  This doesn’t really seem to line up with my reality.  But I might not expect it to since these genetic tests are so limited right now.

This kind of test can be informative with the yes answer—yes I carry a certain version of a gene that might lead to a disease.  But the no answer isn’t that useful.  It doesn’t mean that they've looked at all the possible genetic differences that can lead to a disease and I don’t have any of them.  Basically it means that they didn’t find the specific genetic difference they were looking for.

Now I wouldn’t necessarily have predicted that any genetic test available right now could tell me a lot more than that.  Type 2 diabetes is too complicated for that and a whole lot more research will need to be done to get a genetic test useful to lots of people.

But still, this is probably what people are looking for with these sorts of genetic tests.  Will I get cancer, type 2 diabetes, Alzheimer’s, Parkinson’s, etc.?  For most of these cases, the tests can tell you a lot about rare forms of these diseases but little about the more common forms.

So the no answer didn’t really help me much.  Here I am on my way to being a diabetic and the test said I was at average risk.  Of course, I suppose I didn’t even need to take a test… all four of my grandparents came down with type 2 diabetes.  Like lots of these complex diseases, family history is the best predictor.

The second part of my question is a hypothetical one.  Let’s say they had a perfect genetic test that said that I was at an increased risk for type 2 diabetes.  Would it have changed my behavior?  I’m not sure but probably not.

I certainly wouldn’t have changed any of my behaviors when I was young.  I was invincible, remember?

Now that I’m a bit older, such a test might have influenced my behavior a bit.  I already knew about my risk because of my grandparents but my thought has always been that maybe I got lucky and didn’t inherit their tendencies towards diabetes.  But if they were tested and we shared the same genetic differences that led to type 2 diabetes, then I might be worried enough to change what I was doing.

Most likely though, my behavior modification wouldn’t be perfect.  What I’d probably do is keep watching TV and eating Twinkies but get my blood sugar tested more often.  Once I was headed for diabetes, then I’d modify my behavior and keep it at bay.  (I’m sure doctors scream into their pillows at night because of patients like me.)

This is different than some people’s reactions to other genetic tests.  For example, some women who find out they have the version of BRCA1 that greatly increases their chances of breast and ovarian cancer have a double mastectomy and/or a hysterectomy before there are any signs of cancer.

I might react much more strongly with a valid cancer genetic test.  Cancer is scary, nasty and not really reversible.  Type 2 diabetes is different.  You can start down the road, modify your behavior and then nip it in the bud.  Carpe diem and then pay the piper.




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Posted in Biology, Health, Partners | 4 Comments

Genetic Tests: When No Means Maybe (Part 2)

September 28th, 2009 by Dr. Barry Starr

Are they related to me? I still don't know…When last I left you, I was searching for my great-great grandmother’s DNA in my own DNA.  Remember, legend has it she was Cherokee and I wanted to confirm the legend with a genetic test from a company called 23andMe.

In my last blog post, I showed how the two most powerful ancestry tests, mitochondrial DNA (mtDNA) and Y chromosome, were useless to me in my hunt. Now I want look at the rest of my DNA.  So here we go!

The Y chromosome and mtDNA are a small fraction of my DNA—something like 0.8% of the total DNA in one of my cells.  But they are incredibly useful because they change very little from generation to generation.  The mtDNA I got from my mom is probably exactly like hers.  Same with most of the Y I got from my dad.

The other 99.2% of my DNA is a lot trickier to look at from an ancestry perspective because it has changed a lot from generation to generation over time.  For example, the chromosomes I inherited from my parents are not the same as the ones they have.  I got a mix of their chromosomes

For example, my mom had two copies of chromosome 1 (and two copies of her other 22 chromosomes too).   As you know, she passed one chromosome 1 to me (my dad gave me my other one).  But, through a process called recombination, her two copies of chromosome 1 swapped DNA so that I got a hybrid of her two copies.  I inherited a unique chromosome never before seen.

This is all well and good from a survival of the species point of view, but it is a problem for ancestry testing.  Imagine that instead of my mom, we look at my Cherokee great-great grandmother.  She has just had a child who inherited a mix of her chromosome 1’s.  This chromosome will look Native American and the child would appear half Native American.

Actually, the test isn’t perfect yet and so there isn’t yet a “Native American” set per se.  Instead, here is how 23andMe describes Native American DNA in their tests:

“…people who identify themselves as Native American exhibit fairly consistent Ancestry Painting proportions of about 75% Asian and 25% European, plus or minus 10%.”

This means the chromosomes the child got from his or her mom won’t look Native American but instead will look 75% Asian and 25% European.  (See a realted post of mine elsewhere for why it looks like this.) Now imagine that this half Native American child grows up and has my grandfather as his or her son.

My grandpa will inherit a mix of his parents’ DNA too.  In this case the Native American DNA will mix with the European DNA to create a hybrid.  On average, you would now see something along the lines of 37.5% Asian (this is a simplification but it gets us into the ballpark of the number we might expect).

Each generation would see, on average, a continued dilution of this Asian part.  My dad would have 18% Asian, I would have 9%, etc.  Here are my ancestry results (click the image to enlarge):



Not a hint of Asian.  Looks like my great-great grandma wasn't Cherokee.  Or was she?

There are lots of ways she could still be Cherokee.  First off, I don’t know how solid the 75% number is for all Native Americans.  I don’t know how many Native Americans are in their database.  I also don’t know how much variation there will be tribe to tribe.

Secondly, you may have noticed that I was very careful to always say, “on average.”  This is because the recombinations don’t have to be a 50-50 swap.  It is true that if you look at a large number of recombination events, the average will be 50%.  But individual recombination events can be biased towards one or more chromosomes.  Occasionally you’ll get mostly one chromosome and sometimes mostly the other.

Sort of like flipping a coin—do it enough and you’ll get pretty close to half heads and half tails.  But if you flip a coin twice, you might get one head and one tail.  And you might not.  Half the time you’ll get two heads or two tails.

This is less a problem than you might think with our chromosomes since the recombination is spread over 23 pairs with each pair being independent of the others.  But it can still throw a monkey wrench into the works.  23andMe actually has a nice chart that hints at this by giving the most likely range of possibilities.  Unfortunately, this chart didn’t come up with my results and I had to stumble on it while I was playing around.

Using the chart, I can see that the bottom end of my expected results in 0.24% “Native American” (if I am reading the chart correctly).  That is pretty low and it seems like a pretty minor mistaken assumption at the beginning might knock this down to zero.

So where am I after this?  Still in the dark.  This is actually how many genetic tests end up.

The positive result tells you a lot.  Had there been Native American DNA, that would have been a slam dunk.  (This isn’t always the case with genetic tests but it would be here.)  But there wasn’t.  Which means, given that I was on the edge of detection, that she may or may not have been Cherokee.

Now, this isn’t 23andMe’s fault.  The test itself couldn’t be conclusive given how far back we need to go and the DNA tests that 23andMe offers.  In fact, 23andMe does an excellent job of presenting the data.  There are pretty chromosome paintings, graphs superimposed on world maps, etc.  All very nice.

I am still worried that the explanations that go along with these images assume an awful lot of knowledge that most people might not have.  Without that knowledge, it can be hard to assess the significance of a certain result.  Next blog that’ll become even more important as I tackle health conditions.




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