6 ms·

UC Berkeley Students Denied Genetic Test Results

14 points by miked 16y ago

carbocation 16y ago
There is a discussion to be had about whether or not the students should receive their test results. However, the author does not seem to fully understand what he's discussing. First, there is the issue of our limited genetic knowledge. Genetic tests are currently based on a sample of 1 out of every ~3000 nucleotides in your genome. Therefore, although they do cover the vast majority of common variants, they cannot tell the full story. You may have a detected SNP that predisposes you to some risk of disease, but at the same time you may have a rare variant - not picked up by the tests - that is virtually guaranteed to protect you from the same disease. This is not trivial, as rare variants are common (everyone has lots of rare variants; however, few people share the same rare variants). Furthermore, most SNPs that are associated with disease have not been demonstrated to be causal for disease. In fact, I'm aware of only a small number of SNPs that are not in exons (coding regions of genes) that are nevertheless known to be causal: one is rs12740374, which causes a decrease in LDL production via a novel pathway. I suppose my point is that there is a large ethical debate that hinges on our scientific knowledge of the limitations of genetic testing. This author seems not to know about this, or not to care, and instead has chosen to write a polemic. I find this unfortunate.
- bmallerd 16y ago
  The article says students were only going to receive their SNP profiles for three genes (lactose digestion, alcohol digestion and folate absorption). I can't imagine how access to this information would radically any student's life paradigm. This sort of demonstration would've vastly increased my interest in first year introductory biology. It's unfortunate that such a great educational opportunity has been lost.
  - carbocation 16y ago
    It is unfortunate that they didn't set up their procedure in a way that was compatible with informed consent. Surely that could have been done easily, had it been considered in advance. They thought things out pretty well - choosing genes that aren't exactly disease oriented - but just not all the way. It would definitely have been fun for the students who chose to participate.
- AngryParsley 16y ago
  There is a discussion to be had about whether or not the students should receive their test results. An extremely one-sided discussion. Genetic testing is already very useful, and it's only going to get more useful. First, there is the issue of our limited genetic knowledge. Our knowledge is incomplete, but it's far from useless. Genetic testing lets us know what foods or drugs are particularly harmful or beneficial. It lets people know of future disease risks. Knowing about these risks helps people change their lifestyles to reduce risk, or at least plan for the future. While today's test results aren't 100% accurate, they give the best probability estimate based on currently available science. To say that no information is better than this is absurd. People don't want to restrict other diagnostic tests, even though they can be similarly inaccurate. It's simple technophobia that causes newer tests to be regarded with suspicion. Also, there's the issue of rights. It's my DNA. I have trillions of copies of it in my body. I am literally made of this stuff. If human beings have any right over their own bodies then they should be able to read their DNA.
  - carbocation 16y ago
    I'm not sure that we're talking about the same type of genetic testing. Perinatal genetic testing is highly useful, because you can literally save a person's life by early knowledge of genetic diseases. Getting GWAS data from 23andMe, on the other hand, is generally not so much useful as it is entertaining. The best probability estimate for most adult diseases still comes from history and the physical exam, not from genetic tests. > Also, there's the issue of rights. It's my DNA. I have trillions of copies of it in my body. I am literally made of this stuff. If human beings have any right over their own bodies then they should be able to read their DNA. I am most sympathetic to that argument.
    - AngryParsley 16y ago
      Getting GWAS data from 23andMe, on the other hand, is generally not so much useful as it is entertaining. I mostly agree, although 23andMe did tell me something very useful. I have the two G alleles for rs4680. (http://www.snpedia.com/index.php/Rs4680 http://www.snpedia.com/index.php/Rs4680) One research paper said I am likely to respond well to Modafinil. I now find Modafinil extremely useful. While 23andMe is mostly for the coolness factor right now, it's only going to get better. For a small fraction of people, data from services like 23andMe is undeniably useful, since it will tell them things we do know with high probability (drug interaction/metabolism, early-onset Alzheimer's from ApoE4, etc). The best probability estimate for most adult diseases still comes from history and the physical exam, not from genetic tests. I meant that genetic testing along with a physical exam is more useful than just a physical exam.
- bhickey 16y ago
  I think the parent is spot on. Just some background in brief: Single nucleotide polymorphisms (SNP in the singular) are single base changes in the genome. Given the size of the genome (approximately 3 billion bases), the mutational rate, and the time since all modern human populations diverged from a single ancestral group (sorry, no number off the top of my head) we should expect that each position has mutated no more than once. So, for the most part SNPs come in two flavors, a minor allele and a major allele. If the SNP is associated with disease, one allele is called the risk allele, while the other is the protective. Down to business. For a SNP and a disease, we can compute the odds ratio or relative risk (there is a difference) for that SNP. Suppose you have the risk allele, the relative risk is 2, and the frequency of disease is 1% -- congratulations, you have a nominal 2% chance of developing the disease. Alright, onto the problems: For most complex diseases, this doesn't help us in the slightest and is non-informative. There are a lot of markers, these diseases are rare, genetic risk might well be subsumed by environmental effects. (Good rule of thumb: Don't smoke cigarettes, don't be obese. Eat your vegetables. I'm a scientist, not a doctor.) If you test someone, you'll invariably get a pile of risk alleles for some disease, just because there are a lot of diseases and a lot of SNPs. This will invariably cause distress in at least some people. The harm done to the subjects would clearly exceeds the benefits to them. Given the study design there's no reasonable way to obtain informed consent from the subjects if they're to be informed of the results. Without informed consent, you can't gather the data in the first place.
- Dylan16807 16y ago
  On the other hand, the fact that it's inaccurate and weak suggests even more that it's not 'clinical'.

14 points by miked 16y ago

There is a discussion to be had about whether or not the students should receive their test results. However, the author does not seem to fully understand what he's discussing. First, there is the issue of our limited genetic knowledge. Genetic tests are currently based on a sample of 1 out of every ~3000 nucleotides in your genome. Therefore, although they do cover the vast majority of common variants, they cannot tell the full story. You may have a detected SNP that predisposes you to some risk of disease, but at the same time you may have a rare variant - not picked up by the tests - that is virtually guaranteed to protect you from the same disease. This is not trivial, as rare variants are common (everyone has lots of rare variants; however, few people share the same rare variants). Furthermore, most SNPs that are associated with disease have not been demonstrated to be causal for disease. In fact, I'm aware of only a small number of SNPs that are not in exons (coding regions of genes) that are nevertheless known to be causal: one is rs12740374, which causes a decrease in LDL production via a novel pathway. I suppose my point is that there is a large ethical debate that hinges on our scientific knowledge of the limitations of genetic testing. This author seems not to know about this, or not to care, and instead has chosen to write a polemic. I find this unfortunate.

bmallerd 16y ago
The article says students were only going to receive their SNP profiles for three genes (lactose digestion, alcohol digestion and folate absorption). I can't imagine how access to this information would radically any student's life paradigm. This sort of demonstration would've vastly increased my interest in first year introductory biology. It's unfortunate that such a great educational opportunity has been lost.
- carbocation 16y ago
  It is unfortunate that they didn't set up their procedure in a way that was compatible with informed consent. Surely that could have been done easily, had it been considered in advance. They thought things out pretty well - choosing genes that aren't exactly disease oriented - but just not all the way. It would definitely have been fun for the students who chose to participate.
AngryParsley 16y ago
There is a discussion to be had about whether or not the students should receive their test results. An extremely one-sided discussion. Genetic testing is already very useful, and it's only going to get more useful. First, there is the issue of our limited genetic knowledge. Our knowledge is incomplete, but it's far from useless. Genetic testing lets us know what foods or drugs are particularly harmful or beneficial. It lets people know of future disease risks. Knowing about these risks helps people change their lifestyles to reduce risk, or at least plan for the future. While today's test results aren't 100% accurate, they give the best probability estimate based on currently available science. To say that no information is better than this is absurd. People don't want to restrict other diagnostic tests, even though they can be similarly inaccurate. It's simple technophobia that causes newer tests to be regarded with suspicion. Also, there's the issue of rights. It's my DNA. I have trillions of copies of it in my body. I am literally made of this stuff. If human beings have any right over their own bodies then they should be able to read their DNA.
- carbocation 16y ago
  I'm not sure that we're talking about the same type of genetic testing. Perinatal genetic testing is highly useful, because you can literally save a person's life by early knowledge of genetic diseases. Getting GWAS data from 23andMe, on the other hand, is generally not so much useful as it is entertaining. The best probability estimate for most adult diseases still comes from history and the physical exam, not from genetic tests. > Also, there's the issue of rights. It's my DNA. I have trillions of copies of it in my body. I am literally made of this stuff. If human beings have any right over their own bodies then they should be able to read their DNA. I am most sympathetic to that argument.
  - AngryParsley 16y ago
    Getting GWAS data from 23andMe, on the other hand, is generally not so much useful as it is entertaining. I mostly agree, although 23andMe did tell me something very useful. I have the two G alleles for rs4680. (http://www.snpedia.com/index.php/Rs4680 http://www.snpedia.com/index.php/Rs4680) One research paper said I am likely to respond well to Modafinil. I now find Modafinil extremely useful. While 23andMe is mostly for the coolness factor right now, it's only going to get better. For a small fraction of people, data from services like 23andMe is undeniably useful, since it will tell them things we do know with high probability (drug interaction/metabolism, early-onset Alzheimer's from ApoE4, etc). The best probability estimate for most adult diseases still comes from history and the physical exam, not from genetic tests. I meant that genetic testing along with a physical exam is more useful than just a physical exam.
bhickey 16y ago
I think the parent is spot on. Just some background in brief: Single nucleotide polymorphisms (SNP in the singular) are single base changes in the genome. Given the size of the genome (approximately 3 billion bases), the mutational rate, and the time since all modern human populations diverged from a single ancestral group (sorry, no number off the top of my head) we should expect that each position has mutated no more than once. So, for the most part SNPs come in two flavors, a minor allele and a major allele. If the SNP is associated with disease, one allele is called the risk allele, while the other is the protective. Down to business. For a SNP and a disease, we can compute the odds ratio or relative risk (there is a difference) for that SNP. Suppose you have the risk allele, the relative risk is 2, and the frequency of disease is 1% -- congratulations, you have a nominal 2% chance of developing the disease. Alright, onto the problems: For most complex diseases, this doesn't help us in the slightest and is non-informative. There are a lot of markers, these diseases are rare, genetic risk might well be subsumed by environmental effects. (Good rule of thumb: Don't smoke cigarettes, don't be obese. Eat your vegetables. I'm a scientist, not a doctor.) If you test someone, you'll invariably get a pile of risk alleles for some disease, just because there are a lot of diseases and a lot of SNPs. This will invariably cause distress in at least some people. The harm done to the subjects would clearly exceeds the benefits to them. Given the study design there's no reasonable way to obtain informed consent from the subjects if they're to be informed of the results. Without informed consent, you can't gather the data in the first place.
Dylan16807 16y ago
On the other hand, the fact that it's inaccurate and weak suggests even more that it's not 'clinical'.