On BioScience and Life and Such

Posts Tagged ‘genetic testing’

I am less likely to support environmental laws – not

In Uncategorized on June 23, 2021 at 12:30 pm

I while ago, I uploaded my 23andMe data to Genomelink. Partly because 23andMe stopped reporting traits, partly because I was curious and partly because I just finished writing up my genetic counseling master thesis where consumer genetics was a central topic.

Unfortunately, I haven’t been able to practice much genetic counseling and 23andme still doesn’t have traits, – so I continued following my Genomelink-results as a way to keep me on my toes. The reports they make are questionable at best and horrifically misleading at worst. No better way to sustain interest than reading things that upset you – … right ?

The latest example is my genetic result-report on “Views on Environmentalism”. Based on two SNPs (rs1397924 and rs4902960), according to Genomelink, I am “less likely to support environmental laws by the government, and that regulations for the environment are needed.”.

So, this was a report that immediately fell squarely into the “misleading” category even before I started fact checking, – hence sorted into a box that already contained “Dog allergy” (which they claim I don’t have while I do), “Vulnerability to Computer Frustration” (which they claim I don’t have, but everybody does, – especially me) and “Left-Handedness” (which they got wrong).

The good thing though, – and the reason I keep looking into these results, is that it got me looking into behavioral genetics. A cool, but also scary field of research. There is a genetic component to all behaviors studied to date and the nature/nurture interaction is particularly fascinating when it comes to genetics in the social sciences.

A really good intro into one of those interaction mechanisms is the story of the MAOA-gene. Again misleading, this gene has been called the “warrior gene”, because one finds a link between MAOA-variants and aggression. However there is strong evidence to support that these agression effects will not manifest unless there’s a environmental trigger (like being abused or paid money to be cruel):

“These findings suggest that some behavioral traits are co-dependent on (1) the possession of genetic risk and (2) exposure to environmental stressors in order for them to manifest.”

Tanksley PT, Motz RT, Kail RM, Barnes JC, Liu H. The Genome-Wide Study of Human Social Behavior and Its Application in Sociology. Front Sociol. 2019;4:53. Published 2019 Jun 26. doi:10.3389/fsoc.2019.00053

So, when it comes to your predisposition to a certain behavior, your genetic risk may never be exposed, or conversely your lack of risk may never benefit you, unless you experience that external trigger.

The nicest possible way then to interpret this clearly wrong conclusion from my Genomelink report, is that I just haven’t experienced that environmental trigger to turn me into a climate-denialist.

Turns out however, that the paper cited for the finding, by Genomelink themselves, directly warns about making conclusions such as those made. Here it is:

“In summary, our molecular-genetic–based estimates of heritability partially corroborate the twin-based estimates and suggest that molecular genetic data could, in principle, be predictive of preferences. Our other results, however, suggest that excitement about the practical usefulness of molecular genetic data in social science research needs to be tempered by an appreciation that much of the heritable variation is likely explained by a large number of markers, each with a small effect in terms of variance explained. As a consequence, for economic and political preferences, much larger samples than currently used will be required to robustly identify individual SNP associations or to generate sizeable predictive power from many SNPs considered jointly.”

Benjamin DJ, Cesarini D, van der Loos MJ, et al. The genetic architecture of economic and political preferences. Proc Natl Acad Sci U S A. 2012;109(21):8026-8031. doi:10.1073/pnas.1120666109

No sizeable predictive power. Sorry Genomelink: no sigar, not even close.

I’ll keep supporting that “regulations for the environment are needed” then.


Certifiably certified

In Uncategorized on December 20, 2010 at 10:41 am

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Our lab is now ISO-13485 certified. Let me assure you that a lot of hours went into this.

If you for any reason, need a lab to make you a molecular biology diagnostic test, we’re the ones to call.

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Finally some serious genetic testing (post I)

In Uncategorized on September 18, 2009 at 12:49 pm

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The structure of Cholesterol
Image via Wikipedia

Despite some ridiculous legal obstacles in this country, we are finally able to set up some proper genetic tests. I need to update myself on these tests – and what better way than to do it while blogging about them at the same time.

We are setting up 8 tests in this first stage of expansion, which I plan to cover in 5-6 posts.

1. Familal Hypercholesterolemia. A disease leading to highly elevated levels of cholesterol and increased risk of heart disease (good review here). Rough numbers: heterozygosity 1:500, homozygosity 1:1000000. Multiple genetic variations (SNPs, insertions/deletions) in LDL-receptor gene. Preferred analytical method: sequencing or genotyping (real-time PCR) a selection of genetic variants.

Normal function of the hepatic low-density lipoprotein (LDL) receptor is obligate for normal levels of plasma LDL cholesterol. The LDL receptor regulates the concentration of plasma LDL cholesterol by internalizing apolipoprotein B-100- and apolipoprotein E-containing lipoproteins by receptor-mediated endocytosis. Mutations in the gene encoding the LDL receptor protein give rise to one of the most common classical autosomal dominant inherited disorders in man, familial hypercholesterolemia (FH). The estimated prevalence of heterozygous FH is 0.2% (1:500) in most populations of the world. – from here

In addition to LDL-receptor mutation analysis (which will take a little while to set up) we’ll be doing SNP-analysis for ApoB-100. One SNP-assay of R3500Q in the ApoB-100 gene.

Familial defective apolipoprotein B (FDB) caused by the R3500Q apolipoprotein B gene mutation may mimic FH but the clinical course, however, is often milder than that seen in patients with LDL receptor gene mutations. -from here

Tests to follow: Thrombophilia, Hemochromatosis, Lactose intolerance, Osteoporosis, Macular degeneration and Crohn’s Disease.

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On testing for Downs syndrome

In Uncategorized on March 4, 2009 at 12:42 pm

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Photograph of child with Down's syndrome showi...
Image via Wikipedia

The following is my response to this Mary Meets Dolly post on prediagnostic genetic testing for Downs Syndrome.

To add some facts arguing against your view on genetic testing for Downs syndrome:

In my home country, where the right to abortion has been established many, many years and where every women (public healthcare) over the age of 38 is offered genetic testing for trisomy 21, the number of children born with Downs has remained unchanged also after the introduction of genetic testing. Thus, your assumption that this testing leads to less children born with this syndrome may not hold true. Also, I do not think that most people believe that the world would be a better place without Downs. I think however, that most people understand that this is a severe disease and that life with Downs is a challenge for the family as a whole. As for the lessons of life, it is truly sad when someone says that we need the sick and disabled to learn these lessons. Such a statement demeans these patients by saying they function as tools for us to understand the less fortunate.

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The need for restraint III

In Uncategorized on February 21, 2009 at 5:38 pm

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Missionary style sex position.

Just too much fun! via Wikipeda

I once thought overselling science was the biggest threat to scientific credibility. Credibility scientists need to achieve general acceptance in the public, and subsequently continued funding (progress).

Recent developments have made me think that rushing into commercializing new biomedical technology,  like embryo sorting and genetic testing may pose a larger threat. Examples are genetic tests for athletic ability and embryo sorting based on more or less uncertain predictions of phenotypes without medical significance.

Granted, athletic testing and embryo sorting will  not become a reality for most of us for a long long time. Athletic ability one can usually assess wit the naked eye, and having sex to create offspring is far too much fun for it to go away.

– Then all the more reason to pause and think twice before unleashing commercial products to the unsuspecting and unschooled (in genetics) lay man. Even more reason to pause, when those products have disputable accuracy and are of questionable value

These are the early days of the genomic era, there are many, many things we still do not know, especially when it comes to the nature vs. nurture relationships. Since the future keeps evading finite predictability,  absolute disease risks (or any other risks or absolute probabilities for that matter) within the full time span of a human life, remains utopic.

We are moving in the right direction, all-encompassing disease prevention and/or treatment is on the horizon together with increased longevity.

Let’s not screw it up for ourselves. Our credibility is all we have, – please people show some restraint…..

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By this certificate I am certifiably decision-certified

In Uncategorized on December 9, 2008 at 11:40 am

Christmas came early this year. Thank you Andrew of ThinkGene:

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This pisses me off a little

In Uncategorized on November 19, 2008 at 9:47 pm

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From this Nature News piece on preimplantation SNP scans of embryos (my highlighting).

[Jacques] Cohen [research director at Reprogenetics, a genetic-testing company in West Orange, New Jersey] says that as the understanding of disease genetics progresses, use of tests that seem controversial now may become more acceptable in the future: “If you had the chance to decrease your child’s risk of a disease like diabetes and you didn’t, society would blame you.

So much is wrong with this statement.

First he is taking the focus away from the very real and disturbing issue of embryo-sorting based on uncertain risk estimation of predisposition to complex disease.

Secondly his statement underscores the importance of the environmental factor in such complex diseases, but it completely misses the point. If you want your children to avoid diabetes, then make them eat right and exercise. You can do that today without any knowledge of their genetics.

Thirdly, currently, society doesn’t seem to blame parents that neglect their children’s health by feeding them unhealthy food or fail to encourage (enforce) physical activity, – why would a genetic test change that.

Lastly, putting such blame on parents has some very problematic socio-ethical issues attached to it.

I hope this is an example of misquoting, I really do….

Update – more on the company Reprogenetics in this post on Sandwalk.

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DTC-testing concluded for now

In Uncategorized on November 6, 2008 at 11:15 am

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{{es|The Doctor.

Image via Wikipedia

A lot has been said about (and argued over) Direct To Consumer (DTC) testing. For extensive coverage of the pros and cons of regulation of such genetic testing please go see The Gene Sherpa and Genetic Future (also, check out a number of recent papers in Nature, – to find them, go read the relevant posts at The Genetic Genealogist or Genetic Future). I have voiced opinions on this too, but have decided to desist more arguing (for a while) after reading this editorial in Nature biotechnology:

1. We need to move from late to early diagnosis

It is virtually impossible to conceive of a sustainable form of healthcare that operates as the current systems in industrialized nations do. At present, healthcare is based on the late diagnosis of disease and the division of diseases into a few categories based on some overarching gross similarities. And it firmly places physicians as the central gatekeepers of information.

2. To do this we need find ways to utilize the potential unleashed by large scale analysis of genetic-material.

The healthcare of the future, on the other hand, if the technical potential to provide personalized medicine is ever to be realized, will probably require a greatly expanded emphasis on diagnosis and monitoring, early and subtle intervention, monitoring of the impact of intervention, and gradual adaptation of treatment with the evolving physiology, metabolism and lifestyle of the individual.

3. But, the medical professionals and healthcare systems do not currently have the capacity to adequately respond.

Faced with this huge expansion of data on ‘my’ health, it will simply not be affordable to maintain our dependence on medical gatekeepers, whether they are physicians or genetic counselors, without individuals taking a much greater responsibility for their own wellbeing. Whether the medical establishment likes it or not, it will be too cumbersome and too expensive to conduct personalized medicine if all diagnostic-to-therapeutic decisions depend on doctors.

4. Therefore, In order to adapt to this new situation, we need to find the golden mean between no regulation and over-regulation.

For personal genomics not to be stillborn, the medical community and regulators thus need to reevaluate their role as gatekeepers. Clearly, they need to be involved in the medical actions that might follow as a consequence of genetic or other diagnostic testing. And for any gene test, regulators must ensure that companies make claims to consumers that are both truthful and accurate. But simply shutting down the whole direct-to-consumer gene testing enterprise because it departs from the traditional genetic testing paradigm of doctorordered test will both retard progress and stifle investment in more advanced whole-genome sequencing technologies—technologies that have the potential to ultimately deliver the promise of genomedirected medicine.

Regulation is obviously needed at some level. However, I reside in a country where regulation completely stifles any attempt to do personalized medicine, even at the most innocent (Cyp 450) level. I strongly advise against such an approach. Transferring all testing currently offered by DTC companies, to existing health-care programs will flood the system, and hence is not an option either.

In my opinion, there is an imminent need to define the subgroup of genetic tests that needs to be accompanied by counseling/medical advice. Group those out sensibly, grade them according to counseling importance, and you have a solution.

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No I do not need a genetic scan to know my kids

In Uncategorized on October 31, 2008 at 10:40 am

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I have three children. I know them very well. Every parent should. I know that they have strengths, – some things they do very well (they know it too). I know that they struggle with other things (they are aware of this too). I tell them to tell me if I can help them learn something new or manage something they find complicated. I encourage them when I see that they are enjoying something they are good at. I tell them that it does not matter if there are things they do not master, – everyone can’t be good at everything I tell them. They accept that. We all do.

I can see if they are sick or are feeling unwell. I tell them to tell me if they feel sick or uncomfortable for some reason. I tell them I will do my best to make them well again. I comfort them and tell them that this will pass, and you’ll be fit as a fiddle again soon. I tell them to eat right, I tell them to stay active. We do this together. I tell them this is because we do not want to be permanently ill in the future.

I know my family, not only my kids. I know which diseases my father and mother have had, and their fathers and mothers too. I tell my kids to do things that will minimize the risk for similar ailments in the future. I try and minimize risk myself too, because that benefits me as well as my children.

When they grow up and can make informed medical decisions, I will tell them that they are free to scan their genetic sequence if they choose to.

I do not however, need a genetic scan to see what is good for them and what is not. I know them.

If you do not know your kids, – please start getting to know them now. To do that you do not need genetic testing, you need attentiveness and presence.

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And now suddenly, we don’t need genetic counselors anymore…..?

In Uncategorized on May 30, 2008 at 12:16 pm

With this post, my posts on genetic counseling are now a trilogy (which somewhat unfairly puts them in the same category as some amazing literature, – and films).

From a recent Nature News Special Report:

No one denies that genetic test results can be life-altering for some individuals. But research by Theresa Marteau, a health psychologist at King’s College London, and others has shown that most people are remarkably resilient in the face of traumatic genetic test results. They typically report feeling anxious or depressed around the time of testing, but these effects dwindle within a few months.

This fits well with my first post where I argued that the need for genetic counselors was overrated. After reading an article on Huntington’s disease however, I changed my mind, and wrote another blog post. But now, this quote contradicts what I thought was my final conclusions and I am left wondering where I stand … again:

Studies by Aad Tibben, a psychologist and psychotherapist at Leiden University Medical Centre in the Netherlands, and his colleagues showed that people who took predictive tests for Huntington’s disease mostly recovered from the shock. Many actually felt more in control after testing because they could make arrangements for care, or even for euthanasia.

And I am not the only one who is confused on these matters

With so much uncertainty about how people deal with genetic risk, is genetic counselling necessary or helpful for people undergoing the less definitive tests for an increased propensity for heart conditions or diabetes? “I’m convinced it’s necessary,” says Tibben. But he and others in the field acknowledge that there is little in the way of controlled trials to support their belief.

I have decided to go with the conclusion that the best thing to do is probably to do the genetic counseling,… and then evaluate,… and then stop doing it if it doesn’t work. This simply because to my knowledge, genetic counseling doesn’t do any harm. It may even do some good even if the effect is all placebo:

“……….Did the counsellor help the patient understand complicated risks, or just provide some face-to-face contact and empathy in a confusing medical world?

So, until someone comes out with a study that says that genetic counseling is harmful, this post will reflect my final (!?) postition. End of story (trilogy).