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Calculating your health predictions

In Uncategorized on December 2, 2009 at 3:01 pm

: Image by psd via Flickr

In our lab we’re setting up the PCA3-test designed to aid prostate cancer diagnostics. The test is representative of many emerging diagnostic tests in that it is a) a supplement to existing testing and b) useful only in a subset of conditions.

The PCA3-test complements results from digital rectal examination, PSA tests, and prostate biopsies. Three tests that until recently have constituted the cornerstones of prostate cancer screening and diagnostics. The relationship between the results from these tests is dynamic and interpretation of test results is often complicated, sometimes very confusing and can, in the worst case, be very uncertain. Add the gene expression results from the PCA3-test and you have a lot of valuable information, but a tough time filtering it into useful clinical information.

Physicians will learn how to combine the information either in med-school or in update learning courses later in their career. A slow and sometimes insufficient way to convey diagnostic information to the clinic, treating physician and ultimately, the patient.

Thankfully, we live in the information age and medicine 2.0 is well underway. Now the doctor or the patient can separately or together get online assistance in interpreting prostate cancer test-results. Well designed and user-friendly calculators like the “Risk of Biopsy Detectable Prostate Cancer” calculator or prostatecancer-riskcalculator.com (professional use) will help anyone undertand and begin to interpret lab-results. A big step forward in my opinion since information flow becomes quick and targeted.

Such calculators have also been made available for cancer risk prediction: nomograms.org, for Marevan/Warfarin dosing: Warfarindosing.org, and as demonstrated in a previous post, for Testosterone: Testosterone.

There are probably a lot of calculators out there that I haven’t found yet and it’s highly likely that many more will be developed.

It seems clear to me that interpretation of clinical lab-results may not remain entirely in the physician domain much longer. Hopefully such automated interpretation will lead to patient empowerment and make deciding on clinical action an easier task.

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quote

Quote of the month November 09

In Uncategorized on November 26, 2009 at 9:32 am

It is a sad truth, but we have lost the faculty of giving lovely names to things. Names are everything. I never quarrel with actions. My one quarrel is with words….The man who could call a spade a spade should be compelled to use one. It is the only thing he is fit for.

Oscar Wilde, Irish playwright, poet, and novelist, The Picture of Dorian Gray, 1890

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Influenza, Vaccination

Swine flu. A family history

In Uncategorized on November 20, 2009 at 11:30 am

: Image via Wikipedia

Here’s how the flu season has played out in my own family (parents (38 and 40) and three kids, a daughter 10 years old, and twin boys 6 years old). I’ve added a couple of references for comparison with public health recommendations and published swine-flu info.

Late August 09: The boys were coughing and had slight fever, our daughter was coughing only. One son, the daughter and the father (me) tested positive for fluA, but negative for SwineFlu. At this time the public health information available said that only SwineFlu was going around since “Any widespread influenza activity in August is uncommon.” (ref). Clearly not in our family though – we had seasonal flu of some sort.

Late September 09: Our daughter gets high fever and headache. I felt scruffy, but did not have any fever. None of us were tested since we were abroad on holiday. We, gave our daughter Tamiflu®, since symptoms suggested possible SwineFlu infection.

Early November 09: One of the boys gets Swine flu vaccinated since he is in one of the risk groups (asthma). I get vaccinated for seasonal flu.

Mid November 09: The other boy gets high fever and headache. He is given Tamiflu®. He is later tested positive for SwineFlu. I tested negative. The rest of the family was not tested since they had no symptoms.

Late November 09: Our daughter is scheduled for SwineFlu vaccination.

This fall our family has had influenza two times, possibly three. We had seasonal flu first and this at a time where seasonal flu is not expected to be common. This infection had very mild symptoms in my family. Two of us then had more severe flu symptoms a month later, but this infection was not confirmed by testing. Some weeks later one of us gets a confirmed SwineFlu infection while the rest of the family apparently escapes disease.

One should not draw epidemiological conclusions based on results from one family, but nevertheless, working in a diagnostic lab being able to test so often has been an interesting experience. If i may, I’d like to speculate a little bit:

1. Seasonal flu may not be as “seasonal” as we think since seasonal flu can give very mild symptoms and remain undiagnosed.

2. Vaccination has worked fine in our family since the vaccinated boy did not get infected through his brother.

3. Seasonal flu does not protect against SwineFlu in children (same boy tested positive for seasonal flu and later on SwineFlu), but may protect against SwineFlu in adults. This is supported by a recent NEJM publication.

4. Following infections longitudinally could give valuable insight into the epidemiology of influenza and other seasonal viral infections.

5. Frequent testing reduces worrying to a minimum. While I realize that I am subjective since I have my own laboratory to develop tests in (and run them as often as I want), I strongly recommend that such frequent testing be performed for everyone.

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Testosterone, Transhumanism

The Testosterone Project II

In Uncategorized on November 10, 2009 at 2:58 pm

: Image via Wikipedia

Previous post in series: The Testosterone project.

Recap: Project Testosterone is my main project aimed at alleviating mature age growing pains.

Plan is as follows:

Test my testosterone levels.
– Done. Twice now. Turns out I’m still at the low end of the normal spectrum. This second time I also measured Sex Hormone Binding Globulin (SHBG) to get an accurate measure of Bioavailable Testosterone. Detailed results were: Testosterone – 8,1 nmol/L (normal level 8-35 nmol/L), SHBG – 12,6 (normal level 8-60 nmol/L), Bioavailable Testosterone (calculated from here) – 10,20 nmol/L (normal level 3,85-13,67 nmol/L).
If low (and yes it feels low, even if it is within the normal spectrum, it’s my manliness we’re talking about after all), then learn more.
– Done, but will continue reading about this.
If not to scary, find out how to get a hold of it.
– Have gone to see a gullible physician, but was turned down because I was in the normal range. Plan was to measure a second time to see if values were lower and then go back, but it seems values are reasonably stable. Legally prescribed testosterone plan scrapped. Next: probe the illegal substance market.
If not too illegal, then get some. Topic for next blog post.
Try low doses. Future posts.
If adverse events acceptable, continue and report effects continously on blog.

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Transhumanism

Thoughts on H+

In Uncategorized on November 5, 2009 at 2:38 pm

The last H+ magazine is full of articles telling us that we’ll soon rid ourselves of various body parts, mood swings and even the physical acts of sexual relations. I am still a transhumanist, but will have to distance myself from H+ if this continues because:

Bodies are nice – I like them. Mood swings are nice – I like them too. Sex is also nice, and anticipation of physical sex can be even nicer. Probably because constant and unhindered sexual interaction is unattainable. Consequently, such anticipations are major drivers of behavior. Messing with the availability of sex is not something one should do without caution.

Fellow transhumanists, please put some restraint on your desires to remove yourselves from the physical world. And, do not underestimate our biology – it isn’t always as bad as you’d think.

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communicating science, diagnostics

Nothing is ever absolutely negative

In Uncategorized on October 31, 2009 at 1:19 pm

: Image via Wikipedia

On a late Friday afternoon

Quality control department: “You missed the last two samples in this dilutions series”.

Me: “Yeah, that’s kind of why we use dilution series – to find our detection limit”.

Quality control department: “But, even though very diluted, those two samples were positives. That means this was an error and needs an error-report”.

Me: “Well no, we define a limit where we can be 99,99% certain that we can reproduce a positive result, these dilutions will be well below that limit”.

Quality control department: “But, that means that you can newer be 100% sure of a negative answer”.

Me: “That’s correct, although the concept you are touching upon (the lack of absolute negation/negativity) is valid for any test and consequently, of a philosophical nature”.

Quality control department: “Then we can never give out a negative answer, at least not without saying that there’s a chance it may be positive after all”.

Me: in silence “¤%%”&&¤…doh” and out loud “”Would that be wise ?”.

Quality control department: “We believe so !!”.

Please notice the use of the word “believe”.

So there you go, hit in the face by the same arguments that created the vaccine-autism wars, the ID vs. natural evolution discussion, the religion meets atheism quarrel……..you cannot prove the absence of something, ergo – it must be there. The mother of all fallacies, but impossible to scientifically refute.

I’ll keep trying though.

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Health care, meeting summary

The Scheveningen Meeting: a Thrilling and Uncensored Story of European Molecular Diagnostics

In Uncategorized on October 27, 2009 at 11:30 am

: Image by Harm Rhebergen via Flickr

Well, while the title alluringly suggests so, this was not a conference for reporting spicy hot ground-breaking news like twelfth generation ultra-high through(the roof)put sequencing, full biome DTC chiponomics or gene-enhanced elisaluminetics or what have you. I’m kind of glad it wasn’t.

Instead this was a down to earth meeting where labs presented their experiences with molecular methods that are used every day in labs. Tests actually ordered by physicians in real-life medical settings. Methods are still PCR and sequencing…..and they are still used in microbiology (including virology), oncology and genetics… but, that’s it basically.

Being a diagnostic lab-professional I had many valuable insights to help in my everyday routines, which is what was expected from the meeting. I’m not going to blog that since it has limited general interest. I’d like to however, expand on three trends that made me especially happy to see:

1. Economy: Many of the speakers emphasized the skewed nature of health care funding. Diagnostics normally receive between 0,5 and 5 % of the total health care budget. Usually, diagnostics is also one of the first places were budget cuts are effectuated. This stands in a mind boggling contrast to the potential savings one could achieve by investing in more testing. A sobering example is the swine flu testing policy applied by my own country which is……..don’t test. In fear of capacity problems and over-diagnosing, the recommendations have been to stay home for a week if you have flu like symptoms – in addition you are strongly advised not to go see your doctor and doctors are advised not to test those patients that violate these recommendations. Of course, this does not work very well, labs are still swamped by swine flu samples, but the net result, nevertheless is the huge cost of absence from work and an immense amount of people worried for no good reason. Testing everyone, I strongly believe, would have been a lot cheaper……and…..although I am admittedly not objective in the matter, I think extensive testing should be a general principle. Investment in diagnostics is a good investment…..over diagnosing I simply do not believe in. Feeding diagnostic knowledge down to the treating physicians on the other hand is a real problem. But, a solvable one.

2. Networks: Many speakers spoke of collaborations between labs. In the research field such collaborations are common and acknowledged by most as a necessity. Not so much in the diagnostic lab until know. It makes me very happy to see that this is changing.

3. Web-tools: The above collaborations are of course aided by interaction on internet. It would be strange if not at some point, the facebook spirit didn’t reach diagnostics too. Now it seems, it have or at least is starting too. In addition, web 2.0 diagnostic tools are becoming more and more accepted, and several talks mentioned such tools. This I found so exiting, I will cover them in a separate post.

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application, open access

My tribute to open access week

In Uncategorized on October 20, 2009 at 8:25 pm

Image by Gideon Burton via Flickr

I am all for open access, my own initiative being sciphu.com – still in early stages and with several unresolved issues. Issues that may prove to be altogether unresolvable, because of the extreme openness of the blog-publishing concept. Still, as a tribute to the open access initiative and in the spirit of such extreme openness I am proposing another open access category: “open access job-applications”. Please find my first contribution below.

Norwegian Biotechnology Advisory Board
PO Box 522 Sentrum
0105 Oslo
Norway

Oslo 14/10-09

Nils Reinton

Open * application for your position as senior advisor for the Biotechnology Advisory Board
I hereby apply for the above position. My background is biochemistry / molecular biology. I earned my Ph.D. in 2000. I’m now working in diagnostics research and development, mainly using gene technology methods.
I write two blogs commenting on the use of biotechnology: one in Norwegian (genom.no) and one in English (BIOpinionated.com). I participate in forums that discuss biotechnology and biomedicine on a daily basis. I have previously written contributions to the debate in Norwegian newspapers (see attached CV for references). I am passionate about my discipline and nurture a strong desire for an advisory board with a proactive commitment.

I have the following two reasons for applying for the position:

1. Correcting past sins. Including i) the biotechnology advisory board’s predominantly negative attitude to GMOs and Biomedicine with populist statements about HPV vaccination as the most glaring example, ii) the boards warm support to the world’s strictest regulation of genetic tests and other medical applications of biotechnology wherein the definition of pharmacogenetics as “presymptomatic testing” is the grossest example, and the mandatory stamp of approval given to only very few selected laboratories is a generally descriptive example of contributions to over-regulation, iii) the board’s support for a biobank law that has nearly eradicated clinical trials in a country that could have contributed enormously.

If hired, I will attempt correct this by involving qualified persons that can inform about the harmful effects to research and development, of such over-regulation.

2. Change the current technology-hostile attitude of the board. Our country is in a unique position to develop technologies for the future, we have money and we have human resources. We should also be very well positioned to address ethical issues related to biotechnology since we are a law-abiding people living in a well-functioning (and thoroughly regulated) democracy. Norway’s prerequisites should ignite a wholehearted investment in biotechnology to help solve medical, environmental and economic problems to the best of both Norwegians and the rest of the world. Instead, fear of technology has won out among politicians and bureaucrats, including the biotechnology advisory board. Combined with a precautionary approach that is more pronounced with us than any other country natural to compare to, we have been left behind in what could have been thriving industry oriented biological technology development.

One suggestion for improvement is tolisten to resourceful people with constructive ideas for the ethical use of biotechnology. Furthermore, I propose to include a technology-friendly mission statement that ensures that the biotechnology advisory board always keeps technology’s potential as a starting point rather than focusing on (real or non real) damaging effects of biotechnology.

There are tremendous opportunities in biotechnology, and in recent years advances in the field have shown us that much of the fear of this technology have been exaggerated. A natural skepticism should be maintained, but a shift towards a basic positive attitude is needed.

I have professional skills, I am flexible, outgoing and self-sustained. I can contribute in a positive and challenging manner if I was offered this job.

Regardless of the application outcome I request that my appeal for a more technology friendly attitude be considered carefully.

Sincerely,

Nils Reinton

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Genetic diversity, genetics

I wish I wrote this

In Uncategorized on October 8, 2009 at 7:42 am

An excellent excellent opinion piece in Nature by Bruce T. Lahn & Lanny Ebenstein. Since I cannot write as elegantly as they have, I’ll just urge anyone reading this to go and read the whole thing because it contains grains of gold like this on “biological egalitarianism”:

We believe that this position, although well-intentioned, is illogical and even dangerous, as it implies that if significant group diversity were established, discrimination might thereby be justified. We reject this position. Equality of opportunity and respect for human dignity should be humankind’s common aspirations, notwithstanding human differences no matter how big or small.

and this:

For now, to intentionally overlook the influence of group diversity on disease susceptibilities and treatment outcomes is to practise poor medicine.

followed by this:

….there is a much larger reason to embrace human diversity in all its forms, in our view. Humanity’s genetic diversity — small or large, within or among groups — is a resource for, rather than a detriment to, creating a more fulfilling and prosperous society. Just as people have come over time to cherish cultural diversity, so we hope that attitudes will warm towards genetic diversity.

topped off by this:

For example, although IQ is a useful metric of some aspects of intelligence and it is partly heritable, it is far from a complete measure of total mental capacity. Therefore, acceptance of human genetic diversity in its totality necessarily leads to the rejection of unidimensional rankings of the capacity of human individuals or groups. If anything, the study of genetics is taking us towards an ever greater appreciation of the multidimensional nature of human potential.

And summarized like this:

Promoting biological sameness in humans is illogical, even dangerous
To ignore the possibility of group diversity is to do poor science and poor medicine
A robust moral position is one that embraces this diversity as among humanity’s great assets

Beautiful reasoning. I hope it impacts like a large meteor.

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communicating science, junk DNA

How to have your cake, eat it, and then complain

In Uncategorized on September 20, 2009 at 3:26 pm

: Image by Getty Images via Daylife

First: State that most of our genome is junk.

Second: When more and more promoters, enhancers, repressors and other regulatory elements are discovered, claim that this of course was not included in the definition of “most of the genome”. The perfect excuse because it means you’ll never be wrong.

Last: Complain when the press does not understand that “most of our DNA” actually meant “much of our DNA , but with a lot of exceptions” and that science reporters don’t intuitively know which exceptions these are.

Post written using the zpen in dire agony over extremely poor science communication from the same persons who most eagerly criticize science communication from others.

Paper in question added to junk DNA coffin post.

Update: response from Professor Laurence A. Moran here.

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On BioScience and Life and Such

BIOpinionated

Archive for the ‘Uncategorized’ Category

Calculating your health predictions

Quote of the month November 09

Swine flu. A family history

The Testosterone Project II

Thoughts on H+

Nothing is ever absolutely negative

The Scheveningen Meeting: a Thrilling and Uncensored Story of European Molecular Diagnostics

My tribute to open access week

I wish I wrote this

How to have your cake, eat it, and then complain

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