Personalized Medicine – a personal story

I came across this story on Reddit, but it’s clearly of interest to anyone who wants to know what personalized medicine is – and how it can be used to save people.

http://matt.might.net/articles/my-sons-killer/

Of course, since we’re at the dawn of the era of personalized medicine, this particular story is a slow moving lament, rather than the fast paced race to a cure it should be.  But, that’s science.  Every day, we get better at making cures and treatments available, and stories like this are just one more good reason to get up in the morning and go to work.  Hopefully, future generations will be able to get results earlier and will have more actionable outcomes that lead to cures.

For the record, I don’t know the person who wrote the story and have never heard of if this particular disease before.   However, the techniques (whole exome sequencing, finding mutations, etc) are the same as those used at sequencing centres around the world – and require large teams of people to perform. The field that I personally study is making sense of the raw data generated, but it’s just one big piece of the puzzle.  Behind all the science discussed in the article is a great team of researchers who work REALLY hard to make stuff like this happen.

Contentment

It’s always easier to blog when you’re upset about something than when you’re feeling content.  Content isn’t a strong emotion that motivates people to get out of their chair and write something, but today, I feel content enough that I wanted to share it.  That’s a huge change from the past 6 months.

Yes, the arrival of my daughter has something to do with it – she’s already impressed me with her wonderful personality – and she’s not even two weeks old yet.  As a father, I couldn’t be any happier.

But, it’s not just that.  A LOT of my complaints about our relocation to denmark have been solved.  Not all of them, but enough of them.  Relocating to a house that suits us has made a massive impact on our quality of life, and is probably most responsible for the change.  We’re close enough to the city that I was able to bike out to get take-out dinner from a Thai restaurant – and the Pad Thai was awesome. (Thanks to a colleague for the recommendation!)  The day before, I was able to bike out to our favorite bakery and pick up some great bread.  Little things like this were impossible from our last house and it’s amazing how much of a change it is to be able to run errands without a 45 minute bus ride into town.

Additionally, the weather in Denmark suddenly “snapped” into summer mode a few days ago.  From the dismal highs of 12C and blustery winds, to suddenly becoming 20C with a wonderful gentle breeze, the weather is gorgeous by any standard.  And the long summer days stretch late into the evening, and start early in the morning.  The 4:30am diaper change this morning was done without turning on the lights, as the sky was already bright enough to illuminate the room. Truly, Danish summers are shaping up to be glorious.

And finally, after about 6 months, I’m starting to understand the language around me.  I was able to listen to a few minutes of news and grasp the point of the discussion (Aarhus had to buy bigger ambulances because the patients they’re transporting are too fat…)  – a new high point in my life in Denmark.  I’m also able to read emails and I’ve begun to read the local weekly newspaper.  I use my phone to translate a lot of words, but I’m learning and I can make sense out of things.  I no longer dread walking into stores and not understanding anything, and having even a basic comprehension feels like a huge weight off my back.

So, there you have it.  Nearly 6 months in, and suddenly, Denmark isn’t so bad after all.

On the bright side, I think I’ve learned a lot about myself – about being more aggressive in going after what I want and need, about not making assumptions, about being more understanding of those who have the courage to move to a new country.  This has been a valuable lesson for me in so many ways, and has probably helped shape me into a better person, which is worth some amount of pain.  Now, the goal is to build off of it and use this to become a more productive person.

It’s a bit late for a new years resolution, but I’m not going to bask in my contentment today – I have things to do.  Blogging it was just the first on my list.

One more Fejes!

Well, she’s half a Fejes, anyhow!

If people are wondering why Fejes.ca has been way off topic for so long, a good part of it has been that I’ve been pretty preoccupied with getting ready to expand the family.  This week, we’ve welcomed our daughter Amelia into the world – and she’s a cutie! She’s already let us know her favorites are: sleeping, eating, having her fingers played with and long walks in a bassinet.

However, because I’ve been blogging all about our experiences in Denmark, I thought I should share a few of the surprising events we discovered for those ex-pats who might be having a child in Denmark.  If you’re not interested, I suggest you stop reading here.

First off, the whole thing went well – Overall, it was a pleasant experience and the hospital staff was always supportive.  And, we only met one person who didn’t understand English – a member of the cleaning staff.  People always went out of their way to be helpful, regardless of what else was going on.

The biggest issue we had was communication, however.  Like every other experience in Denmark, people feel awkward communicating in English, so they rarely go out of their way to explain what will happen, or what should happen.  Thus, I spent a lot of time “taking control” of the situation by asking questions – constantly.  I often had to pin down a nurse and say “Why are you doing this, and what do you expect to happen?”  Once I realized that the only way to make sense of things was to insist the staff take the time to explain things, our experience became infinitely better.

Also, learning a few words of Danish made all the difference.  Staff frequently spoke to each other around us in Danish, and just being able to figure out what they were talking about in vague terms was sufficient to make me feel a bit more part of the process.  Considering I only recognize a couple hundred words in spoken Danish, it’s not like I could have communicated – but knowing the words for simple concepts (like nurse, newborn, mother, father, etc) was a great big help in not feeling so isolated.

Beyond communication, there were a few other surprises.  We had attended a class on childbirth education in English, where they explained what we should expect during labour.  The first thing that they explained was that the process would be nothing like the movies, where the mother’s water breaks, then the rush to the hospital, followed by a lot of drama.  Actually, it was EXACTLY like in the movies – including the speeding cab ride at 1:30am.  The biggest difference was the final stage of labour, where there were only 3 of us in the delivery room – including the midwife who was shy about speaking English. That left me to do all of the coaching and communicating – a task I was utterly unprepared for, and had to learn “on the job”.  My wife was very patient about it, all things considered.

We did have a few communication breakdowns as well – such as the discharge from the maternity ward to the patient hospital.  The midwife sent us away too soon, before the IV port was removed from my wife’s hand and before they had checked to see if my wife was ok. (She wasn’t.)  They sent us to the patient hospital, where we sat for a few minutes, before a nurse discovered us and realized we’d been sent to the wrong place.  While she did identify the problem, her solution was to have us walk to another ward – about 400m away,  (a 12 minute walk in my wife’s condition) where it was discovered that my wife wasn’t doing well. She wasn’t supposed to have been walking and she shouldn’t have been allowed to walk that far so soon after delivering a child.  After completing all the checks and finally having been treated for pain, swelling and completely crashed blood pressure – 4 hours later – we were allowed to return to the patient hospital by shuttle.

Once in the patient hotel, we were provided with pamphlets (in Danish), brochures (in Danish) and a kind nurse tried to accomodate us by passing some of the information on the web through google translate. ( It was completely unreadable.)  Despite being friendly, the information wasn’t particularly forthcoming, and we failed to understand the purpose of the hotel, which turned out to be nothing more than a space in which families can relax, the mother can learn how to breastfeed and to make sure that the parents have some indication of what they’re supposed to do with a child before leaving the hospital.  It wasn’t until I asked on the second day that they explained it to us – and that we discovered those are the criteria that you must fulfil before they let you go home.

In any case, the nurses were incredibly helpful and came immediately upon request.  They were surprisingly non-challant about the child’s health, however, claiming that weighing the baby should only be done if they think there may be a serious problem with feeding – because all babies lose weight the first day, and it is too “depressing” for the mother. (They weighed our daughter in the evening on the second day, anyhow)  A healthy baby will only ever be “eyeballed” by the nurses to make sure that they’re doing well.

Fortunately, my ability to read Danish has improved by leaps and bounds since we arrived, so I started reading through what I could in the brochures.  By about the 28 hour point, however, the lack of information was overwhelming and frustrating., and I ended up compiling a full page of questions that hadn’t been addressed, such as

  • Am I going to have to pay for staying here with my wife? (Yes, and meals are extra for the father.)
  • Is there an internet password that we can use for the wifi (Yes, but only if you specifically ask for it.)
  • How do we get a birth certificate for our child  (no one knew, but I found it later online, through borger.dk)
  • Can you give us the information on how to care for your child that you provide to Danish speakers in the course offered in the afternoons, to which we weren’t invited? (Yes!)

and so on and so forth.  It was much like playing 20-questions, however, as you might miss something by asking a question that was close, but insufficiently accurate.

For the first 24 hours, our best lifeline to information was our smartphones – and thank goodness for them!  Email, Google searches and advice all in English.  Without it, we would have been lost and uncertain about a lot of the little trivial things that we didn’t know, and that no one had volunteered. (For instance, letting a newborn baby suck on your thumb is a bad idea, because the child is supposed to be learning how to breast feed and it will develop bad habits if the thumb is offered – no soothers for 2 weeks!  Who knew?)  Once we became much more aggressive about demading information, our stress level dropped considerably, and things became quite a bit easier to deal with.

The other fascinating thing about the patient hotel was the room we were put into, which was on the edge of a rennovation zone for the hotel.  At times, there was a backhoe that was litterally 3 inches from our window, moving dirt, breaking up concrete and separating metal from the construction debris… and despite that, we managed to rest, learn to breastfeed  (well, I didn’t do much on that front personally) and stay comfortable for 48 hours.

 Anyhow, that’s just a summary of what went down. My wife and I have already spent an hour passing along the details to a friend of ours who’s expecting a child imminently, with the hope she’ll be able to put some of the information to good use. Hopefully the above will be useful to other people as well.   If you would like more information or details, as usual, feel free to send me an email or leave a comment.

Masterchef Australia 2011

This is going to be a rather off beat post, as if the whole last year wasn’t off beat enough for my blog.

Since moving to Denmark, there’s been one thing that’s been constant the whole time: Every night except Saturday, at 7pm (19:00 for the Europeans), MasterChef Australia 2011 has been on. We’ve watched the entire season, and other than maybe the first week, the only episodes I’ve missed were when I went back to Vancouver to defend my thesis and one or two nights when we visited with friends.  That’s probably a good hundred or shows that we’ve watched.

From MasterChef, I’ve dutifully read the Danish subtitles and “reverse-engineered” enough Danish to be able to read the written language.  Everything I’ve bought at the grocery store has been enabled by the words for food I’ve worked out from the tv show.  Additionally, I’ve followed the contestants and learned and tried new recipes from the show.  We even adjusted our dinner time to match the time slot for MasterChef, so that we could make it a part of our evening.

It has been one of the few scheduled items of our life in Denmark.

I’m sad that it is now over.  Even more so, I’m depressed that it’s being replaced by “Backstage with Oprah Winfrey” or whatever it’s called.   I’m *really* not a big Oprah fan.

So, as strange as this is, thank you Master Chef.  Thanks for teaching me Danish.  Thanks for entertaining me for nearly five months, and thanks for all the recipes.  I’m going to miss you, and my evenings won’t be the same anymore.

Learning Latex – Resumes

After writing my PhD thesis in LaTeX, you might think I’d be completely burned out on the topic.  Much to my surprise, the exact opposite is the case.  I’ve been using LaTeX at work, and I still enjoy it.  I have a lot to learn, still, but I’m finding it oddly amusing, and there are some serious parallels in the pleasures of compiling a LaTeX document and those of compiling and running software successfully.   Yes, I am now entirely a geek, and any hope of changing that has now been completely banished.

In any case, what got me started on a resume was a Google+ post that linked to this page: http://texblog.org/2012/04/25/writing-a-cv-in-latex/

It’s a nice template that served as the start for my resume, this time around.

The fact that I’d lost access to my previous resume during the move probably also helped spur on this project as well – and with a few recent papers coming out, I wanted to make sure I had somewhere to keep track of it all.

In any case, if you’d like to see what the resume has become, after playing with it for a while, you can find it here:  http://blog.fejes.ca/wp-content/uploads/2011/09/resume.pdf

I’m aware of a few “mistakes” in the formatting, particularly in the authors’ names in the posters section, but I’ll iron those out eventually.

Suggestions, criticisms or source code, if you’d like to do your own version, can be shared in the comments.

Spring time

A bit of a different post from the usual.  While I’m still not enjoying the rainy weather we’re getting, I am finally a bit encouraged by the slow changes.  First, the days are becoming ridiculously long, having passed the long Vancouver days this week.  second,  I was walking home the other day and noticed that the green spaces have started to smell like spring.  You know the earthy small of things growing again?  That’s a good sign that the plants are at least trying.  Now, if only the weather would cooperate and warm up a bit.

5 months in Denmark

So, its been about 5 months since we arrived in Denmark, so I thought I’d try to capture what’s going on at this point, and to give a bit of perspective.

About a month ago, we moved into our new apartment. It has made all of the difference.  We’ve walked downtown a few times and even found a few places we’d like to try for weekend brunch – and we were able to take the dog with us on those walks (no, the dog doesn’t come for brunch).  It wasn’t like our usual weekend jaunts in Vancouver, but it felt reasonably comfortable.   Seeing people on the streets, having somewhere to walk to and being in town has made a HUGE difference for us.

We’ve also discovered we live near to a couple we’d met at our childbirth education class, and it’s so nice to have friends in the neighborhood!  They’re fascinating people, and time just flies by when we’re hanging out with them.  I also have to admit, they have a fantastic library of English books in their house, which is quite impressive, especially since neither of them is a native English speaker.

In any case, things are finally starting to settle into a bit of a routine.  We have our favourite (English) shows to watch, we manage quite well at the grocery store, we seem to pay our bills on time and we can find stuff to do on the weekends.  I’m even able to read a bit in Danish now, at least to the point where I can skim an article and work out what its trying to say.  Spoken Danish is becoming a bit more tractable, but damn, Danes don’t make that easy!

At any rate, just as we have our routine down, we’re up to the last few days of waiting for our child to arrive, which will happen any day now.  Our last visit with the midwife is scheduled for tomorrow, so whatever routines we have will probably be tossed out the window and have to be started over fresh.  That’s just the way it goes, I suppose.

There are a few odd things that still irritate me: Lunch times, Danish surprises and the weather are at the top of the list.

Lunch times, because they feel incredibly awkward for me.  If I join the rest of the company, and they chose to speak English for me, the conversation is often slowed down and drags along because not everyone is comfortable in English.  If they chose to speak in Danish, then the conversation is lively, fast paced, good natured – and I understand one out of every 10 words.  Damned if you do, damned if you don’t.  In reality, as a foreigner that doesn’t speak the native language, it shouldn’t be a surprise that this is how interactions go, but it is an irritation that is a part of daily life.  I’ve at least gotten over my usual conversation starter of “I’m sorry, I don’t speak Danish but…”   After a while, you realize that everyone knows that, as soon as you open your mouth.

“Danish surprises” are my own way of expressing those things that just blind side me when I least expect it.  For instance, this week it was paternity leave.  The rules are really designed to support working couples, or working mothers, but they’re really quite poor for single income fathers.  An example of that is the rule that fathers get two weeks off after the birth of a child, but the pay is (if I’ve done the calculations right) stripped down to about minimum wage for the time you take off.  After that comes a 12 week period in which the father is not allowed to take any further parental leave, followed by some ridiculous amount of time that can be spread over 9 years – but again, at minimum wage.  If there are problems, and the father needs to take more than two weeks after the birth, it’s just not allowed by the state.   I imagine one could use vacation time for that purpose, but if you’ve recently moved here, you won’t have acquired any.  I’ve already posted about the no vacation for 18 months rules before.  That probably wouldn’t be a concern if I had family here to support my wife after I go back to work, but that’s just not available, as we’ve left our families in Canada.

(I should point out that my company has been quite flexible about these things, to make life much more bearable – but the default rules are strict and obnoxious.)

Finally, the weather here has just been lousy.  We’ve had two weekends in the past 5 months where the temperatures have been decent – Once it went up to 16C, the other time to 19C.  It’s not like I’m expecting summer to arrive in May… but well, ok, actually I am expecting summer to arrive in May.  Hey summer, where the heck are you? At least the days are long, stretching well into the late evening, with a light sky at 10:30pm – even if it’s only 7C outside.

At any rate, life goes on, and bit by bit, we become more comfortable. Still, we’re not getting too comfortable, with some life changing changes in the works. But, with the new house, some basic Danish comprehension skills and a few new friends, life has been looking up for us.  A very welcome change!

Culture Shock

Someone asked me to explain culture shock to them, a few weeks back. After thinking about it for a while, I figured out what it is – at least in my Danish experience.

To me, culture shock is the complete lack of security in one’s actions and behaviors in a new culture.  It’s the sum total of all of your insecurities coming to the surface, when you realise that all of those things you’ve learned about how to behave and how to interact with the world have suddenly been taken away.

It’s not one big thing.  It’s really just a million little details.  Do you shake people’s hands when you meet them?  Are the things you say going to be misunderstood?  Is it rude to not say please when asking for things?  How do you fill a prescription at the drug store?  How do you get on the bus? What store sells the items you’re looking for?  Why aren’t there bathtubs anywhere in the country?

Every little thing you’d learned about the world has to be re-framed into a new context – from the small to the big.  All the details you’ve taken for granted are suddenly clearly highlighted as peculiarities of the region you’ve just left, and you can never be sure about what to expect.

In fact, that sums up yesterday’s experience quite well: At noon, hundreds of alarms all went off at once, filling the air with the sound of air raid sirens.  Being alone in the office, at the time, I had no idea what to do about it.  In fact, I simply decided to ignore it.  No one outside appeared to be panicking, so why should I?

When my colleagues returned from lunch, I asked them what was going on, and was given the perfectly reasonable answer that “at noon on the first Wednesday in may of every year, all of the warning sirens in Denmark are tested, of course.”   Just in case they ever need to warn about chemical spills, invading Germans or otherwise.

Like everything else, since moving to Denmark, it appeared to me to be totally unexpected and out of place.  I couldn’t have predicted it, and there was no warning that it was going to happen.  At the end of the day, I just have to rely on my ability to not be phased fazed by anything going on, and try to figure out – once it’s over – what happened.
And that is exactly what culture shock is about – the never ending feeling that you can only react to events around you, and you have no idea what or when they’ll happen.