Work
It’s the end of the work-day as we know it
Feb 10th
Things we’re getting so snowed under in Tarrytown that most of us (who were silly enough to come into work in the first place) decided to pack up and brave the trip to the station… while we still could. I saw cars sliding off the road, sliding backwards on hills and general mayhem the whole way back into the city (….ok, twice).
On the plus side: snow-day-working-from-home: so very awesome. Here’s some pics I took as I was fleeing the scene:
Very often I am terrified of my own workplace
Oct 27th
…and mostly of phrases like “gown up” which I’m pretty sure aren’t referring to slipping into something slinky and off-the-shoulder.
The Times on cancer drug development – recommended reading
Sep 2nd
My love affair with the New York Times, the international gold standard of arrogant journalism, is well known. I most admire how opinionated and forthright they are as an institution, yet can occasionally admit when they dropped the ball (see: Iraq war).
Today’s article on cancer drug development is so well thought out and composed, it’s a shining example of health care and research reporting. The debate on the ‘worth’ of treatments that cost ~$10k per month and ‘only’ offer marginal survival benefits is interesting, contentious and probably not likely to be resolved any time soon.
This piece is very relevant to my work and other interests on a number of different levels – some of which I hope will come to light in the not too distant future.
The Times also do very pretty things with data:
..be still my beating statistics package.
See here for a take on the usual standard of biomedical reporting. So true!
New publication (finally) out this week!
Jul 2nd
International Journal of Cancer
Early Detection and Diagnosis
Implementation of a novel microarray-based diagnostic test for cancer of unknown primary
Ryan K. van Laar, Xiao-Jun Ma, Daphne de Jong, Diederik Wehkamp, Arno N. Floore, Marc O. Warmoes, Iris Simon, Wilson Wang, Mark Erlander, Laura J. van’t Veer, Annuska M. Glas
Abstract:
Patients with carcinoma of unknown primary (CUP) present with metastatic disease for which the primary site cannot be found, despite extensive standard investigation. Here, we describe the development and implementation of the first clinically available microarray-based test for this cancer type (CUPPrint), based on 633 individual tumors representing 30 carcinoma and 17 noncarcinoma classes.
Tissue of origin prediction for either fresh frozen or paraffin-embedded tumor samples is achieved with the use of a custom 8-pack 1.9k microarray and robust classification algorithm. An expression profile of 495 genes was used to predict tumor origin by applying a k-nearest neighbor algorithm. Internal cross-validation and analysis of an independent, previously published, 229-sample dataset revealed that clinically informative predictions were made for up to 94% of samples analyzed. Analysis of 13 previously published CUP specimens yielded predicted tumor origins that supported the clinical suspicion in 12 cases (92%).
Microarray profiling presents a promising tool to assist in the identification of the primary tumor and might direct a more tailored treatment for CUP patients. © 2009 UICC
Received: 27 August 2008; Accepted: 20 March 2009 [yes, 7 months!]
[Link]
Introduction to Bioconductor workshop, Seattle 2009
Apr 29th
For the past 3 days, I’ve been attending a workshop at the Fred Hutchinson Cancer Center (iPhone pic above) on a data analysis package called BioConductor. Disappointingly, it was not exactly what I was expecting. And by “exactly”, I mean “in no way”.
There was no avenue for providing any feedback during or after the workshop and as I’m sure everyone can tell; I was raised to say nothing at all if I don’t have anything nice to say. However my parents didn’t have any rules about blogging, so I will post a few comments and suggestions for organizers of future “workshops” here, based on my experience over the past few days.
- Introductions: If you advertise for, and receive, attendees from industry who travel across the country and pay $1,200 to attend your workshop; make an effort to greet or at least acknowledge them in some way. Even just a casual few words during the coffee break on the first day would be both professional and cordial.
- Backgrounds: In a group size of 15 people, you have time to briefly allow attendees to introduce themselves to the group and organizers and detail their experience and research aims. Not only does this encourage interaction, it will allow you to tailor your program and language accordingly.
- Room setup: Adults do not enjoy being squashed into small rooms, with 3 people on desks clearly designed for one or two. Also, do not use a whiteboard that you acknowledge is out of view for half the room. Just don’t.
- Deliver what was promised: Let’s say you are running an introductory course for a new type of bonsai pruning. Spending 70% of the time talking about the pros and cons of soil and water, then handing out a pre-packaged DIY tutorial for your new method, is not what those attending your workshop were expecting.
- Questions: If you ask for questions and there are none, that is not a good sign. Good scientists give presentations that stimulate intelligent discussion and questioning. If you ask for questions and someone does ask one, allow them to finish their question before you start answering what you think they were asking.
- References: If you are giving a lot of information and opinions to an educated audience, you need to provide references and follow up reading material. Handing out copies of a text book with your name on the cover, from which you presumably received royalties (via a course-fee-funded bulk purchase), does not seem very independent.
- Common sense: When planning an introductory course, try to think like someone who isn’t already an expert in the field. Skipping over the steps of how one goes from a raw bonsai tree, to one that is ready for your specific and new method of pruning, is frustrating to the audience. If I don’t feel confident I can use this new technique when I get home and back to my own trees, rather than those provided in the course, it’s difficult to summon the energy and will power to learn new, advanced methods.
On the plus side, the lunch boxes were delicious and constant access to pastries, coffee and ice water will be missed!
AACR 2009: Omg actually interesting!
Apr 18th
Day 1 of the conference and shock of all shocks, I’m really enjoying it.
Today I went to sessions about epidemiology, clinical trial design and careers in translational research - and stayed awake and interested all day! That is very possibly a first, in 10 years of conference attendance.
A few interesting tidbits below:
Somewhat depressing slide showing progress in heard disease, CV disease, influenza and cancer between 1950 and 2005.
Male lung cancer rates over time, comparing overall US rate (decreasing from 1991) to California (decreasing even faster) to Kentucky (increasing, still).
Proportion of cancers in the US that are attributable to obesity.
The real take-home message from today was that the best way to prevent sporadic cancer (which makes up about 90-95% of all cases) is engaging in regular physical activity, maintaining a low BMI (seems to the the most important), breastfeeding and a eating a diet rich in fruit and vegetables.
Who would have thought?
Oh, and if you get smoke, you’re going to get lung cancer. Expect it. More people die every year of smoking-induced lung cancer than people who die from breast, colorectal and ovarian cancer combined.
The next person who blows smoke in my face on the sidewalk is going to get an ear full.
Bitching