Posts tagged science
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]
Who says scientists aren’t creative?
Mar 19th
Awesome slideshow I just came across via Biotechniques. Click on the button with the four arrows for full-screen glory.
The three winning images from the GE Healthcare Life Sciences’ 2008 IN CELL Image Competition were displayed on the high-definition screen located in New York’s Times Square earlier this month.
Yay for science!
This reminds me of work I did for my undergraduate thesis [PDF]. Check out my wicked attempt at immunofluorescence (apologies for the awful drop-shadow, it was the mid-90’s):
Ding dong, the scientific witch is dead
Mar 10th
Some sentences from President Obama’s speech about freeing science from the ideological chains of the Bush administration (which maybe should have been one of them) deserve to be re-read and appreciated over and over.
“…in this new administration, we base our public policies on the soundest science; that we appoint scientific advisors based on their credentials and experience, not their politics or ideology; and that we are open and honest with the American people about the science behind our decisions. That’s how we’ll harness the power of science to achieve our goals — to preserve our environment and protect our national security; to create the jobs of the future, and live longer, healthier lives.
And:
There’s no finish line in the work of science. The race is always with us — the urgent work of giving substance to hope and answering those many bedside prayers, of seeking a day when words like “terminal” and “incurable” are potentially retired from our vocabulary.”
Today, using every resource at our disposal, with renewed determination to lead the world in the discoveries of this new century, we rededicate ourselves to this work.
*Swoon*
As someone who was mortified to the point of speechlessness by Bush attempts to dress up his faith-based “beliefs” and inflict them on the world in the guise of science, hearing these words is truly magical. Almost the point of being surreal; is this really happening?
Do we really have a president who actually ‘gets’ the scientific process, realizes that it transcends religion and politics AND looks good in a swimsuit?
Now if he could just do something about the salary difference between those who research cancer for a living and those who destroy economies by creating ridiculously flawed investment models on Wall St, I’d be even happer!
Greetings from San Fran
Oct 26th
Coming to San Francisco feels like visiting an old friend.
I was first here 20 years ago this year (or maybe next year, but anyway), with my Dad. Also on a work-junket; the more things change hey. I think this is my 3rd or 4th visit since I came here as a spoiled, fat, teenager. Having been here during some very different periods of my life, I feel a strange sense of connectedness to this city.
My impressions this time are again tarnished by the huge number of homeless men that rove the street – every street – and seem so entrenched here that I feel like I am trespassing in their homes by walking around the city. I cannot understand how a state with so much money can not have solved this problem yet.
Today I almost drowned, at the beach above. Yes there were signs warning people not to swim, but I don’t trust signs. Turns out they were kind of correct, it is really dangerous – and REALLY cold. I managed to dive under a couple of waves, but got totally cleaned up by a gigantic 4-5m monster, which slammed me against the sand, sucked me back up into the middle of it and spun me around a few times before I could figure out which way was up and fight my way to the surface. It was very dramatic.
I’ve been taking some great pics – it’s a super picturesque city – but I didn’t bring the cord for my camera, so they will have to wait. The weather has been perfect, maybe a little too warm, so I’ve got some good shots, including of the bridge above.
There are a few things that have been annoying me though, including:
- How sloooow people walk.
- How much it smells like dope (which I guess explains #1) and homeless people.
- How confusing the public transport system is (bart? muni? what are these words??).
This also has to be one of the most environmentally hyper-conscious places on the planet, which is semi-annoying. The key for my hotel room is even made of cardboard (with text instructing me to recycle it when I check out… puhlease…) and every second car is a Prius. Damn hippies!
Uugh… time for bed. I’m presenting my poster tomorrow, so I have to be perky and enthusiastic about science!
Conclusions of every cancer conference
Sep 24th
The following are the conclusions of every cancer conference in history (that I’ve attended):
- Clinicians are way better than scientists! At everything!
- Science is hard!
- There’s not enough samples!
- Old people: “The old ways are best”. Young people: “The old ways suck!”
- Stem cells, stem cells, stem cells!
- Experiment doesn’t validate? Blame tumor heterogeneity!
Sigh….
Hot off the press
Sep 19th
A study I collaborated on (quite some time ago) is out today in the Journal of Clinical Oncology:
Gene Expression Profiling to Identify the Histogenetic Origin of Metastatic Adenocarcinomas of Unknown Primary
Hugo M. Horlings, Ryan K. van Laar, Jan-Martijn Kerst, Helgi H. Helgason, Jelle Wesseling, Jacobus J.M. van der Hoeven, Marc O. Warmoes, Arno Floore, Anke Witteveen, Jaana Lahti-Domenici, Annuska M. Glas, Laura J. Van’t Veer, Daphne de Jong
From the Divisions of Pathology and Medical Oncology, the Netherlands Cancer Institute; Agendia BV, Amsterdam Science Park, Amsterdam; and Department of Medical Oncology, Medical Centre Alkmaar, Alkmaar, the Netherlands
Purpose: Patients with adenocarcinoma of unknown primary origin (ACUP) constitute approximately 4% of all malignancies. For effective treatment of these patients, it is considered optimal to identify the primary tumor origins. Currently, the success rate of the diagnostic work-up is only 20% to 30%. Our goal was to evaluate the contribution of gene expression profiling for routine clinical practice in patients with ACUP.
Patients and Methods: Formalin-fixed, paraffin-embedded (FFPE) samples were obtained from 84 patients with a known primary adenocarcinoma and from 38 patients with ACUP. An extensive immunohistochemical panel classified 16 of the patients with ACUP, whereas 22 patients remained unclassified for their histogenetic origin. Information about staging procedures and clinical follow-up were available in all patient cases. The expression data were analyzed in relation to clinicopathologic variables and immunohistochemical results.
Results: The gene expression–based assay classified the primary site correctly in 70 (83%) of 84 patient cases of primary and metastatic tumors of known origin, with good sensitivity for the majority of the tumor classes and relatively poor sensitivity for primary lung adenocarcinoma. Gene expression profiling identified 15 (94%) of 16 patients with initial ACUP who were classified by immunohistochemistry, and it made a valuable contribution to a potential site of origin in 14 of the 22 patients with ACUP.
Conclusion: The gene expression platform can classify correctly from FFPE samples the majority of tumors classes both in patients with known primary and in patients with ACUP. Therefore, gene expression profiling represents an additional analytic approach to assist with the histogenetic diagnosis of patients with ACUP.
[Link]
Never one to shy away from gratuitous self-promotion, it turns out this my 10th (co-authored) publication!
I swear, I must be only one spontaneous head-shave away from being photographed getting out of a limousine, sans-panties, and attacking a car with an umbrella*.
Bitching