sample quality

It’s now been over ten years since John Ioannidis published his now famous paper, Why Most Published Research Findings Are False.   What response has John seen from the scientific community? How has the paper changed his career and role in the scientific community? Join us for a look at science itself.

Here on the show, we’ve talked about the lack of reproducibility for much of biological research. We’ve bandied around various percentages--is it 50% or up to 90% that can't be replicated? And we’ve poked around various issues that may be causing such poor science.

Nicole Perfito is the manager of the Reproducibility Project: Cancer Biology, an effort between Science Exchange and the Center for Open Science. The goal of this project is to take nearly forty “high impact” papers in the field of cancer and try to replicate them.

The team has reproduced several studies already. What are the main issues that are coming up? How helpful are the original authors being? And are there some low hanging fruit which might lead to dramatic improvements to research if adopted?

The project is still underway, but already Nicole and her team have some interesting hunches.

What is a human genome? Well it’s the three billion letters of our DNA. But how is it measured? How do we know when we have it accurately represented?

These are questions that will have to be answered as precision medicine takes hold; for we must have defined standards that will be the basis for regulatory policy, commerce, and better research. These are also the questions that are foremost on the mind of today’s guest.

Marc Salit is the leader of the Genome Scale Measurement Group at the National Institute of Standards and Technology or NIST. In today’s show, he explains how NIST played a pivotal, foundational role in enabling the ‘Century of Physics.' Now Marc and NIST are looking for the right set of standards to enable the already-upon-us “Century of Biology.”

The human reference genome is an example of a standard that Marc and his team are developing. Currently they are piloting what they call “Genome in a Bottle,” a physical reference standard to which all other human genomes can be measured. How far is the team to having a complete reference genome, and what is an example of the way they are working with the FDA to ensure safe and meaningful genomic tests? Join us as we peer in at the foundation of genomics.

In the second part of our interview with Tim Triche, Director of the Personalized Medicine Center at Children’s Hospital Los Angeles, Tim says that micro arrays are still a vital technology for today’s cancer researcher. Making use of both next-gen sequencing and arrays for his research, Tim confirms that arrays still have advantages in the clinic as well, such as quicker turn around time. 

Tim also weighs in on some ongoing questions about whether poor biospecimen quality is hampering research efforts and whether genomic medicine is paying off for patients. 

Go to Part 1:  Want Answers? Look to the Non-Coding Region of the Genome, Says Cancer Researcher, Tim Triche

When science journalist Ivan Oransky co-founded Retraction Watch, a blog with the express purpose of making scientific retractions more public, he didn’t think he would be posting much.

“Adam Marcus, my co-founder, was quoted as saying, ‘yeah, we figured we’d post periodically, our mothers would read it, they’d be very happy, nobody would read it other than them.’ Obviously that hasn’t been the case,” says Oransky in this first of a series of podcasts on scientific integrity.

Now putting out almost a post a day and funded in party by a grant from the MacArthur Foundation, the blog has revealed - and no doubt helped drive - a boom in retractions the last few years.

What is leading to so much bad research, and just how is Oransky’s blog keeping scientists honest?

Oranksy points to science career pressures and financial incentives as part of the problem. He also explores the issue of cell line authentication, a particular quality concern in cancer research.

We couldn't resist the chance to pull this veteran journalist into our recent debate over whether the genomics revolution is delivering on its promise.   

And finally, Oransky was at the now infamous woman's luncheon in South Korea last month when a nobel laureate, Tim Hunt, blew the crowd away . . .  and not with brilliance.