Wednesday, June 25, 2008

summer vacation and protection

by Beyond Lab

There are a lot of reasons to avoid exposure to strong sunshine. This should be especially noticed during this summer travel time. -- Being tan might make you look good and feel good. But does your body feel good as well? -Most likely not.

There is clear scientific connection between heavy sunburn and melanoma (a kind of skin cancer) occurrence. People received multiple severe sunburns are at higher risk of developing melanoma. Children are at even higher risk.

Protect yourself and your family by doing necessary things, high SPF sunscreen (and reapply every 2 hours if in heavy sunshine), protective clothing and hats, and so on. What's the best solution? -- avoid the sun during peak hours -10am to 2pm.

Just my 2 cents.

Tuesday, June 24, 2008

A graduate student oath -- will it help?

by Beyond Lab

University of Toronto created a graduate student oath to let the students remember their social and moral responsibilities, in other words, to conduct research ethically. I think one of the reasons is to try to avoid so many scientific misconduct in the scientific research area. To name a few, the Korean tem cell scandal, the recent retract of an important paper by Linda Buck, a Nobel prize laureate. There are not only irreproducibility of their data, but also the way they put all responsibility to one of the co-first authors. All these are absolutely not normal and should not happen in the pursuit of science.

Will this oath help? I completely doubt it. -- The overall scientific environment is so competitive, mainly financially, that researchers have to publish before their competitors and have to publish in good journals to secure enough support for their continuing research, and their personal salary in many cases.

Is there any way out? Things have to be changed gradually. Higher NIH budget (in US) is definitely one of the first things to do.

Monday, June 16, 2008

what's wrong with those consumer genomics companies?

by Beyond Lab

After the action of New York state about 2 months ago, California is taking a similar approach to try to regulate consumer genomics (personal genomics) companies from offering genome services without prescription from doctors. With many posts in my blog talking about the current situation of personal genomics, you might understand that one of the basic reasons is that it is not ready yet. (Most) Consumers feel what they got from the services didn't worth the money. As many experts suggested, the current consumer genomics services should be considered as "recreational genomics" -- therefore whichever company marketing these services should not relate them to health or medical implications. Otherwise, you have to get physician's prescription. So, at this point, it is reasonable for New York and California two states to initiate some regulations.

This is a good thing!

Saturday, June 14, 2008

to make use of genome

by Beyond Lab

Human genome is huge. Individual variations are also extremely common. Most of these variations don't have any effect on any function. But some, either by itself or in combination with others, do. What, how, when, and where these variations matter is something we have to know before personal genomics really mean anything.

As one of my earlier posts indicated, some companies, in collaboration with research institutes, have projects on their target diseases or conditions. But that's obviously not enough. We have to know everything - eventually.

So, there is a "genome-wide association studies" from NIH which involves "rapidly scanning markers across the complete sets of DNA, or genomes, of many people to find genetic variations associated with a particular disease". Many diseases are under study now. This sort of "national" or global initiative, like the previous human genome project, is really the drive to our understanding of our genome and therefore could make use of genome information.
More detail information could be found here:

Wednesday, June 11, 2008

One gene, one disease??

by Beyond Lab

Obviously not. Life is so complicated that it is impossible for one gene to be solely responsible for one function and therefore one disease. Almost all genes identified have multiple domains (function units) with different "potential" function. So, mess up one gene would certainly have more than one consequences. This has been confirmed in many species, from bakers yeast to human.

So, it is almost impossible to predict the occurrence of one disease just by analyzing the function/structure of one gene or its product. It has to be a combination of various information. With that being said, is it helpful to analyze one gene if it is know that this particular gene (or its mutant formats) always associates with certain disease. Absolutely!. But how accurate is it? No one knows when it comes to one individual -- yes or no. Probability means nothing for one individual.

Why am I saying this? Because one company Orion Genomics just licensed JHU technology to analyze IGF2 gene (insulin-like growth factor 2) with the hope to be able to predict the outcome (progression) of colorectal cancer. -- Beyond Lab personally thinks this is not very wise. I don't know how they will promote their future product to analyze one single gene. --Most current genetic or genomic detection products for breast cancer all involve many genes. One gene? Unlikely mean anything.

Sunday, June 8, 2008

More on presentation

by Beyond Lab

Last month's Nature Methods had an editorial named "talking points".

The short list of advice is:
1. Plan for the allotted time.
2. Know your audience.
3. Define your goals.
4. Structure your talk.
5. Keep your slides simple (content).
6. Keep your slides simple (design).
7. Beware of animations and multimedia.
8. Watch your delivery.
9. Choose your words.
10. Rehearse!

One thing Beyond Lab wants to point out here is that it once again recommends serif font just as Tomjoe's comment to one of my earlier posts.

So, use it!!!

Big money on personalized medicine

by Beyond Lab

Luxembourg government decided to take the challenge to push personalized medicine researches with big money. In collaboration with three U.S. institutes, U. of Luxembourg will establish several research centers to build a BIOBANK which collects huge amounts of disease samples and genetic information. This proposed system will be used to promote translational research and systems biology and in the long run will build the basics for personalized medicine. Of course, this has to be helped with modern personal genomics studies.

To Beyond Lab, this initiative is an important step toward personalized medicine. With U.S. economy going slow and U.S.federal funding being flat, other countries like Luxembourg, Japan, Singapore, and even South Korea are putting big amount of money in life science. At this point, the whole thing is still at data/information collection stage. But very soon, really useful knowledge/technology will come out and some of them will bring money back to those countries who invested in the research. Although it is difficult to predict exactly a time frame, the fast growing technologies will sure prove this is the case.

Wednesday, June 4, 2008

Personal genomics -- not only cancers

by Beyond Lab

A significant part of personal genomics studies have been focusing on the relationship to cancers. But that's definitely not the whole case. Recent gene analysis showed the potential use of personal genomics in other diseases related to our everyday life such as metabolic disorders -- folate (a kind of vitamin) metabolism.

Sequencing of a vitamin-dependent enzyme (critical proteins which carry out most of the molecular reactions in our body) methylenetetrahydrofolate reductase (MTHFR) from about 600 persons' genomes found that there are some variations in the populations. Some of the variations actually affected the enzyme function. More importantly, increasing folate level could rescue its function to normal level. --This is really direct evidence that simply changing what we eat everyday could interact with personal genomes and therefore have obvious benefit.

How useful is your personal genomes? Studies like this will gradually prove it. - Some time in the future, sequencing your genome will be like buying a car. Of course, by then genomics counselors will be a good job :)

Monday, June 2, 2008

colorectal cancer and patient personal genomics

by Beyond Lab

Here, another example showed that colorectal cancer patients with normal K-RAS gene have better response to a FDA approved drug (an EGFR antibody if you are interested).

The study was a multi-center multinational prospective clinical trial (Phase II) of Cetuximab where about 600 colorectal cancer patients were examined for K-RAS gene mutations and related to response to drug treatment (in combination with standard chemotherapy). --More wild-type K-RAS carriers showed reduced cancer and decreased risk of cancer progression. The numbers are not dramatic, but are significant considering the number of patients studied.

This kind of study will gradually build the foundations of personalized medicine and the eventual application of personal genomes (genomics). As mentioned in one of my previous posts, those personal genomics companies should collaborate with researchers to expand this kind of correlation studies (especially with NIH funding is limited).