Monday, May 12, 2014

PSPG hits the streets to explain how genes make us who we are

           With help from the University of Pennsylvania and GAPSA, PSPG was able to run a volunteer booth at the Philly Science Carnival on May 3rd. The carnival was part of the annual 9-day Philly Science Festival which provides informal science educational experiences throughout Philadelphia’s many neighborhoods. The title of the PSPG exhibit was “Who owns your genes?” and featured activities for children and adults alike to educate visitors about how genes make us who we are, what we can and cannot learn from personalized genomics services like 23andMe, and how several biotech companies have attempted to patent specific genes.
           Kids learned how genes act as the instructions for building an organism by drawing alleles for different traits out of a hat and using the genotype to decide how to put together a “monster.” In so doing, they were exposed to the basic principles of genetics (dominant vs. recessive alleles, complete vs. incomplete dominance, and codominance), and they got to leave with a cute pipe-cleaner monster too.
           For our older visitors we presented actual results from a 23andMe single nucleotide polymorphism (SNP) report generously provided by one of our own members (advocacy coordinator Mike Convente). This part of the exhibit walked visitors through the process of sequencing for SNPs, which are single nucleotide bases that vary widely between individuals and can give hints about ancestry, physical traits and possibly diseases, and the implications of bringing these types of tests to the general public. Right now the Food and Drug Administration is trying to figure out how to regulate services like these, which provide genetic information directly to consumers without a qualified middle-man (such as a doctor or geneticist) to explain the complicated results.
           Our exhibit also featured a section entitled “How Myriad Genetics Almost Owned Your Genes” which highlighted the recent Supreme Court case brought against a biotech company that wished to patent two genes (BRCA1 and BRCA2) involved in the development of breast cancer. The genes were discovered at the University of Utah in a lab run by Mark Skolnick, who subsequently founded Myriad Genetics. Myriad went on to develop a high-throughput sequencing assay to test patients for breast cancer susceptibility and eventually obtained patents for both genes. This was controversial for several reasons: 1. These genes exist in nature in every human being and are not an invention; 2. The genes were originally discovered with public funding; and 3. Myriad had a monopoly on testing for BRCA mutations and prevented universities and hospitals from offering the tests. Last year in Association for Molecular Pathology v. Myriad Genetics, several medical associations, doctors and patients sued Myriad to challenge the patents and the Supreme Court decided that patenting naturally occurring genes is unconstitutional (however synthetically-made complementary DNA is still eligible for patenting). It is likely that the patenting of DNA sequences will continue to be an issue in the future considering recent advances in the field of synthetic biology.

Monday, March 3, 2014

Genetically-modified food is not going to give you cancer

Last week PSPG and the Penn Biotech Group hosted Dr. Val Giddings, President and CEO of the consulting firm PrometheusAB and Senior Science Policy Fellow at the Information Technology and Innovation Foundation. Dr. Giddings specializes in issues concerning genetically-modified organisms (GMOs) or as he prefers to call them, “biotech-improved” organisms, which have been genetically engineered to have certain beneficial traits. This usually means that a gene from one organism is inserted into the genome of a different organism to alter its properties or behavior in some beneficial way. GMO crops are frequently altered to improve tolerance to herbicides (think RoundUp) and resistance to insects and pathogens. They can also be modified to change their agronomic qualities (how/when they grow) which helps farmers to be more productive. Crops can also be modified to improve their quality: for example Golden Rice has been engineered to produce beta-carotene, the precursor to vitamin A, which is an essential nutrient that many children in developing countries don’t get enough of1,2.  GMO crops are quite prevalent within the US agriculture, with over 90% of soybeans, 80% of cotton and 75% of corn crops in the US being genetically modified in some way3. Outside of the US, GMO crops are grown in 27 countries by 18 million farmers, most of whom are smallholders in developing countries4. So what are the consequences of all these genetic modifications in our food supply?

Tuesday, February 25, 2014

The unintended impact of impact factors

Dr. Mickey Marks of UPenn stopped by PSPG yesterday to discuss the San Francisco Declaration on Research Assessment (DORA) which calls for new metrics to determine the value of scientific contributions. The system in question is the Thomson Reuters’ Impact Factor (IF) which was developed in the 1970s to help libraries decide which journals to curate. Since then IF has taken on an inflated level of importance that can even influence promotional and hiring decisions.  But can a single number really summarize the value of a scientific publication?
IF is calculated by dividing the average number of citations by the number of citable articles a journal has published over the last two years. One reason Dr. Marks became involved in DORA is because he is co-editor at a journal whose IF had been steadily dropping over the last few years, a trend experienced by numerous other cell biology journals. This led many in the field to question whether IF was really accurate and useful. As you might imagine there are many factors that can skew IF one way or another: for example, in some fields papers are slower to catch on and might not start accumulating citations until well past the two year IF has been calculated. Journal editors can game the system by reducing the number of “citable” articles they publish: citable articles must be a certain length, so if a journal publishes many short articles they can decrease the denominator and inflate their IF. So how reliable is the IF system? Are journals with a high IF really presenting the best science? A few years ago the editors at one journal (Infection and Immunity) set out to address that very question and the answer may (or may not) surprise you. The editors found a strong correlation between IF and retractions (see graph).

Infect. Immun. October 2011 vol. 79 no. 10 3855-3859
          Why are these high impact journals forced to retract at such a higher rate? It might be because these editors are looking for sexy science (because that’s what sells) and might be willing to overlook sloppy research conduct to print an exciting story. Another reason may be that researchers are under extreme pressure to publish in these journals and are willing to omit inconsistent data and allow mistakes and even misconduct slip through to keep the story neat. And this brings us to the real problem presented by IF: in some circles individual researchers’ scientific contributions are being judged almost entirely on what journals they publish in. Scientists learn very early in their careers that if you want a faculty job you need to publish in Science, Nature and Cell. This is because it is faster and easier to draw conclusions based on a journal’s reputation rather than actually read an applicant’s publications.
There are a few alternatives to IF, including Eigenfactor and SCImago which are similar to IF but take into account the overall impact of each journal, and Google’s PageRank which ranks journals based on search engine results. These alternatives generally result in similar rankings to IF, however. The real issue isn’t the rankings themselves but how we as scientists use them. If the system is going to change it will have to start with us.  Scientists must decide together to de-emphasize impact factors and publication rankings when making decisions about promotions, hirings and grants.

Nicole Aiello
PSPG Communications

Friday, January 24, 2014

Bioethics/Policy Discussion: 23andMe vs. FDA

On Wednesday, members of the Penn Science Policy Group met to discuss the current regulatory friction between the FDA and the genetic testing company 23andMe.

23andMe provides personalized DNA results that are interpreted to provide information about ancestry and health risks for various diseases. Because the results provided by 23andMe border on medical information, the FDA has been working closely with the company since 2009 to ensure that their marketing and analysis were accurate and in accordance with federal regulations. However, in May of 2013 23andMe ceased communications with the FDA and simultaneously ramped up marketing of their Personal Genome Service (PGS) for providing “health reports on 254 diseases and conditions.” In retaliation, the FDA sent a letter to 23andMe on Nov 22 warning them to stop marketing their PGS without approval or face harsh regulatory actions. This letter sparked a public debate about how much regulation should be imposed on this new technology, which was the focus of our discussion on Wednesday.

The question at the heart of the debate is: do individuals have the right to access their own genetic information (and interpretations of it) without medical (and hence FDA) oversight?