Archive for April, 2012

Welcome to the “narciss-omics” era

Saturday, April 28th, 2012

Everything started more than a decade ago, in 2001, when the first draft of a human genome was finished, published and made available for the whole scientific community through an array of bioinformatics tools. After this important milestone, a new field of study emerged named “omics”. The suffix -ome is generally used in molecular biology referring to a totality of some sort – in this case the total genome or sequence of bases of the DNA of an organism. The genomics field started before the human genome sequencing, since several organisms had their genomes sequenced; for example viruses and bacteria. Technology evolved fast since 2001 and now we are entering the “personalomics” era. The cost and time spent to sequence a human genome has dropped considerably, and today one genome can be sequenced in a few hours costing a few thousand dollars. A decade ago, the first human genome consumed millions of dollars from the government of the United States for years. These new advances in technology have enabled important studies in the “omics” field. The blog post today will discuss two recent studies that did whole genome sequencing applied to personalized medicine. Different methods can be used to generate not just whole genome sequencing of an individual but all sorts of measurements such as transcriptomics (all genes or RNAs expressed by the cells), metabolomics (all metabolites in the bloodstream of a person), imunogenomics (auto-antibodies from that individual) and so on. “Omics” studies mark the beginning of a new era of personalized medicine in which we will be able to track diseases before they are diagnosed. The first study discussed in this post was published on Science Translational Medicine and analyzed the “genometype” or the predictive capacity that a genome sequence has in detecting a disease using genome sequencing of a large number of monozygotic twins (to read more check the article “The Predictive Capacity of Personal Genome Sequencing”). In this case, just the genomes of twins were sequenced and the results of the study suggested that genetic testing will not be the determinant of patient care and will not substitute preventive medicine such as risk assessment based on family history, physical status and lifestyle. This study provides strong evidence that whole-genome sequence of individuals alone does not tell much, and a model of gene-environment interaction should be considered. For example, the future of personalized genomic medicine can be glimpsed in a second report published in the journal Cell in which Michael Snyder’s genomic sequence (who is also the lead author of the study) with the other “omics” were uncovered to give a read-out on his predisposition to disease, and his body’s response to viral infections and the onset of type 2 diabetes. As a proof-of-principle example of personalized genomic medicine, it is distinct from other studies because it applies whole-genome diagnostics to a healthy person rather than to individuals with disease, before the disease appears. Snyder, a geneticist at Stanford University School of Medicine in California, joins other researchers who have publicly aired their own genome sequence (others include J. Craig Venter, James Watson and celebrities such as Ozzy Osbourne from the rock band Black Sabbath). Snyder’s ‘Integrative Personal Omics Profile’ named iPOP, was created by merging his genomic sequence with RNA, protein, metabolic and auto-antibody profiles taken 20 times over a 2 year period (for more information see the article “Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes”). The results revealed Snyder to be genetically predisposed to type 2 diabetes, despite no family history or other risk factors. During the study, his blood glucose levels escalated following the second of two viral infections, and he was subsequently diagnosed with the disease. Snyder has since made drastic dietary and lifestyle changes to manage his blood sugar levels and the glucose levels went down showing the power of such study. However, there is a lot of criticism and skepticism about it. For example, Richard Gibbs of Baylor College of Medicine in Houston, Texas, has humorously dubbed it “the narciss-ome” or the beginning of the “narciss-omics” era according to a Nature magazine journalist (check the article “The rise of the narciss-ome”). The geneticist George Church of Harvard Medical School in Boston, Massachusetts says that a criticism of this paper is that it’s anecdotally about one person, but that’s also its strength since it shows an integrative “omics” in a timeframe of 2 years. Well, when comparing both studies (of course each one has its limitations) it is clear that “personalomics” should incorporate different measures with time since our bodies are constantly changing based on the environmental cues (diet, lifestyle, infections, etc…). The conclusion is that the sequence of the human genome is important; however since it is static, it is not enough to give us all answers. Genomic sequences should be integrated with other “omics” technologies to guide doctors in the new era of personalized medicine. Or should I say “narciss-omics” era? (Image credits: deviantART)