Personal Genomics

The raving about personal genomics has been ongoing for a while now that sequencing has become increasingly common. I have been thinking about different applications of personal genomics. It seems the most direct impact is clinical.

1) For the first time, science is being directly in touch with the masses, through companies such as 23andMe, Genetic Alliance are reaching out to the public at a large scale. People are getting in touch with microarrays, DNA, SNPs, genomic mutations - technical jargons - thought to be associated solely with just scientists. At this interface, the interplay between scientific ethics, communication, education and journalism is gaining importance. A great summary of the "Personal Genomes" conference at Cold Spring Harbor 2011 at Finchtalk gives a good summary of an outlook of this.

2) Pharmacogenetics is translational. Elucidating individual genomes means a more customized healthcare at the population and individual level. But medical informatics at the hospitals has not caught up to this. The deluge of data with just selected sequences is giving the clinicians and informaticians at the hospitals a hard time, let alone integration of full sequence data. While basic and translational research might have caught up, we would have to wait before medicine can fully utilize these information. A recent excursion to the Yale-New Haven Hospital jolted me to the fact that this is more than a technological affair, especially when healthcare becomes an enterprise.

3) Genome information is the first level of the central dogma. The primary sequence and the most fundamental, and the first to be done at high throughput. The next milestone, should be the full integration of this first level of information into healthcare. At least variability of drug dosing must be incorporated.

4) I have never thought I would be surprised by adamant resistance to knowing about your genetic material until I come here. I realize things are getting tricky with religion and insurance companies. At the other end of the spectrum, there are the apathetic people, who did their profiling and do not really care. It's scary because this nonchalance, if persists, kills the interest of the general public in the long run. When that happens, the use of such a fantastic clinical tool seems like a farce of the educated.

5) Is there anything about personal genomics that might be important beyond just being clinically relevant? The ability to distinguish maternal and paternal parts of a genome at high resolution allows a different scientific perspective of variability in the genome. But can we glean anything further? Interplay with the different other omes: transcriptome and proteome and metabolome?

M has an entry of the summary of the NIH Proteome Meeting that he spoke at: http://blog.gerstein.info/2011/10/summary-of-data-integration-session-at.html. That should be the next frontier that science is going to in clinical research - where CSI's instant mass spectrometry comes alive. Or perhaps science fiction might be gaining the most out of this.

EDIT: new science blog entry on CSHL conference on PG
http://scienceblogs.com/digitalbio/2011/10/genomes_with_benefits.php?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+scienceblogs%2Fdigitalbio+%28Discovering+Biology+in+a+Digital+World%29

Genome-Transcriptome-Proteome Triad

The buzz has mostly been about the three entities separately. I was trying to squeeze out a proposal for my research project for a fellowship application. Was doodling on a piece of paper.

Drawing first genetic interactions: epistasis, linkage. Then RNA interactions, among themselves, where for example you can have 22-nucleotide microRNAs (miRNA) interacting with messenger RNAs (mRNA) or you can also have RNAs regulating genes (pretty good symposium review: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088955/). Finally, proteome can be regulated by RNAs, such as tRNA, and they can also regulate the genes via transcription factors. Basically, I drew some edges and nodes on a scrap piece of paper.

The same day, I stumbled upon this article in ScienceDaily:

http://www.sciencedaily.com/releases/2011/10/111013121514.htm

Four Cell papers, published back to back. I haven't read the papers but four independent studies showing the influence of non-coding RNAs and its networks in cancer, on four different ncRNAs: long coding, miRNA, mRNA and a new ceRNA (pronounced SIR-na, competing endogenous RNA)... It shows that it seems quite a big deal. But I thought it's quite obvious for the levels in the central dogma to be interconnected. Perhaps the novelty lies in the context. 

I am working on ncRNAs for now too. So might actually good to take a look at the papers.