A Genetic Poem
December 24th, 2010 § Leave a Comment
A poetry contest is being organized by 23andMe. The five lucky winners each get a free entry to the 2011 edition of the Personalized World Medicine Conference. The rules are simple, include at least 5 words from a list provided and send it by December 31st. Any formats and number of tries are allowed. Unfortunately I am not eligible because it is only open for US residents and travel costs are not covered.
Since Christmas is a time that tends to be free of distractions for me :-) I decided to give it a try and write a genetic poem, even though I am not eligible for the prize. I will share it for now but I might take it down later if I feel more embarrassed about it.
My Genes and Me
Genes between probes
Vary my transcription
Condition their relation
And length of ear lobes
My credit card spelled out
The questionnaires went
I too gave consent
To have my test done, no doubt
A saliva drop fell
As the parcel came home
I shook it all well
The lab got it, I logged on
Risks and Ancestry I found
Some were fine, some were high
I Scrolled up, I scrolled down
Browsed data through the night
Then something else happened
A 5th cousin had chatted
That shared my haplogroup
Was she part of my troupe?
Yet it was all the genotypes
That 23andMe found alike
Without it I wouldn’t know
Such tales of my chromosomes
For how can a little SNP count
If these traits are all mine
My phenotypes all defined
When I had just DNA out
And if this was not enough
Hope you’ll let me certify
GWAS is good for some stuff
Even if it’s hard to identify
On the Need for Ontologies that Encode Environment Health Factors
May 23rd, 2010 § Leave a Comment
Complex genomic diseases are well known to be affected by environmental factors. Despite the obvious association of Genotype and Environment (G x E) to Phenotype (= P), current efforts to understand the etiology of complex diseases have been focused mainly on G, ignoring the E part. It is not surprising that this is the case, since environment variables such as diet, education, exposure to pollution, etc., are not easily to measurable, let alone be encoded in a computationally friendly format.
This difficulty in measuring E however does not justify its conspicuous absence in Genome Wide Association Studies (GWAS) or other genomic studies. Providing a proper controlled vocabulary or ontology that describes environmental phenomena amenably should help overcome barriers in following and annotating E.
In the field of Genome Medicine, ontologies have been extremely useful for characterization of phenotypic traits in patients. For example, the London Dysmorphology Database, the Human Phenotype Ontology and the Gene Ontology all have proven invaluable for description of clinical traits, molecular processes, biological function, etc.
The current situation of lack of environmental health factors in genome association studies could be comparable to years ago when diseases were being characterized without formal descriptions of phenotypes. Unfortunately, it seems that so far the efforts to include E have been rather limited and not enough drive has been produced to formally encode it. A simple search in google shows no ontologies applied to E and neither E is included in the NCBO Bioportal for anything related to health and disease.
Collection and encoding of environmental factors in a formal structured ontology will surely help shed light on the missing heritability of complex diseases and beyond. Let’s hope that such efforts are soon embraced. Perhaps such an initiative could help reverse the traditional trend to ignore the E part of the G x E = P equation.
