October 3, 2013 § Leave a Comment
I cannot believe that 4 years have passed by since I bought my first 23andMe spitting kit. I was recently invited to give a talk at a course on Synthetic Biology and was able to present an overview of all the findings of my years working with my own personal genome and those of my family.
I would like to thank specially my cameraman and friend Phil Tobitt for his brilliant work in filming and editing this talk. Although this started as a hobby, a lot of my scientific efforts and after-work hours have gone into this.
There will be more developments happening in the near future but meanwhile I leave you with the present state of the art of our personal genomics adventure:
September 13, 2013 § 7 Comments
I came across this article in which a graduate student decides to leave academia just several months before the submission of his/her PhD. His/her frustration and acute appreciation that the academic/scholar system is inherently flawed by the constant drive to publish, the sclerotic hierarchy of untouchable professors and the ruthless exploitation of those at the base of the pyramid, has led him to give up.
Well, I understand all those concerns and I am personally affected by them. The fact that I am married with three small children, one of them with severe discapacity, limits me greatly as a scientist. I agree with a colleague who recently told me that the way to become a leading scientist or academic is really cruel and unjust, perhaps more than most professions, but that the system is corrupt does not take away the idealism of the academic enterprise.
If you really love politics, should you stop being a politician, even if the system is corrupt? Why not try to do whatever is in your power to make it better?
If you like banking and genuinely want to make a contribution to society, should you not do it?
The problem this article highlights is a deeper one than a problem with academia: our society has forgotten living according to high moral standards. It is more acute in academia though because by its nature this place is supposed to be idealistic and live by really high standards. Yes, standards are low in academia, so I understand this person’s frustration.
I do not claim academia is apt for everyone, but for those who have high ideals of scholarship, it is still a very rewarding and worthwhile path, even though the system may be corrupt in some aspects. Academic achievement should never be an end in itself, it must be the means for a better society. When academic achievement does not truly fulfils its role, it is not being true to itself. That is why we need people with high and strong ideals who are able to give their life for them. That is what is needed in academia and in every other sector of society: individuals who are able to truly live up to their high values regardless.
July 25, 2013 § 3 Comments
ISCB, the International Society for Computational Biology, elected me as a member of the Board of Directors during the last #ISMBECCB conference. I thought it would be a good idea to publish in this blog the actions I intend to work on during my 3-year tenure starting in January 2014.
I bring to the table a lot of experience in setting up networks, organizations and events at an international level. Things that I started include ISCB’s Student Council, ISCB’s Regional Student Groups, the series of Student Council Symposiums, the ISCB Africa ASBCB Conference and Itico.org, a non-for-profit company of which I am director.
I consider I have strong presence in social networks with a blog that has been independently voted among the top 15 bioinformatics blogs, a twitter account with >1,000 followers and >1,000 contacts in LinkedIn.
As an ISCB Board of Directors (BoD) I pledge to:
- Help create a structure within ISCB to represent and give opportunities to contribute to “middle layer” members. I would like to work really hard to ensure that a new organisational structure is brought about within ISCB to accommodate the flourishing of a new initiative targeting the “middle layer”. By middle layer I mean scientists who are in between the two main groups ISCB currently caters to: students and highly accomplished scientists. I want to discuss with this constituency new ways in which scientists at this middle level can be effectively engaged to work within the Society, through specific work tasks, committees or entirely new initiatives.
- Advocate for students and scientists in developing countries. As a BoD member, I would be particularly interested in overseeing, encouraging and stimulating members of Regional Student Groups (RSGs), particularly in Africa. African scientists have specific needs that require special attention. I would do this by continuing my collaboration with Nicky Mulder and Dan Masiga (present and former Presidents of the African Society of Bioinformatics and Computational Biology, ASBCB). I would also like to organize periodic teleconferences with RSG leaders to discuss their issues and to act as a voice for them within BoD meetings.
- Engage in a process of “evangelization” of the constituency; an Ambassador program, where recognized scientists talk about the benefits of becoming an ISCB member.
- Promote public recognition of service to the Society. A simple yearly award during ISMB could be a good start. People who have demonstrated their commitment to the Society should be recognized publicly through positions of responsibility, promotions, awards, etc. I know that this is done privately to BoD members who receive a certificate. My proposal is that these awards are made public through the website, the newsletter and other media if necessary.
Please submit comments or suggestions using either the comments below or contacting me directly.
June 21, 2013 § Leave a Comment
Risking being called ‘Narcissome’ (as Michael Snyder’s work or Snyderome has been called), we not only have written about the Corpasome, we now have it published as well. Today the article “Crowdsourcing the Corpasome” appeared in the journal Source Code for Biology and Medicine. In this article I define the word, but most importantly, I describe the motivations for crowsdsourcing the genomes of my whole family (with their informed consent). Our final aim is to raise awareness of the huge benefits that open personal genome data could bring for the development of open, easy-to-use tools. Don’t forget however, to find the little pearls of satiric humour disseminated in the text!
In this article I also provide a list of all of the data that can be freely downloaded via figshare. To accompany the publication of this article, I have created a video in YouTube, encouraging scientists to analyse these data and to use them in any way that can help them develop new open source tools for the analysis of personal genomes. Enjoy!
April 12, 2013 § 4 Comments
Is it weird for a Spaniard to have red hair? The typical stereotype for a Mediterranean person is brown-skinned, not too tall and with dark hair. I do not seem to fit all those stereotypes very well, except for the dark hair. At least so I thought until I posted this picture of my beautiful family on my Facebook profile:
Of the five of us I am the only one without red hair. Seeing this picture really brought it home to me, it was strange that everyone of my three children had inherited my wife’s ‘recessive’ red hair!
I did not give a lot of importance to this until my colleague and Facebook friend Dave Adams, who happens to lead a research group at the Wellcome Trust Sanger Institute, asked me whether I had checked the MC1R gene.
The protein encoded by the MC1R gene is found in melanocytes, the cells that give hair and skin their color. The variants associated with red hair alter the protein’s function, tipping the balance of pigment production in melanocytes from black-brown eumelanin to red-yellow pheomelanin .
Dave is well aware of my efforts to crowdsource my genome data analysis and those of my blood relatives (parents, siblings and aunts and uncles). Since I have had my exome done, and following Dave’s suggestion, I looked for the animo acid changes he suggested (r151c, r160w and d294h) in the MC1R gene. Below you can see some of the comments of our conversation on Facebook:
I have a VCF file for all variations in my genome available in figshare for public download. I searched the file for the 89978527-89987385 interval in which the MC1R gene is located in chromosome 16 and found:
16 89986091 rs11547464 G A
This indicates that in position 89986091, there is a small change of one letter (SNP rs11547464) that makes my DNA in that position differ from the one of the human genome reference. The reference genome has a G whereas I have an A.
I also looked at my 23andMe genotype using myKaryoView, which also includes this rs11547464 SNP, and found that my genotype is ‘AG’. Doing some research with this I found that AG in the rs11547464 SNP encodes a missense change on the protein sequence (R142H), making me a ‘carrier’ state for ‘red hair’ .
More information about the relation of this SNP the phenotype showed that this mutation has been shown to be deleterious  and that this MC1R variant is “functional” .
According to Dave, I am a carrier for this red hair mutation and presumably my wife is homozygous for another variant with my kids being compound heterozygous. This means that perhaps my wife has another variant somewhere that also contributes to my children having red hair.
This explains, at least partly, how my offspring’s red hair is so strong, something that in principle should be self evident from the picture above. There is something satisfying though about being able to confirm the obvious with scientific evidence.