A Family Experience of Personal Genomics Paper Out
January 9th, 2012 § Leave a Comment
I have the pleasure to announce the publishing of the case study “A Family Experience of Personal Genomics” by the Journal of Genetic Counseling today. An accompanying Commentary Note written by ethicist Anna Middleton is also published. Both papers are open access. [Correction: these papers will be open access shortly.]
The case study paper is an invited contribution for the Journal of Genetic Counseling in a special issue on Direct-To-Consumer (DTC) genetic testing. This paper describes the journey I went through with my family when we all embarked into analysing our personal genomes via a DTC genetic testing company. I believe my experiences could be related to many other people in the world as they gain access to this technology. In the commentary Dr Middleton discusses the implications of the difficulties I went through when communicating my relatives their genomic information.
A Genome Blogger Manifesto
September 28th, 2011 § 9 Comments
Have you ever wondered why some people have no reparation in sharing their genetic profiles? Why do they openly talk about something supposedly so private? I believe that no contradiction exists between wanting to protect one’s privacy yet sharing one’s genomic data with the world. I am more concerned about the information that Facebook collects about my profile than my genome data (provided that I live in a country where there I public health).
Sharing and comparing one’s genome with other personal genomes is a matter of necessity if one is to shed light on the meaning of one’s personal DNA.
This is why I became a genome blogger myself. Why one should be constrained by the information that genomic test reports provide? No personal genome analysis report can ever be complete, they will always be influenced by the biases of whomever is providing such a report.
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Although no formal document seems to have been produced on what the core values for genome blogging should be yet, core beliefs driving personal genome-sharing should be made explicit. Here I present an initial and inherently imperfect first attempt to put in writing of what I believe genome blogger values could be. I do not expect every fellow blogger to agree with them, but I hope that at least they inspire some debate. These are not a fixed set of rules; on the contrary, I expect this thinking to evolve with the genomics technology itself. I base some of the ideas below on Marcus Wohlsen’s ‘Biopunk’ book, Meredith Patterson’s ‘biopunk manifesto’, Misha Angrist’s ‘Here is a human being’ book and Pekka Himanen’s ‘Hacker’s ethics’ book.
Core Values for Genome Blogging
- Intelligent exploration, experimentation and trial to push the boundaries of knowledge are a right for ordinary people. The days in which genetic science was only done by university professors or people working in corporate labs are now over. Now everyone should have the power and legitimacy to be able to discover, develop and find new things about their own genome data. « Read the rest of this entry »
Not All Genetic Discrimination is Illegal in the US
June 24th, 2011 § Leave a Comment
It struck me that the Genetic Information Nondiscrimination Act (GINA), the flagship US law against genetic discrimination, signed by President George W. Bush in 2008, does not cover life insurance, disability insurance, or long-term care insurance.
In other words, in the US it’s still possible to be discriminated against for genetic reasons. How is this situation likely to change in the near future?
When I look more closely at it in the NIH factsheet for GINA it is stated that
As genomic medicine is poised to revolutionize medicine, patients will be able to utilize advances in genetic testing to create highly personalized care and treatment plans without fear of discrimination.
I have two main objections with that:
- The current level of protection is not near enough to dissipate the fears for people to ‘utilize advances in genetic testing’. The law itself states that GINA sets a ‘minimum standard’ but still does not cover some crucial scenarios where being discriminated against may be devastating (e.g. life insurance).
- If Direct-to-consumer (DTC) genetic testing is only going to be available via medical prescription, as many in the FDA are seeking to implement, does this approach help in any way the advancement of personalized health care? According to Misha Angrist [1], the top requestor for genetic tests in 2006 in the US was a Spa company; i.e. rich people with disposable income who wanted to understand their health risks. The impression I gather is that private demand is the main driver for DTC genetic testing and not the institutionalized health care. If the worst fears of DTC providers become a reality it may well be the end of an open, accessible, democratized personal genomics field as we now it. This does not take away the grave obligation DTC providers and relevant governmental agencies have to educate the public to ensure that they understand their results and that rigorous standards are met in reported findings.
Genetic Information Nondiscrimination Act Factsheet
It also strikes me that, in GINA, concepts like ‘privacy’ and the ‘right not to know’ are not even mentioned. My family and I chose to share our genotypes with the world, which should be as respectable as not sharing this data in the strictest sense. Both being open or protective of one’s genetic data should be an informed personal choice and not something imposed. I thus think this should be an important aspect that remains to be addressed at the juridical level.
In the NIH GINA factsheet it also reads that
Insurers cannot use genetic information obtained intentionally or unintentionally in decisions about enrollment or coverage.
To my mind this means that there is no restriction in collecting genetic information even though it cannot be used. I’ve heard say that some insurers may be collecting genetic data in anticipation of changes in laws that would allow them future use of the data.
Ignorance is the worst possible kind of discrimination
The need to educate the public and help them make an informed decision on genetic testing should remain the single most important priority by governments and regulatory agencies alike. Trying to impose on the public tight regulations on access to DTC genetic testing may create the wrong public opinion and backfire in the same way as GM food and crops did in Europe. Now is the time, when opinions are still to be formed, to make people aware of what DTC can or can’t tell them about themselves. The worst form of discrimination I know is ignorance and only ignorance can lead to the wrong interpretation of test results. Perhaps the solution does not lie so much in restricting access to DTC genetics testing as it is in helping consumers choose the right option for themselves.
[1] Here Is a Human Being: At the Dawn of Personal Genomics (2010) HaperCollins Books.
Millions of Genomes
February 15th, 2011 § Leave a Comment
This was that title of a talk recently given by Richard Durbin at the Wellcome Trust Sanger Institute. Excitement and expectation, reassured by a continuous trend of exponential growth, made inspired listeners feel the same way Google or Facebook employees must have felt at their company’s peak time.
Some numbers presented by Richard gave context to the startling prediction that by 2015 millions of individual genomes will be sequenced. This is in fact the expected number if the current pattern of growth continues. Ten years have now been celebrated after the draft for the first Human Genome was released in 2001. By 2006, with next generation sequencing in full swing and sequencing centers churning out many gigabases per week, tens of genomes had been sequenced. Today the number of individual genomes is in the order of thousands, meaning that every year a 4 fold growth is predicted. Extrapolating this estimation to five years from now makes thus the number of genomes sequenced 1024 times (45) our current number, hence millions of genomes.
Having such an incredible amount of data will clearly create challenges which we are just beginning to find. How are we going to hold all this data when processing capacity in computers “only” grows 2 fold every year? The answer is that as more genomes become available, an individual’s data will not be stored in its totality but only the differences that define his/her particular variations.
Although many genomes may have been sequenced by now, accessing them is not a trivial matter. Stored in many different places, with different restrictions and inconsistent levels of detail, the bulk of this data is likely to remain at least mildly challenging to handle. Results of investigations will certainly be accessible, but think of the effort it could cost to access every single database containing public individual genome data. I do not believe that a great number of genomes will be optimally researched unless more straightforward and standardized access protocols are put in place, something that currently is lacking. Times for excitement are reasonably justified, yet base pair to bedside medicine may be delayed if current data sharing procedures are not streamlined.
Anonymizing Patient Records for Next Generation Sequencing Studies
April 25th, 2010 § Leave a Comment
The advent of Next Generation Sequencing (NGS) is proving valuable for Genome-Wide Association Studies (GWAS), allowing identification of specific genomic variants leading to disease. The release of genomic data together with clinical features are of paramount value for validation of biological associations. This data involve real individuals, whose privacy should be protected. Protecting the individual’s privacy while making research findings available to the community for validation is not an easy task. There is a trade-off between how much personal data can be made public and the amount to which this data released may be useful for further studies.
Recently, this topic has been addressed by Loukides et al., in a PNAS paper were they present a method for automatically extracting linkable clinical features, which are then modified in a way that they can no longer be used to link to a small number of patients.
Modifications to clinical features are carried out preserving the associations between genomic sequences and specific sets of clinical features relevant to GWAS-related diseases. The user specifies the sets of diagnosis codes that are linkable to specific disorders and the algorithm modifies the linkable codes so that they cannot be attributed to a small number of individuals. Such code modification is carried out making sure that clinical association validation is retained, where sets of clinical features are replaced with semantically related codes to satisfy the distribution of GWAS-related diseases.
Thus, an attacker who knows a set of clinical features diagnosed for a single visit, would not be able to uniquely identify an individual because each record links to no fewer than say, 5 individuals (k=5).
Some limitations to this approach are also discussed. Data linkage may be performed if additional sources of data are possessed about the individual. Allowing data owners to make the decision of the appropriate level of protection (setting k) may hamper the reproducibility of findings if the attacker’s knowledge is overestimated, as well as compromise the individual’s privacy if underestimated. Their method also does not guarantee that the information loss for the chosen level of protection is minimized.
Personal Genomes Ripe For Social Networking
April 9th, 2010 § 5 Comments
Personal genomics offers the promise of raising quality of life to unexpected levels. Understanding one’s genome and its effects become paramount for achieving this promise. Recreational Genomics has arisen as a field of commercial activity allowing mass scale genome screening. For several hundred dollars it is possible to have one’s genome analyzed and results easily downloaded as a flat text file. In the case of 23andMe, this analysis consists of personal variants (genotype) for more than 0.5M SNPs (single nucleotide polymorphisms). This personal “genome” is interesting in its own right and it would be even more interesting provided that this information is compared and analyzed in the context of other people’s genomes and their phenotypes.
A resource available for social networking to allow mass comparison of people sharing traits and genomic variants, I believe could have revolutionary effects. Such a network could allow one start making sense of specific personal traits, susceptibility to illnesses and determination of potential treatments proven successful by genetically similar people. Exchange of genetic information made easy should be a reality soon.
The time is ripe for social genome networks. Indeed there are lots of potential ethical and legal challenges ahead. How long are laws and social prejudices going to stop the inevitable?
Computational Bioethics: Leveraging Personalized Medicine Ethically
July 14th, 2009 § 1 Comment
Computational Bioethics relates to the appropriateness of use, management of access and discovery of biological insights applied to patient health. A simple search in Google shows that this concept has only been used in the past at a workshop session in the Rocky Bioinformatics conference in 2008. In the resulting publication of this meeting, Computational Bioethics is said to encompass ethical issues that are unique to computational scientists compared with bench and clinical scientists. In addition, it is argued that as medical informatics, computational biology and bioinformatics become more widely used in medical research, these issues will become even more relevant in the future.
And the future is now become a present reality. The rise of next generation sequencing technology, together with the adoption of microarray techniques in normal clinical practice is revolutionizing the way patient’s data is handled. Similarly, the amount of data created is surpassing most software tools available. Projects like the 1000 Genomes are generating an enormous pool of variability of genome data and derived sources of information. This makes necessary the exchange of data between research centers to be able to establish what constitutes normal and pathogenic variation in human beings.
Personalized medicine, a widely used term since the near completion of the Human Genome Project, implies the application and use of personal genome data for the determining genomic changes leading to disease, risk factors and patient’s susceptibilities. The problem with this sort of data is that it may yield information that could severely change the life style of the person, affect relatives and, in many cases, with little ability to do anything to mitigate the effects of findings. As our current knowledge is so fragmented and rudimentary, it is expected that collected information with no current value may be relevant in the future, influencing analyses and results.
Some ethical practices currently implemented in Computational Bioethics include the creation of consent forms that allow putting anonymized patient information in genome databases. This information may be accessed by the scientific community and compared with other previously consented patient data for the characterization of new syndromes, the effect of knockout genes in the general population and the understanding of genome variation in normal individuals.
