Author Archive for Don Conrad

People Have A Right To Access Their Own Genetic Information

This week has seen another FDA meeting seeking guidance on how to regulate direct-to-consumer (DTC) genetic tests in the US. The meeting itself has been covered by GNZ bloggers Daniel at Genetic Future and Dan at Genomics Law Report, and its apparent outcome has sparked furious debate elsewhere. The discussion among the “independent” panel convened at the meeting appeared to converge on the proposal that all health-related genomic tests should be ordered and reported through physicians. However, the outcomes of the meeting in terms of FDA policy remain unclear, and one FDA official has indicated that decisions about the availability of genetic tests will be made on a test-by-test basis.

There is no doubt that the appropriate regulation of personal genomics tests is a complex issue, and there is a diversity of opinion about how best to achieve it within GNZ (as there is throughout the genomics community). However, there are several points we agree on:

  • Individuals have a fundamental right to access information about themselves, including genetic information. While it is important to also consider the accuracy, interpretation, validity and utility of tests, this underlying principle should guide policy.
  • There is currently no evidence that DTC genetic tests pose a danger to consumers. A recent study of over 2,000 participants in DTC testing concluded that “testing did not result in any measurable short-term changes in psychological health”. In the absence of any evidence of harm there is no justification for restricting individual autonomy.
  • DNA does not have magical powers, and does not require special treatment simply by virtue of being DNA. Genetic exceptionalism – the idea that genetics must be treated as special under the law – is an inappropriate basis for policy-making. Tests should be regulated appropriately based on their predictive power, utility and potential for harm, all of which are related concepts.
  • As DNA sequencing becomes cheaper, the line between medical and non-medical testing will continue to blur. Excessive regulation of health-related genetic tests could also unncessarily hinder the ability of people to access their entire genome sequences for other purposes (such as genetic genealogy).
  • Most clinicians do not have the appropriate knowledge to interpret genomic tests, particularly in healthy individuals. This point is almost universally agreed, even by the FDA, and has certainly been the experience of some of the GNZ members upon taking our genetic results to doctors. Physicians in general are therefore a strange choice for ‘guardians of the genome’.
  • Most early adopters of DTC genetic tests are sufficiently well-informed to understand the implications of a genomic test and interpret the results correctly. Putting a general physician between these informed individuals and their own genomes is paternalistic and unnecessary.

While the outcome of the FDA’s deliberations remain uncertain, it is clear that there will be intensive lobbying against any attempt at excessive legislation. In the worst case scenario, the fledgling and innovative personal genomics market could be crushed by the FDA. However, there is still plenty of room for a measured approach that enforces test accuracy, punishes false claims and promotes informed choices by consumers, without reducing the ability of responsible companies to continue to operate and innovate.

We urge others in the genomics community to make their voices heard on these issues. Let the FDA – and, if you’re based in the USA, your political representatives – know that regulation of genetic testing should be based on evidence, not fear, and that any attempt to unreasonably restrict your access to your own genetic information is unacceptable.

Friday Links

Clinician Jacob M. Appel has a refreshing take on direct-to-consumer genetic testing – unlike many of his stethoscope-wielding brethren he rails against the idea that members of the public shouldn’t have access to their genetic information without the supervision of a medical professional:

The underlying belief of DTC opponents is that laymen are incapable of handling their own genetic information without the assistance of physicians. As a physician myself, I cannot help but fear that this approach smacks of the worst aspects of medical paternalism. We may soon find ourselves living behind a genetic Iron Curtain whose drawstrings are held by a cadre of white-coated Platonic guardians. Despite the public triumphs of the genetic revolution, our genetic liberties are slowly and silently slipping away.

Let’s hope this attitude catches on. [DM]

SNPedia’s Mike Cariaso discusses the present and future of personal genomics in a brief op-ed piece in Bio-IT World, which ends on an optimistic note:

While there is considerable trepidation at the marketing of genomes, I’ve been pleasantly surprised by the nearly universal consensus that you have a fundamental right to your genome. The biggest reluctance comes from those who want you to have the data, but only after they tell you what it means for a reasonable fee. But the head of the NIH, Francis Collins, has said, “free and open access to genome data has had a profoundly positive effect on progress.” FDA regulations may curtail the marketing, but it seems increasingly unlikely to limit the fundamental availability of personal genomes for the masses. The learning curve is still steep and much uncertain remains, but the path seems safe with no fundamental barriers to continued progress in all directions. [DM]

23andMe’s Joanna Mountain has a great post summarising the key messages for personal genomics from the presentations at the recent American Society of Human Genetics meeting. [DM]

Genetics chairs across the US read this Nature news piece carefully, which outlines new strategic directions for NHGRI.  We should expect that 15-20% of the current budget for large scale sequencing centers will be reallocated to three areas in the next funding cycle: analysis of Mendelian disease, clinical use of sequencing to guide treatment of difficult cases, and development of more user-friendly software for analysis of next-gen data. The clinical emphasis of these new priorities echoes other exciting developments for sequencing centers in other countries, such as the Wellcome Trust Sanger Institute’s DDD project. [DC]

Over at Genomics Law Report, Unzipper Dan Vorhaus reports from the recent Partners Healthcare Personalized Medicine Conference. The conference included real-time polling of the audience on various topics, including this highlight:

46% of the audience said they would wait until the price of whole-genome sequencing (WGS) dropped to $100 before taking the plunge. 30% would be buyers at $1,000, 9% thought $0 sounded more reasonable and a full 15% answered that they weren’t interested in a whole-genome sequence at any price. Panelist Mark Boguski (Beth Israel Deaconess Medical Center) joked that the audience was “cheap” but, given the rapid decline in the cost of WGS, “patient” may be a better adjective. By way of comparison, at last year’s conference 59% answered that $100 was their preferred price point, with only 10% declining WGS no matter what the price. Is it possible that some people are are getting cold feet as the prospect of actually having their own genome sequenced becomes more realistic? [DM]

Finding the holes in our genomes

In a previous post I discussed copy number variation, a form of genetic variation not broadly reported by DTC companies. In today’s post I provide a very simple program that allows one to identify potential deletions on the basis of high density SNP genotypes from a parent-offspring trio, and report on the results of running this program on data from my own family.

The program uses an approach that I applied as a graduate student to mine deletions from the very first release of data from the International HapMap Project in 2004.  The idea, explained in my last post, is to look for stretches of homozygous genotypes interspersed with mendelian errors, which might indicate the transmission of a large deletion. Let’s be clear, this is a simple analysis that most programmers and computational biologists would find straightforward to implement. It is probably a good practice problem for graduate students and would-be DIY personal genomicists.

I obtained 23andMe data from both my mom and dad, and, with their consent, ran the three of us through the program. I was mildly surprised to find only two potential deletions; I had previously speculated that one would find 5-10 deletions per trio with the 550K platform used by 23andMe.

Continue reading ‘Finding the holes in our genomes’

Dude, where are my copy number variants?

The genome scans currently offered by major personal genomics companies provide information about only one kind of genetic variation: single nucleotide polymorphisms, or SNPs. However, SNPs are just one end of a size spectrum of variation, reaching all the way up to large duplications or deletions of DNA known as copy number variants (CNVs). Over the last decade we have learned that CNVs are a surprisingly common form of variation in humans, and they span a formidable chunk of the genome. While there are about 3M-3.5M bases of variation due to SNPs within an individual genome (in say, a typical person of European descent), there are at least 50-60M variable bases due to CNVs.

For the personal genome enthusiast with their SNP chip data from 23andMe or deCODEme in hand, there are two important practical questions: (1) can I learn about my CNVs using SNP chip data; and (2) will that information be useful?

Continue reading ‘Dude, where are my copy number variants?’

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