Debating the future of genome sequencing in medicine

This is a cross-post from my more technical blog, Genetic Inference. However, I thought that it might be of interest to non-specialists who like to keep up with the ongoing debates about the role of genomics in health and medicine.

Last week many of us at Genomes Unzipped (along with over 7000 other geneticists) were at the International Congress of Human Genetics in Montreal. A highlight of the meeting was a large debate entitled “Current and Emerging Sequencing Technologies: Changing the Practice of Medical Genetics”. The panel and the audience were both packed with research scientists, clinicians and industry researchers (you can see the full list of panel participants here), and as you’d expect the discussion was at times pretty lively.

Different perspectives

Joris Veltman described his exome sequencing of 500 individuals with intractable disease, and noted that there has been much success, and very little evidence of harm. Ségolène Aymé mentioned NIH targts that hope to see almost all genetic diseases diagnosed by 2020, and new treatments for rare diseases to be developed simultaneously. There seemed to be a solid consensus across the panel that sequencing should be rolled out as a standard tool in the diagnosis of genetic diseases, provided that the approach is a targeted one, restricted to finding the pathogenic mutation(s) causing the disease.

More controversial was the role of sequencing of healthy individuals, and the general return of data to patients or doctors for any reason other than directly diagnosing a genetic disease. Rade Drmanac, chief scientific officer of Complete Genomics, was obviously strongly in favour of everyone having their genome sequenced, and made it clear that Complete Genomics intends to start offering sequencing to doctors in the future. In his vision, genomes are sequenced at birth, and an initial analysis of immediately actionable results (e.g. potential genetic diseases) is passed to the doctor and patient, with further analyses being carried out if and when they are required.

Michael Hayden immediately dismissed this as hype. He pointed out how unable the US is to handle medical sequencing, with no good systems of reimbursement, a massive shortage of genetic councilors, and a general lack of training in the medical profession.While more positive in general, Louanne Hudgins also expressed worries about the lack of knowledge of genetics among doctors, with some truly scary examples of MDs failing to understanding even the most basic concepts in genetics.

Squabbling versus consensus building

The debate was lively, and very interesting, but started to get frustrating as time went on, and more questions and comments came from the floor. At times it seemed like a consensus might be in sight, but there was also a whole morass of squabbling that seems to get in the way. Those who are strongly in favor of rolling out sequencing argue against the conservative elements that they see as throwing out obstructions in the form of unfounded worries, and just want to defend their paternalistic tendencies against the onslaught of patient freedom. Those who are against argue against the liberals on the grounds that they are hyping the tech, and haven’t properly considered the welfare of the patients.

However, neither side really seems to fundamentally disagree on the findings of fact. Getting informed consent is difficult, but not impossible, or at least not more impossible than for other medical tests. There need to be more genetic councilors, and better education of doctors, but this is increasingly happening, and good annotation software and communication of genetic results will help things along (and is also happening). Genome quality is still not perfect, we need to ensure things are validated, and the associated costs are still relatively high. There exists some actionable information in the genome (the amount grows every year), and in the right circumstances this could improve treatment and prevent disease, but the efficacy of this approach, and its cost effectiveness, will need to be carefully assessed.

I feel that the time for debate is drawing to a close. If we wanted to we could keep on fighting, accusing each other of being clueless scientists who have never treated a patient, or out-of-date clinicians scared of new technology, or sequencing company shills who are only interested in selling genomes. However, the age of the genome is arriving whether we like it or not as a larger number of companies are now offering genome sequence for commodity prices, and we need to start getting ready. Both Michael Hayden and Louanne Hudgins ended the session with a plea to the American Society of Human Genetics and related societies to start to set out standards for the use of genomes in medicine. Now is the time to be finding things to agree on, to compromise on those that we don’t, and forge a consensus on which the future of genomic medicine can be built.

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4 Responses to “Debating the future of genome sequencing in medicine”


  • The interface between sequencing technologies and patients, if there is to be one at all, might be health care professionals. In fact, most patients would prefer this. However, would patients and/or insurers pay for the clinical time and expertise?

    If this technology has any traction, it will prove itself in the marketplace, not via some ACMG regulatory guideline or CMS dictum, and genetic counselors (note correct spelling) and physicians, including the most qualified – board certified clinical geneticists, and the less qualified – all other physicians, will be bustin’ in the door to get some. It’ll be like Botox! So bring it on. let’s see what it’s made of! Of course, this economic model works for snake oil, too.

  • The death of Steve Jobs made me reflective about what made him uniquely successful. Rather than complain that users would not learn to use computers, he commercialized technology that allow us to guide the computer with skills that we already have.

    I think that we have a similar challenge. Instead of bemoaning the fact that doctors lack knowledge of genetics, we need to develop tools that enable them to use genetic data to extend the knowledge that they already have.

  • As well as practical issues of implementation, a further difference between:

    There seemed to be a solid consensus across the panel that sequencing should be rolled out as a standard tool in the diagnosis of genetic diseases, provided that the approach is a targeted one, restricted to finding the pathogenic mutation(s) causing the disease.

    and:

    In his [Rade Drmanac, chief scientific officer of Complete Genomics] vision, genomes are sequenced at birth, and an initial analysis of immediately actionable results (e.g. potential genetic diseases) is passed to the doctor and patient, with further analyses being carried out if and when they are required.

    is that, in the absence of disease, it is still unclear what most variations mean, for the individual. So, to take a well-known set of deleterious mutations, on which women seek diagnosis and take action (and especially if they have a family history):

    http://www.ncbi.nlm.nih.gov/pubmed/21890493

    Cox, D.G. et al (2011)

    Common variants of the BRCA1 wild-type allele modify the risk of breast cancer in BRCA1 mutation carriers.

    Hum Mol Genet. 2011 Sep 16.

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