Tag Archive for 'genome sequencing'

Genome interpretation costs will not spiral out of control

Mo' genomes, mo' money?

An article in Genetic Engineering & Biotechnology News argues that as the cost of genome sequencing decreases, the cost of analysing the resulting data will balloon to extraordinary levels. Here is the crux of the argument:

We predict that in the future a large sum of money will be invested in recruiting highly trained and skilled personnel for data handling and downstream analysis. Various physicians, bioinformaticians, biologists, statisticians, geneticists, and scientific researchers will be required for genomic interpretation due to the ever increasing data.

Hence, for cost estimation, it is assumed that at least one bioinformatician (at $75,000), physician (at $110,000), biologist ($72,000), statistician ($70,000), geneticist ($90,000), and a technician ($30,000) will be required for interpretation of one genome. The number of technicians required in the future will decrease as processes are predicted to be automated. Also the bioinformatics software costs will plummet due to the decrease in computing costs as per Moore’s law.

Thus, the cost in 2011 for data handling and downstream processing is $285,000 per genome as compared to $517,000 per genome in 2017. These costs are calculated by tallying salaries of each person involved as well as the software costs.

These numbers would be seriously bad news for the future of genomic medicine, if they were even remotely connected with reality. Fortunately this is not the case. In fact this article (and other alarmist pieces on the “$1000 genome, $1M interpretation” theme) wildly overstate the economic challenges of genomic interpretation.

Since this meme appears to be growing in popularity, it’s worth pointing out why genome analysis costs will go down rather than up over time:
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Guest post: Time to bring human genome sequencing into the clinic

Gholson Lyon is a physician-scientist currently working at the Utah Foundation for Biomedical Research and the Center for Applied Genomics at Children’s Hospital of Philadelphia. He will be starting as an assistant professor in human genetics at Cold Spring Harbor Laboratory next month. I asked him to write this guest post to provide some personal context to his thought-provoking commentary in Nature (subscription required) on returning genetic findings to research subjects. [DM]


Photo of Max, who died aged four months from Ogden syndrome. Posted with permission from his family.

I have just published in Nature a commentary discussing the need to bring exome and genome sequencing into the clinical arena, so that these data are generated with the same rigorous clinical standards as for any other clinical test. This way, we can then easily return at least medically actionable results to research participants. In this day and age of consumer and patient empowerment, I can also see eventually returning all data, including the raw data, to any interested participants, as this can then promote crowd-sourcing for data analysis, with research participants controlling and promoting the relative privacy of and analysis of their own data.

As I described in my commentary, my thinking on this matter was prompted mainly by Max  (see picture) and his family. The obituary for Max can be found here, and that of his cousin, Sutter, here. We described their condition here, and we named this new disease Ogden Syndrome in honor of where the first family lives. I am now trying to think about and discuss the human aspects of and lessons from this story. My thinking has also been influenced somewhat by the late James Neel, who wrote a very thought-provoking book called Physician to the Gene Pool.

To me, it was deeply disconcerting that I could not officially return any results to this family (or to another family in a different project discussed here) even when the papers describing the genetic basis of their disease were published, as this was considered “research” and was not performed in a clinically appropriate (CLIA-certified) manner. This was all the more painful when one of the sisters in the Ogden family became pregnant and asked me what I knew. I cannot predict whether it would have helped or hurt this woman to learn during her pregnancy that she was indeed a carrier of the mutation, with the associated 50% risk of her baby boy having the disease. I also do not know if she would have undergone any genetic testing via amniocentesis of the fetus prior to birth (with the associated ~1% risk of miscarriage from the procedure), nor do I know what decisions she might have made prior to the birth even if she had undergone such testing. All in all, it was certainly an ethical and moral dilemma for me not to be able to return the research result to her, given that the results were not obtained in a CLIA-certified manner. It is still an issue, as there are even now financial and systematic barriers for getting all women in the family tested with a CLIA-certified gene test for NAA10 (which was developed over a six month period by ARUP Laboratories). It would have been so much better if we had just done the entire sequencing up front in a CLIA-certified manner.
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