Tag Archive for 'whole-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:
Continue reading ‘Genome interpretation costs will not spiral out of control’

Making sequencing simpler with nanopores

The Advances in Genome Biology and Technology (AGBT) conference, one of the main go-to destinations for those who get excited by DNA sequencing technology, is currently going down in Florida. Sadly, no-one from GNZ could make it this year, but we are keeping up with the various announcements about new genomics tech as best we can. One that caught our attention was the announcement of a brand new sequencing machine from a company that has previously kept very quiet about its technology.

Oxford Nanopore, who we have written about before, today announced two new sequencing machines to come out this year. The announcement has caused quite a buzz amoungst, well, everyone. Nature, New Scientist, GenomeWeb, BioIT World and Forbes all have reported on it, and bloggers Nick Loman and Keith Robison have also had a chance to talk to some of the Oxford Nanopore peeps about their new toys.

A lot of the interest has come from the (very cool) MinION, a tiny, disposable USB-key sequencer (shown in the picture above) that can sequence about a billion base pairs of DNA, and cost around $500-$900 each. The applications of this are endless – the ability to pick up a bit of biological matter, mix it with a few chemicals, and read whatever DNA is in it, could help with diagnostics, epidemiology, ecology, forensics. It is also (though not quite) the price where hobbyists could consider having a play; perhaps in a few years plug-and-play DIY genetics could be a possibility.

Less immediately striking, but still just as interesting, is the GridION sequencing machine. This is the work-horse of the nanopore sequencing world, made for reading lots of DNA, and scaling up to massive sequencing centers. Obviously, many scientists are going to be very interested in many of the features (notably, the ability to read very long pieces of DNA, a trick that has previously been more-or-less impossible to do reliably). However, what will this announcement mean for those of us who are interested in personal genomics?

Continue reading ‘Making sequencing simpler with nanopores’

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]

Max

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.
Continue reading ‘Guest post: Time to bring human genome sequencing into the clinic’

Complete Genomics to sequence 1500 whole genomes for pre-term birth study

Genome sequencing provider Complete Genomics has announced a deal with the non-profit Inova Translational Medicine Institute, under which the company would sequence 1,500 complete human genomes to help explore the genetic basis of premature birth.

The Inova collaboration is one of many large-scale genome sequencing studies currently being planned and performed around the world. In some respects the study is actually quite a small one – only 250 “cases” (i.e. premature babies) are being sequenced, along with 250 normal-term control babies, which means the researchers will have low statistical power by the standards of modern genomics. However, sequencing this number of complete genomes to high depth is (as far as I know) unprecedented, and the inclusion of the parents of all of the children in the study will provide the team with the ability to do some very interesting analyses – for instance, looking at “de novo” mutations that arise in the babies but weren’t present in either parent, as well as exploring potential effects of the maternal genome. Maternal genetics are known to be important in determining the risk of premature birth: girls born prematurely have a higher risk of delivering a pre-term baby themselves (with twin studies suggesting between 15 and 40% of the risk is heritable), while paternal genes seem to have almost no effect.
Continue reading ‘Complete Genomics to sequence 1500 whole genomes for pre-term birth study’

Cracking non-coding variation, carrying cystic fibrosis, and more Alzheimer’s prediction

Daniel and Luke attended the Biology of Genomes conference at Cold Spring Harbour last week. The talks did not have a huge amount of direct relevance to personal genomics, but did show some real quantum leaps in understanding the function of the non-coding DNA that makes up most of our genomes. Understanding mutations that lie outside of coding DNA is largely a prerequisite for transitioning to whole-genome sequencing for personal genomics, as most of the variation that drives genetic differences between people appears to lie there. As we’ve said before, one of the powerful aspects of sequencing is that it allows you to get at the aspects of your DNA that are unique to you, but that is only really useful (and a lot cooler) if we know what this unique variation does. Biology of Genomes showed us that that dream is closer now than it has ever been before.

For a (somewhat technical) account of some of the conference talks, you can read Luke’s blog posts over at Genetic Inference (along with a signficiantly less technical post about chipmunks and wood cabins), and Matthew Herper has a lay-friendly post on his Forbes blog. As has become standard, Twitter was an important way of disseminating knowledge live during talks, and Keith Bradnam and EpiExperts wrote about this aspect. [LJ]

Since GNZ started, Luke has actually been holding back writing about his many and varied genomics woes, and his resulting quest for bodily health, mostly for lack of time. However, one part of this has leaked out somewhat: he has recently given an interview to fellow blogger Elaine Westwick about being one of the two cystic fibrosis carriers in Genomes Unzipped. Read the interview at Elaine’s blog The Stuff of Life. [LJ]

On a similar subject to our recent post about calculating Alzheimer’s risk, over at Genomics Law Report Dan has written a detailed post about the regulatory challenges ahead for both direct-to-consumer and clinical tests for Alzheimer’s. [LJ]

Next-Gen Sequencing Heading to Madison Avenue?

For companies seeking to make their mark in the ultra-competitive next-generation sequencing (NGS) market, new technology and lower prices may no longer be enough.

As the size of the NGS sequencing market grows, and an increasing number of NGS purchasers evaluate an expanding array of providers and technologies (see William Blair’s Next-Generation Sequencing Survey), NGS companies are beginning to look beyond price points and product specs in an attempt to stand out.

Ion Torrent on the Offensive. Consider Ion Torrent, an NGS newcomer recently acquired by Life Technologies, which launched its first product (the Personal Genome Machine) a scant four months ago. Since then, Ion Torrent has announced improvements to the PGM’s output, read length and sample prep (coverage from Matthew Herper of Forbes here and here).

As it seeks to distinguish the PGM from its competitors’ products, particularly Illumina’s offerings (see J.P. Morgan’s Next Gen Sequencing Survey), Ion Torrent has added a new dimension to its PGM campaign. Ion Torrent recently launched several creative online advertisements, with its side-by-side comparison of the PGM and Illumina’s MiSeq system—modeled after Apple’s popular “I’m a Mac/I’m a PC” campaign—raising the most eyebrows.
Continue reading ‘Next-Gen Sequencing Heading to Madison Avenue?’

A Googol of Genomes?

[Editor's Note: this was originally posted over at the Genomics Law Report but we'd like to survey Genomes Unzipped readers as well. How many complete genomes do you think will be sequenced in 2011? Poll is at bottom.]

Earlier this week we took a look back at 2010 and offered our projections for the coming year in personal genomics. Topic #1, just as it was last year: the $1,000 genome.

In hindsight, it might have been ill-advised to offer predictions about the near-term future of genome sequencing during the same week in which one of the year’s major industry conferences (the JP Morgan annual Healthcare Conference) is taking place.

Continue reading ‘A Googol of Genomes?’


Page optimized by WP Minify WordPress Plugin