Tag Archives: illumina

Tip of the Week: one iPad app to rule them all

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There is none.

Ok, so that is the simple answer. The complicated answer is this: my ideal genome browser iPad app would have the flexibility to go from a mass market browser to look at an individual’s genomic variants in a genomic context with information about the research, genes, etc presented in such a manner so that any thoughtful person or doctor could understand, to a full fledged UCSC genome browser type research tool.

So, that’s not feasible. Instead, I’m going to look at three genome browsers for the iPad, two for research, one for the mass market. The former are GeneWall by Bioskoop and Wowser by the Children’s Hospital of Philadelphia, the latter is MyGenome by Illumina (links take you to iTunes app store).

The iPad and other touch tablets are perfect research assistants and the day is fast approaching, if it’s not already here, where most researchers will have one on the lab bench for entering and accessing data.

So what am I looking for in a iPad genome browser?
Navigable: it should have a very intuitive, iPad native navigation. I should be able to pinch and swipe my way through the genome with finely controlled ease.
Comprehensive: I should be able to access my genome of choice, past assemblies, and a huge range of annotations.
Flexible: I should be able to upload my own annotations with ease.

Why not just go to the UCSC Genome Browser? You could, but it fails the first test. It’s definitely usable, but many features available on a computer are not available on the iPad and navigation is obviously not iPad native.

20120509-091620.jpgGeneWall works nicely on the first criteria, but zooming in and out takes several (sometimes many) pinches of the fingers. There is no simple way to zoom in and out or walk the chromosome in a more fine tuned manner. On the second, though it comes with a single genome (human) with only a few annotation tracks so it’s not very comprehensive to start, you can easily add annotation tracks downloaded as bed files. So it has some flexibility. The pathway search and gene list function are nice too. A quick YouTube intro here.

20120509-091959.jpgWowser is somewhat different in that it is an iPad interface to the UCSC Genome Browser. It works natively with the iPad and so is easy to navigate. Zooming and walking was intuitive. On a few different wireless networks it was slow to load, but not excruciatingly so. It is quite comprehensive, including the latest human reference sequence and many, but not all, of the UCSC tracks. The tracks are simple to hide or add in. Future updates are said to be including other genomes and more tracks. I could not find a way to add your own custom tracks or data, so on flexibility GeneWall wins out.

Both apps are great, if not quite “there” yet. I think either would be useful if you are looking at the human genome for research.

20120509-092126.jpgMyGenome is a different beast. From Illumina, it’s audience is not the researcher but the medical professional and patient. It’s a beautiful app with a nice interface. Easily navigable, it was simple to get to the information wanted. There is a lot of information there, but it is still quite limited. I took several variations that effect propensity for prostate cancer and other diseases and was unable to find information on them either because the variation is listed but no information, of variation was in an intergenic region which seemingly isn’t included. A user can not yet upload their own data,or other annotations, which is understandable since by Illumina’s own account this is only the beginning. Currently it’s a great educational tool (though I was a hung for more gene information), in the future it will be a good way to browse your own data.

So the bottom line for all three of these are that they are useful as they stand and for their stated purpose, but I’m looking forward to the future of browsing genome data like I was on an Avatar set :). It’s coming.

The cost of genomics, revisited

1,000 dollars to sequence the entire 3 billion ‘basepair’ long human genome is the holy grail. Last year, on this blog, I predicted that we’d reach that goal ‘within a year’. Well, it’s been a year and we aren’t there. I did hedge a bit in the comments later, but the main point was that the cost was plummeting and headed for $1,000 for an entire genome. The graph at the left is cost of a single genome from 2003 to 2010… 300 million, to 10 thousand.

The cost is still plummeting. Illumina* has lowered the cost of sequencing the genome to $5,000. Half.Complete Genomics* today announced that their first quarter revenue was 6.8 million, up from 300 thousand last year. They have 2,000 complete genomes to sequence in their backlog. They charge < 10,000 for small orders, down to $5,000 for bulk orders (in research groups). The cost of sequencing large groups for research is getting much smaller.

So the price plummets still.

The price for genomic scans also plummets. 23andMe, which scans about 1 million variable sites in your genome (most of the human genome is not variable from person to person), cost 400 dollars last year, in December they price went to 200. After a one-day free sale, it’s now $100.

Of course, the question remains how expensive will it be to analyze that data.

 

*full disclosure, I own a (very) small amount of stock in both Illumina and Complete Genomics.

 

Bulk sequence pricing

Illumina announces that they are slicing their price of whole-genome sequence to 19,500 . This is half what they were charging before. Hey, you can get it at 14,5000 per genome if you do it in bulk, 5 or more people. Perhaps you and your family for a cool 72,500?

As I mentioned before, the price of personal genome sequencing has been plummeting and I predicted 1,000 by the end of a year’s time. Admittedly, that is a bit (understatement) of an optimistic prediction, but the trajectory definitely is headed that way.

Another step to personal genomics

I was just having this discussion with in-laws, both in the medical field, that personal genomics was on it’s way. We discussed how this was going to affect our health insurance and health care, in both good and scary ways. Well, as Genetic Future blogs, Illumina delivers its first commercial personal genome sequence.

The service cost 48,000 US dollars, which is of course a far cry from the millions it would have cost a decade ago. Complete Genomics, a new company to do just this, says it will offer genome sequences for 5k US dollars. So pricing will only go down all around as competition heats up.

That light you see might be the train of personal genomics.

A genome a day

I want to say ‘keeps the ? away” but can’t think of anything. This is just a quick post. Mary’s first line on the corn genome post, “sometimes it feels like ‘another day, another genome‘ round here got me to thinking”, it isn’t so far off the mark. According to GOLD there are 905 ongoing eukaryotic genomes (according to Entrez Genome Project,  it’s 225, but those are only ones reported to NCBI). The cost of sequencing and completing a genome has drastically decreased. For example, Illumnia recently reported sequencing a human genome in 1 month for $100,000.

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