Happy Holidays to All!

happy holidays

As 2012 winds down, we wanted to take a moment to wish everyone a happy and healthy holiday season. Before we get swept up in the frenzy of a new year, we’ll take this opportunity to look back at what 2012 brought us.

The year kicked off with all sorts of excitement at the JP Morgan Healthcare Conference, during which Life Tech’s Ion Torrent announced that it would unveil a platform that could sequence a full human genome in a single day — for the bargain price of $1,000. While we haven’t heard of anyone achieving that $1,000 milestone just yet, being so tantalizingly close to the target spurred a whole new conversation this year around the informatics implications of it. What will it take to get the genome analysis and interpretation step down to $1,000? We haven’t heard a concrete plan yet, but we’re pleased to see that the discussion is focused on analysis, since that will be critical in getting genomics into the clinic.

Here at DNAnexus, 2012 was a big year thanks to ever-increasing activity from our users. In the past year, our users processed and analyzed more data than they did since the launch in early 2010 (2010 and 2011 combined). It’s great to see that people are coming back again and again — and that they’re bringing more data when they do. This has further been exemplified by the fact that our users have also been busily publishing this year, as we noted recently in a round-up of recent papers using DNAnexus.

Overall, we’ve seen a surge of interest in cloud-based solutions for genomic data; we think that’s partly due to the increasing sequencing capacity as sequencing platforms become more affordable, and partly to people growing more comfortable with the cloud’s usefulness and security. At conferences we attended throughout the year — from AGBT and ABRF this spring to Bio-IT World and ESHG in the summer to Beyond the Genome and ASHG this fall, among others — we saw more vendors joining the space, increasing interest from scientists, and more posters and papers from researchers who have used cloud computing for their genomic projects.

Add this all up, it’s clear that we’re at the beginning of a golden age for genomic analysis and interpretation. We are thrilled to be part of it, and more excited that we’ll soon be launching a new platform catering to bioinformaticians and computational scientists in 2013. In the meantime, enjoy the holidays!

 

Sequence Data: The View from JP Morgan

Last week, Andrew Lee, Vice President of Strategic Operations, and I attended the JP Morgan Healthcare Conference, an annual investor conference here in San Francisco that brings some 25,000 people to the city. The big news this year came from Life Technologies and Illumina, which both announced platforms that will be capable of sequencing an entire human genome in a day. Life Tech in particular noted that its same-day genome sequence will cost $1,000 in reagents — effectively putting an end to a race that began 10 years ago, when scientists first started seriously competing to achieve the $1,000 genome.

With this price point achieved, we expect people to sequence genomes at a much faster clip than ever before. Indeed, a survey from GenomeWeb and Mizuho Securities found that scientists anticipate that sequencing data will increase 32 percent this year over 2011, and increase another 38 percent next year compared to this year. That’s exciting on the data analysis front: As the volume of DNA data grows exponentially, it’s even more important to have a scalable platform to manage, store, and analyze that data securely and efficiently. The GenomeWeb/Mizuho survey also found that people expect to spend more on informatics in 2012 than they did in 2011.

After all, mainstream genome sequencing won’t be possible until the analysis costs come down by orders of magnitude. Even with so much attention on cutting the price tag for sequencing technologies, that didn’t translate to matching improvements for data costs. The race to the $1,000 genome may be over, but as it turns out, that was just the first leg of a relay. Now the baton has been passed to the data management and analysis folks, and it’s our turn to run as fast as we can.

Streaming an entire sequencing center across the Internet

How much next-gen sequencing data do the top genome centers in the world produce? It’s a staggering amount compared to even one year ago: The Broad Institute now has over 50 HiSeq 2000s, and BGI has over 100. Each HiSeq 2000 can sequence two human genomes per week, which means these centers could sequence in excess of 5,000 and 10,000 human genomes per year, respectively.

What would it take to transmit all the sequence data over the Internet? It turns out, surprisingly little. Let’s do some math: Each HiSeq 2000 can sequence 200 Gigabases per run, but takes over a week to do so. Illumina quotes the throughput of the instrument at 25 Gigabases per day, or about 1 Gigabase per hour. With quality scores and some simple compression, each base takes less than 1 byte of storage. In other words, a HiSeq 2000 produces 1 Gigabyte of sequence data per hour, or 290 Kilobytes per second. To put this number in context, today people routinely stream movies over the Internet to their home at a higher bitrate! Yes, these instruments produce a lot of data compared to the previous generation technology, but it’s quite manageable over modern network connections.

Let me go even further: A sequencing center operates sequencing instruments at perhaps 80% efficiency, so 290 Kilobytes/second * 80% * 8 bits/byte (for network transmission) = 2 Megabits per second. That means 50 HiSeq 2000 instruments, or the entire sequencing capacity of the Broad Institute, could fit over a 100 Megabit connection. A Gigabit connection could support four times the sequencing output of the BGI. A much smaller sequencing core, for example one with one or two HiSeq 2000s, can be supported easily with a 10 Megabit connection.

For those of you that operate a sequencing center, it may seem almost ludicrous that this is possible, and there are certainly reasons why these calculations are ideal-case: it’s difficult to get 100% of your connection’s rated bandwidth, your network is often congested from other ongoing activities, individual TCP streams are difficult to scale to Gigabit speeds, etc. And moving further down the analysis pipeline to SAM/BAM files from read mapping and variant calling, the data transfer demands can easily go up 10-fold. But these calculations are nonetheless close to what’s actually achievable today. Even if your actual network throughput is 50% of the ideal, most sequencing centers with a reasonable connection have no bandwidth issues streaming all the sequence data across the Internet.

Why would we want to do this? Once your data has been moved to an outside data center, it opens up tremendous opportunities: You can then decide to store it there long-term, and access it from anywhere in the world. You can give collaborators access to your data instantly. You can tap into vast compute resources available in the cloud, for example 100,000s of CPUs available in Amazon. You’re no longer bound by what your internal computing and networking infrastructure can support, and can grow or shrink your infrastructure as needed. There are so many advantages to moving your sequence data outside your walls, that I’ll leave that discussion for a future blog posting.

Want to test out the bandwidth yourself? It’s easy to do – just sign up for a free account. You’ll be able to upload three samples for free. If you want to upload directly from the sequencing instrument, we can also help you set that up in 10 minutes. Email info@dnanexus.com to find out more information on how to try streaming the data off your instrument to the cloud.