Next Generation DNA sequencing

In our series on why $1000 genomes cost $2000, I raised the issue that the $1000 genome is a value based on simplistic calculations that do not account for the costs of confirming the results. Next, I discussed how errors are a natural occurrence of the many processing steps required to sequence DNA and why results need ... Read more

I had the good fortune on Thursday to hear a fascinating talk on deep transcriptome analysis by Chris Mason, Assistant Professor, at the Institute for Computational Biomedicine at
Cornell University. 

Several intriguing observations were presented during the talk.  I'll present the key points first and then discuss the data.

These data concern the human transcriptome, and at least some of the results are supported by  follow on studies with data from the pigmy tailed macaque.

Some of the most interesting points from Mason's talk were:

  1. A large
  2. ... Read more

These days, DNA sequencing happens in one of three ways.

In the early days of DNA sequencing (like the 80's), labs prepared their own samples, sequenced those samples, and analyzed their results. Some labs still do this.

Then, in the 90's, genome centers came along. Genome centers are like giant factories that manufacture sequence data. They have buildings, dedicated staff, and professional bioinformaticians who write programs and work with other factory members to get the data entered, analyzed, and shipped out to the databases. (You can ... Read more

A couple of years ago, I answered a reader's question about the cost of genome sequencing. One of my readers had asked why the cost of sequencing a human genome was so high. At that time, I used some of the prices advertised by core labs on the web and the reported coverage to estimate the cost of sequencing Craig Venter's genome. As you can imagine, the cost of sequencing has dropped quite a bit since then.

In 2007, Genome Technology reported the cost of sequencing Venter's genome was $70 million. ... Read more

Watching the chIPs roll in,

then I watch them roll away again,

I'm just sitting on the DNA,

wasting time

(sung to the tune of "Sitting on the dock of the bay" by Otis Redding)

Hesselberth et.al. recently published a paper about digital genomic
footprinting that blew me away because it has so much potential. The authors used DNAse I and Next Generation DNA Sequencing to map every site in the yeast genome where a protein might be sitting.

Since I used to do similar kinds of experiments, albeit on a much, much smaller scale ... Read more

For the past few months, the shake-up that began with Next Generation DNA Sequencing has been forcing me to adjust to a whole new view of things going on inside of a cell. We've been learning things these past two years that are completely changing our understanding of the genome and how it works and it's clear we're never going back to the simple view we had before.

What's changed? The two most striking changes, to me at least, are the new views of the way the genome is put together and what the cell does with the information.

They just don't assemble ... Read more

Cofactor Genomics is offering to sequence a genome for a few classes for free using Next Generation DNA Sequencing technology (either Illumina GA or via AB SOLiD).

Quoting from their site:

Cofactor will ask course organizers for a 1 page description of how their ~700Mb sequencing project could be used as an effective teaching aid in their class. We will review and choose the best entries during the month of May. Those entries will be awarded a free

... Read more

One of my favorite web 2.0 technologies is the webinar. When you work at a company and not a University, with constant seminars, it gets a bit harder to hop on a bus and travel across town to learn about new things. Webinars are a good way to fill that gap. I grab my coffee cup, put on my headphones, and I get to listen to someone tell me about their work for an hour and show slides over the web. It's nice.

Our company is even going to be involved in two webinars in the next two months. One of us is giving an Illumina webinar ... Read more

It's a Solexa data directory.

I've held off on blogging about Next Generation Sequencing here, but now that one of my colleagues has started blogging about it, it seems like a good time to write a little about FinchTalk, our company blog.

We've decided that we can serve an educational role for people who are interested in Next Generation DNA Sequencing.

Certainly, FinchTalk is our company blog and it is a place where you can expect to read about our products. But, we've noticed that quite often, the ... Read more