next-generation sequencing
dgmacarthur | January 19, 2009Well, it's a little late, but I finally have a list of what I see as some of the major trends that will play out in the human genomics field in 2009 - both in terms of research outcomes, and shifts in the rapidly-evolving consumer genomics industry.
For genetics-savvy readers a lot of these predictions may seem, well, predictable, so I want to emphasise that my purpose here is not really to make risky forecasts; I'm more interested in laying out what I see as the major big picture trends for the year to come, with a few specific predictions about unknowns thrown in. In any case (as you will…
dgmacarthur | January 14, 2009Still quite a way, based on this survey of second-generation sequencing users (subscription only, I think) conducted by the industry publication In Sequence.
Along with a range of other questions, the survey asked users about the cost to generate one billion base pairs (one gigabase, or Gb) on their platform at the end of 2008, which is about as current as we're likely to get. I've estimated below the total cost to sequence a complete* human genome, assuming an overall depth of coverage** of 30x, for the three most widely-used second-generation platforms:
The fine print
Note that the number…
dgmacarthur | January 12, 2009A press release today describes a potentially exciting partnership between two companies in the DNA sequencing space: Oxford Nanopore Technologies and Illumina.
Illumina is an established player in the field, providing one of the most widely-used second-generation sequencing platforms (the Genome Analyzer, previously known as Solexa). Oxford, in contrast, is a young but promising contestant in the increasingly heated race towards so-called "third-generation" sequencing technologies, which promise even more staggering increases in the ability of researchers to generate vast amounts of…
dgmacarthur | January 7, 2009Daniel G. Hert, Christopher P. Fredlake, Annelise E. Barron (2008). Advantages and limitations of next-generation sequencing technologies: A comparison of electrophoresis and non-electrophoresis methods Electrophoresis, 29 (23), 4618-4626 DOI: 10.1002/elps.200800456
The dideoxy termination method of DNA sequencing (often called Sanger sequencing after the technique's inventor, Fred Sanger) has been the workhorse of pretty much every molecular biology lab for the last 30 years. However, over the last few years the method has been increasingly supplanted by so-called next-generation sequencing…
dgmacarthur | December 19, 2008Sure is news to me - from popsci.com:
Archon X Prize for Genomics
Purse: $10 million
Goal: Sequence 100 human genomes in 10 days for $10,000 per genome or less
Status: ZS Genetics, which is developing an approach that replaces fluorescent tagging with decodable electron-microscope images of DNA, is a favorite to win. [my emphasis]
ZS Genetics is developing an extremely unusual approach to DNA sequencing, which involves directly imaging DNA with an electron microscope (pictured to the left). The potential pay-offs of this approach are huge: in particular, this approach would have minimal costs…
dgmacarthur | December 18, 2008Nature has a list of the top news stories of 2008, and "Personal genomics goes mainstream" comes up second:
In January, an international consortium announced the launch of the 1,000 Genomes Project, which aims to provide a catalogue of human genetic variation. In October, the Personal Genome Project, which hopes to sequence and publish the genomes of as many people as possible, released initial data for ten participants. Meanwhile, as researchers wondered what they could glean from the results coming from personal-genomics companies, the prices of such services dropped. The firm 23andMe,…
dgmacarthur | December 4, 2008David Dooling from PolITiGenomics has put together a handy little table for genomics nerds like me: statistics on the output of the various iterations of the three major competing second-generation DNA sequencing platforms (Roche's 454, Illumina's Solexa/Genome Analyzer and ABI's SOLiD).
It's a little inscrutable for non-genomicists, but it helps to provide some insight into the sheer scale of the DNA sequence data currently being produced by large-scale sequencing facilities. A single Illumina GA II machine, for instance, churns out at least 8 gigabases of sequence (that's almost three human…
dgmacarthur | October 24, 2008Over at PolITiGenomics, Washington University's David Dooling discusses his work as part of the Tumor Sequencing Project. The TSP and a variety of other groups (like The Cancer Genome Atlas) are using large-scale sequencing to create comprehensive maps of the genetic changes that underlie cancer formation.
The cancer genome sequencing community have already made impressive headway - Dooling notes two papers in this week's edition of Nature, one from the TSP on lung adenocarcinoma, and another from The Cancer Genome Atlas on glioblastoma (which received extensive media attention when it was…