Next Generation Sequencing

We have been fortunate to gain a new and very skilled employee in Singapore, Mr Henry Wang, which means that we now have a native Chinese speaker in CLC bio. In this video Henry uses his mother tongue to explains how to assemble data from two different NGS platforms, Illumina Genome Analyzer and 454, in one run. The data set contains both paired-ends and single reads.

Just as economists have a Big Mac index to rate the cost of living in different countries, scientists in genomics are using the full human genome sequencing cost as an index of how much DNA sequencing costs. Judging by this index October seems to be a good month for sequencing customers.

Last month, several sources - including the Genetic Genealogist - quoted George Church for claiming that the cost of sequencing a human genome would drop to 5000$ in October 2008.

Today, Applied Biosystems posted a press release about their new SOLiD 3 system which is expected to enable scientists to sequence a human genome for approximately $10,000.

Earlier this year, AB claimed that they had used the SOLiD system to sequence a human genome for less than $60,000.  Now, technical enhancements to the new platform that enable higher sample and data throughput are expected to further decrease the cost of genomic sequencing.

Church also recently predicted a 1000$ genome already by the end of next year and with AB recent release and Illuminas predicted capacity increase this goal suddently seems within reach.

However, October has only just started and we may still be in for more exiting news!

We have just released a scientific white paper which confirms, that, in benchmarking tests, our new algorithm for assembly of Next Generation Sequencing data is indeed fast. Not only is our algorithm fast, but it also provides a better quality of the results, compared to other algorithms benchmarked in the white paper.

Assistant Professor at Rutgers University, Dr. Todd P. Michael, states,

The speed of CLC bio’s new algorithm for reference assembly of Next Generation Sequencing data raises the bar to a level currently unmatched by any competitor. When CLC bio continues this impressive rate of development, and eventually also handles SOLiD’s Color Space analysis in the same convincing manner, this could easily become a de facto tool for scientists working with Next Generation Sequencing analysis.

The white paper is free to download for everyone at www.clccell.com/ngs

You can read the entire press release by clicking here

Helicos Biosciences have announced a partnership with the Children’s Oncology Group (COG) where Helicos will use their NGS platform to experimentally characterize different tissue types from patients with Ewing’s sarcoma, a rare cancer.

In their press release they state that:

These samples include a normal bone marrow sample and tumor cell lines derived from a Ewing’s sarcoma primary tumor biopsy and the metastasis from the same patient obtained after two cycles of chemotherapy. It is hoped that an in-depth comparison of genomic DNA sequence and RNA expression between the normal tissue, primary tumor, and treatment resistant metastasis will reveal structural and functional genomic changes associated with clinical aggressiveness and treatment resistance.

The study will include an ambitious range of applications for NGS technology as it will aim to identify rare mutations, polymorphisms, copy number variants, true whole-genome RNA transcriptional activity, and global methylation patterns.

The press release does not mention anything about the tissue sample sizes that will be collected as starting material, so I guess I will have to read the papers at some point . However, the ability to characterize very small tissue samples is one of the most interesting features of the single molecule sequencing technologies, so it will be interesting to see how the technology performs for this type of problems.

PolITiGenomics have posted some details about the upcoming update to the 454 system.

According to the blog, the next upgrade will be called Titanium and will have twice the number of cycles increasing  the average read length from 250 to around 400 bases. Furthermore, the new version will have smaller, more densely packed wells on the picotiter plate which will increases the number of DNA fragments sequenced per run. All together, 454 FLX Titanium runs will quintuple their data output from 100 Mb to about 500 Mb.

Obviously, the increased data amount will put even more strain on the downstream image- and sequence analyses pipelines.