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Next-Gen Sequencers Improve, Promise More

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When it comes to tracking price and performance, next-generation sequencing systems are a moving target. In the last year, vendors have improved their performance in several ways — and promised to make them better and more affordable this year.

Since May 2007, Roche has added several new features to its 454 GS FLX platform. Notably, the company kept its promise to introduce mate pairs with increased read lengths of 110 bases, which improved the 20-base length of earlier paired reads.

Roche also came through with its promise of bar-coding tags, offering 12 unique identifiers for complex samples, and 96 for amplicon resequencing.

This year, the company plans to improve the performance of its system and cut reagent prices. A Roche spokesperson says the price cut “will be significant.”

Illumina’s Genome Analyzer has also improved in performance since last May. A specification sheet on Illumina’s website from October 2007, the latest data available, said the system can generate more than 2.3 gigabases per paired-end run, more than twice as much as the 1 gigabase it put out in a single-read run five months earlier.

According to the spec sheet, the system now enables paired-end sequencing. Illumina said in mid-October that it is using insert sizes of 200 to 400 bases, and is working on 2-kilobase inserts.

ABI’s SOLiD system made its early-access debut in the summer of 2007 and formally launched in October. As of Jan. 1, the instrument, which can run one or two slides, can provide up to 3 gigabases of single-read data compared with 1 gigabase in May, said ABI.

In addition, paired-end reads, which were in early access testing in the spring and generated 1 gigabase of data, today yield up to 4 gigabases of data, with insert sizes ranging from 600 bases to 10 kilobases, the company said.

ABI also reduced the amount of recommended starting material, from between 10 and 30 micrograms in May to between 100 nanograms and 20 micrograms, depending on the application.

Julia Karow

Sequencing Notes

The Beijing Genomics Institute plans to use its fleet of 120 Sanger and next-generation sequencing instruments to offer sequencing services to the global market. BGI says it has more than 100 Sanger sequencers, seven Illumina Genome Analyzers, and two ABI SOLiDs, enabling a sequencing throughput of 250 million base pairs per day using Sanger, and 4 billion base pairs per day using the next-generation instruments.

Researchers at Italy’s Istituto Agrario di San Michele all’Adige and Myriad Genetics published the genome sequence of a pinot noir grape in PLoS. The team used both Sanger and 454 sequencing to analyze the plant’s 500 million base pairs.

Data

$12 million

NIH will award up to $12 million over two years to build a resequencing application for genome-wide biomedical research.

Funded grants

$270,667/FY2007
Hybridization-Assisted Nanopore DNA Sequencing
Grantee: Xinsheng Sean Ling, Brown University
Began: Aug. 1, 2007; Ends: Jul. 31, 2010
Ling's goal is to develop a low-cost nanopore sequencing technology taking advantage of the latest advances in solid-state nanopore technology and utilizing the recently proposed concept of hybridization-assisted nanopore sequencing, according to the grant abstract. The proposed sequencing technology has the potential of being fast, low-cost, and portable.

$227,780/FY2007
Genome Sequencing by Ligation Using
Nano-Arrays of Single DNA Molecules
Grantee: Xiaohua Huang, University of California, San Diego
Began: Sept. 29, 2006; Ends: June 30, 2008
This project aims to develop a sequencing technology using a method for fabricating high-density arrays of wells with sub-micrometer dimensions for ordering single nanoparticles and DNA molecules. Huang and colleagues aim to demonstrate the proof-of-principle of single-molecule sequencing by ligation.

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