By Julia Karow
In-solution target enrichment provider FlexGen of the Netherlands has launched a free online cost calculator for targeted sequencing experiments, which it hopes will draw more customers to its website.
FlexGen, based in Leiden, originally developed the tool for in-house use to determine the efficiency of its target-enrichment products, but thought that the information might also be of interest to its customers, according to Joris Parmentier, the company's marketing and sales manager.
"We want a lot of people to use this," Parmentier said. For the last few weeks, FlexGen has been beta-testing the tool and has been "pleasantly surprised" by the amount of interest from the next-generation sequencing community.
FlexGen's NGS experiment cost calculator lets users estimate the consumables cost for a targeted sequencing experiment in humans, assuming 40x coverage. Included in the price are library preparation, target enrichment using FlexGen's technology, and sequencing. The tool also provides the cost of whole-exome sequencing for comparison, but does not specify the enrichment method used.
To keep the tool simple, users type in just five parameters: the sequencing platform, whether the experiment is single-read or paired-end, the size of the region of interest, and the number of samples. From those, the tool calculates the cost per sample and per experiment, with a current output in euros.
At the moment, the calculator supports almost all available next-generation sequencing platforms, including those from Illumina, 454/Roche, Life Technologies, Pacific Biosciences, and Helicos BioSciences. It also includes two platforms that are not fully commercialized yet — Illumina's MiSeq and Ion Torrent's PGM using the 318 chip.
The pricing information underlying the cost calculator comes from the recent "Field guide to next-generation DNA sequencers," published in May in Molecular Ecology Resources by Travis Glenn at the University of Georgia. The information contained in that paper will be updated on the journal's blog, with the next update scheduled for May 2012.
FlexGen also makes its own updates "pretty much all the time," Parmentier said; for example, it recently included a price cut for the Ion 314 chip from $250 to $99.
Based on the calculator, sequencing a 0.5-megabase region in 24 samples using single reads costs about €1,400 ($1,905) per sample on the Illumina HiSeq 2000 using TruSeq v3 reagents and FleXelect custom enrichment kits, and about €33,000 ($44,925) per experiment. Sequencing the exome on this platform would cost about €2,000 ($2,722) per sample.
In the future, FlexGen might adapt its tool to include additional sequencing platforms, other organisms besides humans, more optional parameters for the sample prep and target enrichment methods, and costs in US dollars. It might also include whole-genome sequencing of different organisms, Parmentier said.
Ultimately, the company, which moved into new space in the Leiden Bio Science Park this summer, hopes to use the cost calculator to attract new customers for its target-enrichment products. It currently offers custom target enrichment kits called FleXelect oligopools as well as an oligo synthesis instrument, the FlexArrayer, for customers to make their own target-enrichment probes.
Founded in 2004 as a spinoff from the Leiden University Medical Centre and Dutch Space, FlexGen originally set out to develop the FlexArrayer for custom microarray synthesis, according to its website, but the in-solution target enrichment market for next-generation sequencing has become its "key commercial focus," Parmentier said.
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For FleXelect, customers can choose target regions between more than 10 kilobases and several megabases. The company then designs probes to those regions and generates kits containing pools of RNA probes and capture reagents. Kit prices start at €49 and go up to several hundred euros per sample and typically take four to six weeks to deliver, according to the firm's website. FlexGen does not offer exome kits because of the presence of a number of strong players — for example Agilent and NimbleGen — in that market.
According to Parmentier, one of the key benefits of FlexGen's offering is its probe design. The company, he said, helps customers decide "which parameters are important when designing probes for a specific experiment."
The company's FlexArrayer, which has a list price of €195,000, allows customers to generate their own oligonucleotides, or target-enrichment probes, in house. This reduces the reagent cost of sample enrichment "quite drastically," according to Parmentier, down to €1 per sample for a small genomic region in a large number of samples.
Using the FlexArrayer, for example, would decrease the cost of sequencing 0.5 megabases in 24 samples on the HiSeq 2000 from €1,400 to €1,000 per sample, according to the calculator.
In the future, FlexGen plans to provide additional informatics tools for its customers. For example, it is considering making its probe design tool available to customers of its FlexArrayer instrument.
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