Driving Down Cost
“Process optimization, especially in the synthesis and deprotection steps, leading to increased yields will have a large impact on driving down costs,” predicts Dr. Fettes. “Strategic development of alternative supply chains, however, will likely have the greatest impact on cost of goods. This will occur as large-volume products begin to appear in the market, allowing the supply chain to operate closer to its installed capacity. Improving cycle times to decrease occupancy of assets will also have a role in reducing costs.”
In January, Eurofins MWG (www.mwg-biotech.com) and Operon Biotechnologies (www.operon.com) joined forces to bolster their competitiveness in the custom oligonucleotides market. Operon and Eurofins MWG and Medigenomix will form a network of custom DNA companies with an estimated $50 million in revenues.
“Over the past 10 years, overcapacity in the market has put a lot of pressure on all custom oligonucleotide-synthesis service suppliers,” notes Patrick Weiss, managing director of Operon and future CEO of Eurofins Genomics, explaining the motivation for the merger. “Prices have decreased to a level where few companies are able to keep up with the level of investment and innovation needed to meet the market demand for lower cost and higher quality of products and services.”
Scaling Up to Market
The need to scale up oligo synthesis as compounds in development move through the pipeline creates challenges for maintaining product quality. The demand for large-scale synthesis is particularly strong in the RNA sector, “however, scales have still not approached those of DNA,” says Dr. Fettes.
“This is likely due to the early clinical phase of the compounds and purported increased efficacy of the drugs. As scales increase, focused process-development activities, rather than novel chemistries, are key to maintaining good product quality. Even as the number of RNA compounds is increasing rapidly, many DNA compounds hold a lot of promise such as antisense, aptamers, immunomodulators, decoys, and DNAi.”
At “TIDES,” Dr. Fettes will be participating in a discussion entitled “Manufacturing RNA Oligonucleotides: Can One Hydroxyl Really Make That Much of a Difference?” While the core principles governing successful DNA and RNA production are basically the same and include developing scalable models and implementing Design of Experiments (DoE) methods, “the manufacture of RNA is a more complex process involving the synthesis of two strands with deprotection chemistry that requires careful process control.”
“The management of these parallel processes to maintain equivalent process performance requires predictive development work,” says Dr. Fettes. To ensure that risk-management tools and DoE are integrated across the organization and throughout process and analytical development and manufacturing, “Avecia recently added personnel that have extensive experience in Lean and Six Sigma to drive operational excellence.”
In other recent news, Biosearch Technologies(www.biosearchtech.com) received a worldwide license to the noncoding DNA patients owned by Genetic Technologies (GTG; www.gtg.com.au), granting the oligonucleotide-synthesis company the rights to manufacture and distribute oligos, probes, and primers for research use under GTG patents. The license covers all genomes and includes SNP genotyping and allelic discrimination.
Houston, TX-based CytoGenix (www.cytogenix.com) developed a synthetic cell-free process for large-scale production of biologically active DNA and an expression vector for producing single-stranded DNA sequences inside target cells.
In August, the company broke ground on a new 20,000 sq.ft. facility that will house its offices, laboratories, and DNA production plant and will enable expansion of the company’s internal drug-development programs toward clinical testing and its ability to produce GMP DNA products for customers.
“In the industry today, it is not as much about building general capacity—the major players have enough capacity to satisfy the world market,” says Martin of IDT, “It is more about what you can do with that capacity and with your capabilities.”
According to Martin, IDT is “trying to push the envelope,” for instance, by providing 100% MS-based quality control for all of its oligos. In addition, the company continues to improve its technology for synthesis and QC of oligos of extreme length, called Ultramers.
“We have been able to achieve synthesis above 300 bases in testing and are offering the Ultramer product in lengths up to 200 bases,” notes Martin. IDT developed an MS method for quality control of these long oligos. Ultramers have particular advantages when producing oligos with difficult-to-synthesize regions such as homopolymeric runs or long repeat stretches, Martin reports. “A 200 mer allows for synthesis right through some of those difficult segments,” he adds.
The synthetic biology group at IDT has seen increased demand for longer oligos and whole genes. IDT uses the Ultramer technology for de novo synthesis of double-stranded fragments called mini-genes. These can be used as gene fragments or internal standards or they may be incorporated into larger constructs. Other applications for Ultramers may include site-directed mutagenesis and use as templates for RNA synthesis.
Looking forward, Martin sees a continuing and accelerating shift from the use of traditional Sanger sequencing to higher-throughput, next-generation DNA-sequencing technologies, which at present comprise sequencing-by-synthesis and sequencing-by-ligation methods. The former requires large-scale, high-purity oligos of defined sequence, whereas the latter relies largely on DNA fragments comprised of one or two defined, labeled bases and mostly random oligo sequences.
“These are nasty oligos to make and purify as you want equimolar mixtures of the random bases,” Martin says. “Whereas randomized oligos are not new as research tools, now with a large preparation of randomized oligos going into a $20,000 sequencing run, the customer is more demanding about what they’re putting in.”
The switch from classic Sanger sequencing to next-generation methods “is happening really fast,” with sequencing centers relying less on primer-based methods and shifting to new methods, Martin concludes.