LGC Genomics, a division of the UK-based LGC Group that provides DNA and genetic analysis services, recently expanded its genotyping facilities to keep up with its sequencing-based SNP discovery services.
The new facility opened in London last week and will serve as a complement to the company's sequencing facility, which is located in Berlin.
Knut Mohr, LGC Genomics' business manager of sequencing and genotyping, told In Sequence that the company primarily performs SNP discovery and genotyping services for ag-bio researchers and companies and epidemiology researchers.
The sequencing facility in Germany is equipped with an unspecified number of Illumina HiSeq 2000 and Roche 454 GS FLX instruments, and recently acquired an Illumina MiSeq, Mohr said.
He added that the company does targeted resequencing, exome sequencing, and amplicon sequencing for SNP discovery and validation. The main customers are ag-bio researchers and companies, either looking to discover a handful of novel SNPs from well-characterized plants related to specific traits or phenotypes, or looking to do a broad SNP discovery on lesser characterized plants. Additionally, the company performs SNP discovery on large cohorts for academic researchers in epidemiology and population genetics.
Currently, most of the next-gen sequencing is done on the HiSeq, with amplicon sequencing done primarily on the 454. However, Mohr said that the 454 pipeline will likely be transitioned to the MiSeq instrument.
He said the company recently decided to test the MiSeq and so far it has been working well at about one-fifth the cost of sequencing on the 454.
"With the next step of improvements that the MiSeq will bring … it's going to be a perfect replacement of 454 for targeted amplicon-based resequencing," Mohr said. Illumina has said that it plans to introduce 2x300 reads for the MiSeq in 2013 (IS 11/13/2012).
Additionally, sequencing from both ends of the amplicon will allow for a "much more powerful tagging system that we developed," Mohr said.
"When you have tags on both sides, then you can have combinatorial tagging, which allows sequencing of maybe up to 10,000 different individuals on a known target gene on a MiSeq run," he said.
Mohr said that the company is not looking at other sequencing technologies at the moment. The long reads of the Pacific Bioscience RS, for instance, are not necessary for LGC's specific application of SNP discovery.
Like other relatively small sequencing service companies, Mohr said that LGC's focus on the applications surrounding the sequencing itself help to set it apart and compete with larger sequencing service providers such as BGI, GATC Biotech, and Beckman Coulter.
For instance, the company has a proprietary genotyping assay, dubbed KASP, that it offers as a follow-on to SNP discovery sequencing projects and as a standalone service. KASP is a fluorescence-based competitive allele-specific PCR technique that was developed by KBioscience. LGC acquired KBioscience last year.
Mohr said that the combination of the two firms' sequencing and genotyping technologies has helped provide a complete solution for researchers doing SNP discovery and genotyping.
Additionally, Mohr said the company has developed techniques for DNA extraction specific to the needs of ag-bio researchers. For instance, he said, sometimes researchers will not want to wait for a plant to grow before doing sequencing and will want to use DNA extracted from seeds.
LGC has developed protocols, using chemistry called sbeadex, to enable extraction and sequencing of DNA from plant seeds. The main advance of the sbeadex chemistry is that it helps remove plant ingredients, such as polyphenols and polysaccharides, that are common in plant seeds.
The company already has several protocols for seeds from plants such as wheat and barley, but will also tailor protocols for researchers' specific types of seeds, Mohr said.