Sequencing as a service is available with Illumina, 454, and Complete Genomics.
July 29, 2010 | SINGAPORE—Malaysia Genomics Resource Centre (MGRC) has announced a genome mapping pipeline service starting at $4000 per genome.
“The target market, said Robert Hercus, managing director of MGRC, “is smaller labs, hospitals, and university researchers who perhaps do not have the facilities or the bioinformaticians but want to do some sequencing.”
“We want to un-complicate the lives of the researchers who are doing wet lab biology and research,” Robert told Bio•IT World in a phone interview. He believes the service will help smaller labs that do not have the time or resources to invest in learning 10-20 open-sources packages or pay for software or hardware.
MGRC’s solution is a proprietary pipeline for processing genomic data. MGRC does the processing and analysis and returns their findings to the lab for validation. The service takes about a week for each genome. Data is sent to MGRC on a terabyte disc by courier. MGRC accepts sequence data from Illumina, 454, and Complete Genomics said Hercus, and, “MGRC hopes to later offer Ion Torrent and PacBio as well.”
Once the data has arrived, MGRC does pre-processing to “clean up” the data, maps the reads, and then applies proprietary mutation and structural variation pipelines. All of the processing is done in-house on MGRC servers, and Hercus said the current capacity is about 100 genomes per month.
Results are returned to the customer on the same terabyte disc one week after receipt. MGRC also offers their own genome browser with which researchers can share and interact with their results.
The processing includes identification of SNPs; inserts and deletions up to three bases; and density mapping to flag copy number variations. With paired end data, the pipeline can identify structural variations such as insertions, translocations, inversions, and multi-base deletions. As a separate service, MGRC will do comparative analyses between any number of genomes.
“We have comparative results against other systems that do mapping, for example, Bowtie, SOAP and BWA, and we [make] those statistics available to customers so they can see [that] our results are more accurate than what’s currently available,” Hercus said.
“I don’t think there’s another company in the world that could take a complete human genome at 30x coverage, say 90 gigabases, and process it in one week with complete analysis, 100% finished.”
The service was launched in early April, and Hercus said that the company has already done some genomes, has 15 commitments, and is in talks with another 20 prospects worldwide. When asked for names, he laughed, but then mentioned that Harvard Medical School has sent several genomes. The company website lists some key “customers and partners” including Lilly, The Genome Center at Washington University, and Cancer Research UK.
In the May 13 issue of PLoS One, researchers at Brigham & Women’s Hospital in Boston published the sequencing of the Mesothelioma tumor genome.
Sequencing was done on a “human primary malignant pleural mesothelioma (MPM) tumor and matched normal tissue by using a combination of sequencing-by-synthesis and pyrosequencing methodologies to a 9.6X depth of coverage,” said the paper authors including Hercus. “Read density analysis uncovered significant aneuploidy and numerous rearrangements. Method-dependent informatics rules, which combined the results of different sequencing platforms, were developed to identify and validate candidate mutations of multiple types.”
MGRC has been around for five years and is the services subsidiary of Synamatix, a Malaysian software and bioinformatics tools company that Hercus founded in 2001. Synamatix has developed the software and tools; MGRC “provides the services to customers and looks after the bioinformatics pipeline.” MGRC also has a web portal that provides free online bioinformatics tools to users.
MGRC’s services are constantly expanding, Hercus explained, as new customers bring new challenges and opportunities as the technology advances. “We plan to eventually offer a sequencing service as well,” he said. “We have a lot of local Malaysian research institutes that want to do sequencing of human genomes, and at the moment we send that out overseas. So we believe it will be cost effective for us to have our own sequencing centre here, at least for Malaysia, if not the region.”
This article also appeared in the July-August 2010 issue of Bio-IT World Magazine. Subscriptions are free for qualifying individuals. Apply today.