Roche Nimblegen and 454 Life Sciences present sequence capture microarrays and a genome sequencer, to speed sample preparation and sequencing for research on cancer and diabetes.
Targeted resequencing allows scientists to capture only the regions of interest of the human genome and then use high-throughput sequencing to assess genetic variation within the captured DNA fragments.
The use of Nimblegen sequence capture products simplifies the capture of these genomic regions when compared with traditional laboratory methods, allowing researchers to progress to the sequencing stage much quicker.
Nimblegen sequence capture microarrays and 454 sequencing are integral research tools for sequencing service provider labs, such as Genoscope - CEA in Paris, France.
The head of its Department of Genomic Resources, Dr Gandabor Gyapay, said: 'In our work studying rare monogenic diseases, it is virtually impossible by PCR methods to prepare samples for sequencing if the interval, where the disease gene is localised, is more than a few hundred kilobases.
'Using Nimblegen sequence 385K microarrays, we are able to capture megabase-sized regions and sequence our samples using the genome sequencer FLX instrument.' Dr Gyapay added: 'Roche Nimblegen's detailed protocol is very useful, and it guides you through the procedure in a clear and illustrative fashion.
'At every quality control step you are given a figure showing the expected results.' As an early adopter of Nimblegen sequence capture microarrays in Canada, Dr John McPherson, platform leader, Cancer Genomics and High-Throughput Screening, Ontario Institute for Cancer Research, has firmly established this technology in his lab.
'Targeted resequencing enables us to analyse more genomes, as whole-genome sequencing is still too expensive for the number of samples we want to process.
'We were able to get enrichment of targeted regions on our first attempt and are still optimising the protocol, and have adapted it for use with other sequencing platforms.' In January, Roche Nimblegen launched its human exome product, which uses an optimised design algorithm (launched on the 385K platform in October last year) to provide the highest-performance Nimblegen sequence capture array designs to date.
This optimised design helps capture all target regions with equal efficiency, and reduces the overall sequencing needed, reducing costs.
The human exome product is a Nimblegen sequence capture microarray built on the high- density HD2 (2.1 million long oligonucleotide probes) platform.
This product allows the capture of nearly all regions of the human genome that code for proteins (around 180,000 human coding exons and 700 miRNA exons) on a single array.
It gives researchers an easy, cost-effective system (compared to conventional PCR methods) for exon sample preparation in generating hypotheses for studies aimed at unravelling the complexity of human genetic variation.
Implementation of this technology in customer labs is made easy with three-day on-site customer workshops available from certified Roche Nimblegen sequence capture trainers, who can train customers on the 385K and 2.1M capture protocols.
The genome sequencer FLX system and the GS FLX Titanium chemistry series expand upon the previous series by providing researchers with an even greater sequencing power of more than 400bp sequencing reads and over 1 million reads per run.
The system also includes dedicated analysis tools for mapping reads and detecting variants of data from DNA captured with Nimblegen arrays, allowing straightforward interpretation of results.
The 454 sequencing system for ultra-high-throughput DNA sequencing has the following specific applications: de novo sequencing and resequencing of genomes, metagenomics, RNA analysis, and targeted sequencing of DNA regions of interest.
The hallmarks of the 454 sequencing system are its simple, unbiased sample preparation and long, highly accurate sequence reads, including paired-end reads.
The technology of the 454 sequencing system has allowed hundreds of studies in diverse research fields, such as cancer and infectious disease research, drug discovery, marine biology, anthropology, paleontology and many more.
