DNA Pipelines provides genome analysis services for the Institute’s Faculty. The Pipelines process DNA, RNA and tissue samples received from internal and external sources to generate sequence, genotype and copy number information. The Operations group oversees the delivery of this high-quality data via a range of technologies and platforms.
DNA Pipelines Operations is split into:
- Sample Management
- Illumina Sequencing
- Supplementary platforms that include PacBio, Genotyping, Microarray, Optical Mapping and Capillary Sequencing.
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The Sample Management pipeline registers and processes more than 350,000 samples per year. It provides extraction of DNA and RNA from biological materials and delivers automated high-throughput DNA quantification and normalisation. Sample management serves the needs of Faculty members, Celllular Genetics and Phenotyping, Illumina Sequencing (High Throughput), PacBio Sequencing, Illumina and Sequenom Genotyping, and Microarray pipelines.
The Illumina Sequencing platform uses Illumina HiSeqs and the HiSeq X Ten system, delivered by a high-throughput team and a bespoke team. The capacity of these machines allows the teams to combine multiple sample libraries into a single lane, routinely generating more than 600 Gigabases (Gb) per run (anticipated to rise to 1Tb per run with upgrades). To ensure our processes are robust and scalable, we seek to conform to the standards of Good Clinical Laboratory Practice (GCLP).
The Illumina Sequencing platform delivered more than 70,000 libraries and 12,000 lanes in 2013 across a range of library types, and a total of 400 Terabases (Tb) of data. In addition, there has been an improvement in quality control, with our Libraries now meeting a 99–100 per cent pass rate and a reduction in sequencing lane failure rates to less than 5 per cent.
The PacBio next-generation platform supports research projects that require longer read lengths, such as bacterial and parasite de-novo sequencing and viral sequencing.
The Genotyping Pipelines use the Illumina and Sequenom platforms, which includes five high-resolution Illumina bead chip scanners (iScans) and three Sequenom mass spectrometers. In all, the Institute has the capacity for 110,000 genome-wide scans and 500,000 Sequenom low plex types per year. A large part of the Pipelines’ work has focused on collaborative projects, including WTCCC3, which is a consortium study funded by the Wellcome Trust.
The Microarray Facility provides mRNA expression and array (comparative genomic hybridisation) CGH analysis using the Illumina BeadChip and Agilent platforms respectively. It is used by research groups in the Institute’s Human Genetics, Malaria, Pathogen Variation, and Mouse & Zebrafish Genetics programmes.
The Optical Mapping platform provides services using the Irys system.
The Capillary Sequencing Pipeline provides low-to-medium throughput, sample preparation and sequencing services to Faculty members and a “load-only” service to the Mouse Embryonic Stem Cells (ES) Mutagenesis group and Cancer Genome Project. The platform is also able to provide fingerprinting and clone library replication services.