DNA Pipelines Operations

The Wellcome Trust Sanger Institute's technological platforms underpin our ability to carry out biomedical research on a large scale, allowing researchers to answer questions that can be intractable in other institutions.

Sanger Institute, Genome Research Limited

Here we outline the operation of these platforms and discuss how researchers can access our technologies.

The Wellcome Trust Sanger Institute was founded to exploit DNA sequence in order to understand biology and disease.

That imperative remains as strong today as the Institute capitalises on leading-edge technologies to answer questions that were unanswerable only a few years ago. We have always used and will continue to use the most appropriate technology to provide the data that solve important questions in biomedicine.

The Institute has one of the largest DNA sequencing facilities in the world. Our nextgeneration sequencing capacity is currently at 26 Illumina HiSeqs (comprising 10 HiSeq 2500 V4 and 16 HiSeq2000 V3) , as well as one set of HiSeq X machines (‘X Ten’), 5 Illumina MiSeqs and one Pacific Biosciences machine. For large-scale genotyping, there are 5 Illumina iScan machines and three Sequenom mass spectrometers. The DNA Pipelines are further supported by an automated sample management facility. The platform is capable of producing more than 1700 terabases (1700 x 1012 bp) of DNA sequence per year.

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

Sanger Institute, Genome Research Limited

  • Sample Management
  • Illumina Sequencing
  • Supplementary platforms that include PacBio, Genotyping, Microarray and Optical Mapping.
Sample Management

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.

Illumina Sequencing

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 1Tb per run. To ensure our processes are robust and scalable, we seek to conform to the standards of Good Clinical Laboratory Practice (GCLP).

Typically, our Libraries now meet a 99.8 per cent pass rate and a reduction in sequencing lane failure rates to less than 5 per cent.

Supplementary platforms

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.

Optical Mapping

The Optical Mapping platform provides services using the Argus Optical Mapping system. In spring 2015 the Irys system also became available.