EC0900 Sequencing & Genotyping Services Framework

Tender description

The University of Edinburgh (UoE) is intending to create a framework covering a wide range of sequencing and genotyping services. The UoE have internally available resources and this framework is designed to support these resources. End-users will be encouraged to approach our internal resources first and foremost but if capability, capacity or cost isn't suitable, then successful suppliers on the framework will be able to compete for this business. It is intended that each Lot will work on a ranked basis, with Direct Call-offs being used as a preferred mechanism for speedy purchases but in the case of larger value or more complex requirements, a mini-competition may be run instead which would invite all suppliers from the appropriate Lot. The estimated cost indicated in this notice is a rough calculation from spend across ALL lots. This is an estimate only at this time and does not provide any guarantee on potential spend levels. SUPPLIERS SHOULD NOTE THAT COVID-19 AND BREXIT MAY RESULT IN SIGNIFICANT REDUCTIONS IN SPEND FROM THE INDICATED LEVEL. Minimum standards will focus on suppliers capacity and capability, both from a technical and financial perspective. Technical scored questions will focus on but not limited to; 1. Service delivery e.g. turn-around time, available equipment, storage, order processes/procedures 2. Quality assurance e.g. project references, sample quality assurance, obtained accreditation 3. Logistics/Process e.g. shipping arrangements, tracking ability, weekend storage, shipping formats 4. Technical Support/Contract Management e.g. continuous improvement, invoice procedures, poor/failed sample integrity 5. Sustainability/Community benefits e.g. service elements promoting good sustainable practice 6. Added Value e.g. Suppliers will be asked to provide an example rebate system based on annual spend levels, early payment discounts, re-sequencing charge Suppliers are only to bid for the Lots relevant to them but can apply for more than one. Lots may be awarded on a staggered basis depending on the complexity of submissions and duration of evaluation. PLEASE NOTE: THIS NOTICE IS BY NO MEANS A FIRM INDICATION OF HOW THE FRAMEWORK WILL OPERATE. THE UNIVERSITY RESERVES THE RIGHT TO ALTER THE CONTENT UP TO THE POINT OF TENDER PUBLICATION. LOT NAMES, DESCRIPTIONS MAY CHANGE ALONGSIDE INTENDED CALL-OFF STRATEGIES. IN ADDITION, THE CURRENT AND POTENTIAL ECONOMIC AND PANDEMIC ORIENTATED CLIMATE MAY RESULT IN THE UNIVERSITY PULLING THE TENDER BEFORE IT'S PUBLICATION OR DURING THE TENDER PROCESS. Suppliers are encouraged to get in contact with andrew.helmn@ed.ac.uk for further information. Lot 1: Lot 1 - Short Read Genomic Sequencing & Analysis Paired end library sequencing Long mate pair library sequencing Linked read sequencing Genome Sequence imputation Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 2: Lot 2 - Long Read Genomic Sequencing & Analysis Pacific Biosciences (PacBio) Sequencing Oxford Nanopore Technology (ONT/Nanopore) sequencing VASA-Seq Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 3: Lot 3 - Transcriptome Sequencing & Analysis RNA-Sequencing (mRNA and total RNA sequencing) full length transcript or cDNA sequencing Small RNA Sequencing Nanostring Microarray services Direct RNA sequencing (Oxford Nanopore) Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 4: Lot 4 - Targeted Sequencing & Analysis Exome Sequencing Targeted / Gene Sequencing Custom sequence capture Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 5: Lot 5 - Microbial Sequencing & Analysis Whole Genome PacBio Sequencing (for microbial) Whole Genome Nanopore Sequencing (for microbial) Whole Genome Short Read Sequencing (for microbial) 16s Microbial Sequencing Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 6: Lot 6 - Single Cell Sequencing & Analysis Single Cell Isolation and Sequencing Single Nuclei Isolation and Sequencing Single cell ATAC-Seq Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 7: Lot 7 - Other Genomic Methods & Analysis Methylation Sequencing (reduced representation or whole genome bisulphite sequencing) ATAC-Seq Library Preparation ChiP-Seq Library Preparation HiC library preparation / sequencing RIP-Seq Ribo-Seq Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 8: Lot 8 - Optical Mapping Optical Mapping Including data transfer QC of sequence data - specific to the lot Including Library Prep (and sample QC) - specific to the lot Bioinformatic Services - Data Analysis, Interpretation & Reporting of sequencing services - specific to the lot Lot 9: Lot 9 - Sanger Sequencing / Genotyping Sanger sequencing / genotyping Plasmid DNA extraction Lot 10: Lot 10 - Array-based genotyping Genotyping of Single Nucleotide Polymorphism (SNP) Array-based genotyping Include all-inclusive genotyping services - specific to the lot Lot 11: Lot 11 - Other Genotyping services Genotyping of simple sequence repeat (SSR) Genotyping by Microsatellite Genotyping of low number SNPs Include all-inclusive genotyping services - specific to the lot - specific to the lot Lot 12: Lot 12 - Genotyping of transgenic animals Genotyping of transgenic animals Genetic background characterisation 1-7 genes per animal, with up to 6 different alleles detectable for each gene a panel of genetic markers that can distinguish between the common lab strains of mouse and rat evenly spaced through the genome Lot 13: Lot 13 - DNA/RNA Extraction whole blood Saliva FTA paper Buccal swabs Mammalian cell lines/primary cells (cell pellets) Plant and animal tissue FFPE tissue Bacteria