DNA library preparation reagents

Tampere University Foundation sr (Contracting authority) is publishing direct award notice for 'DNA library preparation reagents'.

BACKGROUND INFO Tampere University is a part of EU Horizon Mission consortium named PREDI-LYNCH. The PREDI-LYNCH consortium mission is to deliver an ambitious, multi-omic approach to address the unmet need for an accurate, non-invasive, acceptable and cost-effective method of detecting precancerous and early-stage cancers in those individuals with Lynch syndrome, the most common inhered cancer predisposition syndrome. The PREDI-LYNCH consortium includes a clinical trial using non-invasive liquid biopsy modalities for early cancer detection. The UroScout assay developed at Tampere University is used as an intervention assay to test its clinical performance for early detection of urothelial cancer. UroScout is a urine-based assay that employs a targeted hybridization capture panel (covering 32 genes) to detect tumor-derived DNA mutations in key urothelial cancer-associated genes in exfoliated DNA in urine. As a non-invasive molecular screening test, UroScout offers potential advantages: (1) earlier detection of asymptomatic neoplasia, (2) higher sensitivity relative to urine cytology, and (3) better stratification of patients for confirmatory diagnostics. If UroScout can reliably detect early urothelial carcinomas in LS patients, interventions may be undertaken at a stage amenable to less radical surgery, lower morbidity, and improved outcomes. The UroScout assay has already been tested in several clinical trials and on-going trials. The results show that urinary tumor DNA testing is feasible, well tolerated, and capable of identifying early, asymptomatic cancers, supporting the need for large-scale validation. The aim of the PREDI-LYNCH international clinical study is to evaluate the clinical performance of the UroScout multigene test in the early detection of urothelial carcinoma in carriers of pathogenic or likely pathogenic variants in the Lynch syndrome gene. NEED UroScout is a urine-based molecular assay that detects somatic mutations associated with urothelial carcinoma through targeted hybrid-capture DNA sequencing. The assay targets a 32-gene panel of genes frequently mutated in bladder cancer and upper tract urothelial cancer. The test analyses urine cell pellet DNA isolated from urine samples collected in preservative solution to maintain cell and DNA integrity during transport. The assay includes automated and manual steps for DNA extraction, library preparation, target capture, sequencing, and informatic analysis. The associated software pipeline performs read alignment, variant calling, quality control checks, and generates a structured clinical report. DNA library preparation reagents by Twist Bioscience allow the highest volumetric input of sample material to library preparation reactions out of the commercially available library preparation methods utilizing enzymatic fragmentation. This allows streamlined sequencing library preparation. The Twist Bioscience Library Preparation kit is based on formulation of a hot-start enzyme that has an improved error rate and high efficiency at low input volumes. The DNA library preparation with the Twist Bioscience reagent kit is combined with the Twist Universal Adapter System consisting of indexes needed for downstream target enrichment and sequencing. The Twist Universal Adapter System is TruSeq-compatible, using 10 bp adapters for all 'T-A' overhang workflows. They reduce adapter dimer formation, improving yield for efficient and high-quality NGS library preparation providing 384 different index-pairing between samples, improving data quality while lowering sequencing costs. CONCLUSION FOR DIRECT AWARD A direct award is justified as the UroScout assay has been developed, tested, and validated using Twist Bioscience reagents for DNA library preparation. As the UroScout assay is used as an interventional test in PREDI-LYNCH clinical trial (NCT07360834), changing the assay reagents would endanger patient safety or require significant additional time and investment on testing and validating an alternative set of reagents. it is not warranted to change the reagents for the UroScout assay, and the direct procurement for the use of Twist Bioscience DNA library preparation kit and Universal Adapter System for UroScout assay is justified.