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Norway - Laboratory, optical and precision equipments (excl. glasses) - Equipment for weekend sequencing for the Department of Medical Genetics at UNN HF Tromsø.

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The Medical Genetics Department at the University Hospital of North Norway (UNN) shall procure a sequentialator from PacBio to read long fragments of DNA and RNA sequencing (long-read sequencing, LRS). The instruments shall be used for diagnostics and shall replace and supplement the current diagnostics based on short-read sequencing (SRS). This is because LRS detects some types of genetic variation better than SRS, e.g. major structural deviations and methylation status. Method transfer shall therefore be carried out from the current SRS to a new LRS for selected medical indications and it is therefore very important that these sequentators deliver a sequence of very high quality and reproducibility. Of the above mentioned reasons, PacBio, as far as the contracting authority is aware of, is the only supplier who can fulfil the requirements. The terms in PPR § 13-4 (b) no. 2 are considered fulfilled. The Medical Genetics Department at the University Hospital of North Norway (UNN) intends to procure 1 sequentialator from PacBio to read long fragments of long-read sequencing (DNA and RNA sequencing). The instruments shall be used for diagnostics and shall replace and supplement the current diagnostics based on short-read sequencing (SRS). This is because LRS detects some types of genetic variation better than SRS, e.g. major structural deviations and methylation status. Method transfer shall therefore be carried out from the current SRS to a new LRS for selected medical indications and it is therefore very important that these sequentators deliver a sequence of very high quality and reproducibility. There are several technical specifications that are decisive for achieving the quality we need for this purpose, for example: - The sequencing must be able to carry out sequencing with long read lengths of DNA and RNA for clinical samples. The read length of sequential fragments must at least be median 10-15 kb. At least 90% of the bases must have a quality of Q30 or higher in a typical 30X human genome. The instrument shall be particularly suitable for detecting major structural deviations and methylation status. - The data quality of SNP variants and short parts <50 bp must be at least as good as that achieved by Illumina SRS. This is important so that the analytical sensitivity of the analysis offer is not reduced for these types of variants and that the quality of the analysis offer is not, therefore, impaired for the patient analyses that shall only be carried out on a new long-read sequentator. - Sensitivity and precision must be documented in a reference dataset for the entire genome (i.e. not just the encoded areas in the genome) with the following parameters met: (i) F1 score > 99 % for SNS. (ii) F1 score > 95 % for INDEL's. (iii) F1 score >90 % for structural variants (SV's). (iv) Recall or F1-score for SNVs and INDEL are for technically challenging medical relevant genes (CMRG, as defined in Wagner et al., Nature Biotechnology 2022: https://www.nature.com/articles/s41587-021-01158-1) at least on par with Illumina SRS. High F1 scores (low false positive and negative variant detection) are decisive in avoiding extremely time-consuming and resource-demanding downstream verification of variants/missing cause variants. - Variantcalling to the mentioned standards must be achieved with an average 30X sequencing depth. This is required to avoid the need for deeper sequencing, including duotone readings, in order to achieve the necessary data quality. The need for deeper sequencing will increase the costs and time consumption, which is not acceptable. - Sequence data cannot have systematic bias in basecalling and variant calculation, including in homopolymer areas. Of the above mentioned reasons, PacBio, as far as the contracting authority is aware of, is the only supplier who can fulfil the requirements. The terms in PPR § 13-4 (b) no. 2 are considered fulfilled.

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