Market consultation: Request for large cancer gene panel for analysis of somatic genetic alterations in cancer

This advance notice is not an invitation to tender, but it is a market consultation for the upcoming procurement. No tenders will be submitted and no advance registration will be made for the actual tender based on the advance procurement notice. This advance notice does not obligate the Acquisition Unit of the Joint Authority of the Helsinki and Uusimaa Hospital District for any actions. The responses to this information request do not obligate the acquisition unit to any service acquisitions nor to commit proceeding with the procurement. The acquisition unit also does not commit to the information provided in this market consultation or its attachments, as the subject or requirements of the procurement may change in the preparation of a procurement procedure. HUS Group (also “HUS”) is preparing a procurement of large cancer gene panel for analysis of somatic genetic alterations in cancer (also "supplies"). The aim of this market consultation is to gather information on potential tenderers and the features of available supplies. Laboratory of Genetics at HUS (Helsinki University Hospital) Diagnostic Center is an SFS-EN ISO 15189:2022 accredited laboratory providing diagnostic genetic testing services to all patients at Helsinki and Uusimaa Hospital District. The services include analysis of both constitutional samples and malignancies. The laboratory provides sequencing services mainly using local sequencing capacity (Illumina NovaSeq 6000, NovaSeq X Plus, Ion GeneStudio S5 Prime equipment). Currently, Laboratory of Genetics is seeking for a large cancer panel test for detection of small nucleotide variants (SNVs), indels, gene fusions, copy number variations (CNVs), microsatellite instability (MSI), homologous recombination deficiency (HRD), and tumor mutation burden (TMB) relevant for the genetic profiling of solid tumor samples and/or hematological malignancies. This test is based on analysis of total nucleic acids (RNA and DNA) extracted from paraffin embedded specimens and/or fresh-frozen specimens. Sequencing of the samples is carried out using next generation sequencing (NGS) on Ion Torrent or Illumina NovaSeq sequencers. The number of cancer panel tests performed annually is estimated to be between 500-1000. The following specific requirements concerning the cancer panel tests are: • The test is validated for Ion GeneStudio S5 Prime equipment. Yes/No • The test is validated for Illumina NovaSeq 6000. Yes/No • The test is validated for Illumina NovaSeq X Plus. Yes/No • The test is validated for paraffin embedded samples. Yes/No • The test is validated for fresh frozen tissue samples. Yes/No • The automatic nucleic acid extraction methods used in the laboratory (Maxwell, QIAsymphony) are suitable for tests. Yes/No • The gene panel covers the most common cancer genes with clinically relevant alterations i.e. according to WHO classification and cancer type specific guidelines. Yes/No • The test is intended for solid tumors. Yes/No • The test is intended for hematological malignancies. Yes/No • The tests for solid tumors and hematological malignancies are separate products. Yes/No • The test is validated for cfDNA. Yes/no • The test for cfDNA is a separate product Yes/No

Please respond to the following questions (a-i/j) for each test (1-3): 1. The test intended for solid tumors: a) Please provide a list of the genes covered by the test, including information whether the whole coding sequence or which hotspots are covered. b) Novel fusion partners are identified. Yes/No c) CNVs can be detected in single exon level. Yes/No d) CNVs can be detected in multi exon / whole gene level. Yes/No e) MSI, TMB, and HRD are identified. Yes/No f) For fusion calls, allele frequency, read depth, fusion breakpoints and sequence covering the fusion breakpoint are reported. Yes/No g) What is the limit of detection (LOD) for each variant type or biomarker? h) How many samples can be run in one chip/flow cell? i) What is the hands-on time of the laboratory protocol? j) What is the total turnaround time of the laboratory protocol? 2. The test intended for hematological malignancies: a) Please provide a list of the genes covered by the test, including information whether the whole coding sequence or which hotspots are covered. b) Novel fusion partners are identified. Yes/No c) CNVs can be detected in single exon level. Yes/No d) CNVs can be detected in multi exon / whole gene level. Yes/No e) MSI, TMB, and HRD are identified. Yes/No f) For fusion calls, allele frequency, read depth, fusion breakpoints and sequence covering the fusion breakpoint are reported. Yes/No g) What is the limit of detection (LOD) for each variant type or biomarker? h) How many samples can be run in one chip/flow cell? i) What is the hands-on time of the laboratory protocol? j) What is the total turnaround time of the laboratory protocol? 3. The test intended for cfDNA: a) Please provide a list of the genes covered by the test, including information whether the whole coding sequence or which hotspots are covered. b) Novel fusion partners are identified. Yes/No c) CNVs can be detected in single exon level. Yes/No d) CNVs can be detected in multi exon / whole gene level. Yes/No e) MSI, TMB, and HRD are identified. Yes/No f) What is the limit of detection (LOD) for each variant type or biomarker? g) How many samples can be run in one chip/flow cell? h) What is the hands-on time of the laboratory protocol? i) What is the total turnaround time of the laboratory protocol? Please respond to the following questions regarding the software: • The test includes a specific tertiary data analysis software. Yes/No • In case the test includes a specific tertiary data analysis software, 1) the software is included in the price of the test, 2) there is an additional cost for the data analysis. Yes (option 1 or 2)/No • In case the test includes a specific tertiary data analysis, this tertiary data analysis solution is 1) SaaS product, 2) software to be installed to a server provided by HUS, 3) software to be installed to a server provided by supplier, 4) something else. Yes (option 1,2,3 or 4)/No • The test can be analyzed using a third-party tertiary data analysis software. Yes (which software?)/No • Please attach a list of laboratory equipment required to run the assay. • The test is CE-IVDR class C certified. Yes/No. If yes, please provide the intended use of the assay. Please respond to the following questions regarding the criteria for tenderer’s suitability: • Is the turnover of the tenderer for the last confirmed 12 -month financial year at least 500 000 EUR? Yes/No. If no, please provide information of the turnover (EUR). • Has the tenderer references regarding prior deliveries of the large cancer panel tests. Yes/No. If yes, please provide information of the number of references. • Does the tenderer have a professional risk indemnity insurance for at least the amount of 500 000 EUR? Yes/No. If no, please provide information of the amount of professional risk indemnity insurance (EUR). • Is the tenderer's credit rating at least satisfactory A or equivalent in the credit rating of Suomen Asiakastieto Oy or in a comparable credit rating verified by an external party? Yes/No. If no, please provide information of the credit rating. All responses to the questions will be treated with confidentiality. The information provided will be used solely for the purposes of evaluating the procurement procedure and will not be disclosed to third parties. The response to this cancer panel test request should include descriptions to the above questions. We wish to receive a response to our request within few weeks, but latest on May 30, 2025, at 12:00 pm (EEU time) by responding via email at: sara.taivainen@ptcs.fi. We kindly request that you send the answers to the above-mentioned email address in the manner that suits you best. For example, you can copy the questions into a Word document, answer them in that document, and then attach the Word document to the email.