Request for information: Large gene panel for analysis of somatic genetic alterations in cancer

HUSLAB is seeking a large gene panel test for detection of genetic alterations in cancer covering genes with the most common clinically relevant alterations (at least 500 genes). The test should detect SNVs, indels, gene fusions, copy number variations (CNVs), microsatellite instability (MSI), homologous recombination deficiency (HRD), and tumor mutation burden (TMB). The test is based on analysis of total nucleic acids (RNA and DNA) extracted from paraffin embedded solid tumor samples using next generation sequencing (NGS) on either Ion Torrent or NovaSeq 6000 sequencers. The number of cancer panel tests annually in HUSLAB is estimated to be between 500-1000. This is not a call for tenders and we are not asking for any offers via this announcement. This prior information notice does not obligate the procurement unit for any actions. All information presented in this prior information notice is preliminary and indicative. This notice is not binding on any kind of solutions or actions. The suppliers are not paid for responding to this request for information or participating in a possible technical dialogue.

HUSLAB Laboratory of Genetics at HUS (Helsinki University Hospital) Diagnostic Center is an SFS-EN ISO 15189:2013 accredited laboratory providing diagnostic genetic testing services to all patients at Helsinki University Hospital area. The services include analysis of both constitutional samples and malignancies. The laboratory provides sequencing services mainly using local HUSLAB sequencing capacity (Illumina NovaSeq 6000, Ion Torrent S5 and Ion Torrent Proton equipment). HUSLAB is seeking a large gene panel test for detection of genetic alterations in cancer covering genes with the most common clinically relevant alterations (at least 500 genes). The test should detect SNVs, indels, gene fusions, copy number variations (CNVs), microsatellite instability (MSI), homologous recombination deficiency (HRD), and tumor mutation burden (TMB). The test is based on analysis of total nucleic acids (RNA and DNA) extracted from paraffin embedded solid tumor samples using next generation sequencing (NGS) on either Ion Torrent or NovaSeq 6000 sequencers. The number of cancer panel tests annually in HUSLAB is estimated to be between 500-1000. This is not a call for tenders and we are not asking for any offers via this announcement. This prior information notice does not obligate the procurement unit for any actions. All information presented in this prior information notice is preliminary and indicative. This notice is not binding on any kind of solutions or actions. The suppliers are not paid for responding to this request for information or participating in a possible technical dialogue. We ask companies interested in this procurement to answer the following questions and requests listed below: - The test is validated for Ion Torrent equipment. (Yes/No) - The test is validated for Illumina NovaSeq 6000. (Yes/No) - The test is validated for paraffin embedded samples. (Yes/No) - The automatic extraction methods used in the laboratory (Maxwell, QIAsymphony) are suitable for test. (Yes/No) - Provide a list of laboratory equipment needed to perform the test. - The number of genes covered by the panel is over 500. (Yes/No) - Provide a list of genes covered by the panel, specifying which genes are covered completely or partially and in the latter case, information on which parts of the genes are covered. Furthermore, the list should specify for which genes can CNVs and fusions be detected. - Novel fusion partners are identified. (Yes/No) - The cancer panel covers the most common exon skipping (at least MET exon 14) in solid tumors. (Yes/No) - MSI, TMB, and HRD are reported. (Yes/No) - Allele frequency, depth, breakpoints and sequence of variants are reported. (Yes/No) - SNVs and indels can be detected in the same sequencing run as fusion genes. (Yes/No) - What is the limit of detection (LOD)? - How many samples can be run in one chip/flow cell? - The test includes a tertiary data analysis software. (Yes/No) - Is the test CE-IVDR certified? (Yes/No) - If No, how does the manufacturer plan to acquire IVDR certification for the test? The response to this request for information should include replies to the above questions. The answers to this request for information are asked to be sent by e-mail to kilpailutus.laboratorio@hus.fi. We wish to receive a response to our request at the latest on August 15th 2023.