EUROPEAN OPEN TENDER IN TWO LOTS IN FRAMEWORK AGREEMENT WITH PRESUMED AND UNGUARANTEED SUM FOR THE AWARD OF THE SUPPLY OF REAGENTS FOR GENOMIC ANALYSIS FOR THE RESEARCH NEEDS OF THE DEPARTMENT OF MEDICINE AND SURGERY OF THE UNIVERSITY OF PARMA WITHIN THE FOLLOWING RESEARCH PROJECTS: "A RADIO-IMMUNO-GENOMIC APPROACH TO IDENTIFY PROGNOSTIC AND PREDICTIVE MODELS FOR THE RESPONSE TO IMMUNOTHERAPY IN NSCLC" AND "IDENTIFICATION OF PROGNOSTIC AND PREDICTIVE RADIO – IMMUNE – GENOMIC SIGNATURES IN SMALL CELL LUNG CANCER (SCLC) AND MALIGNANT PLEURAL MESOTHELIOMA (MPM)".

N. 288 SEQUENCING KIT: PANEL COMPATIBLE WITH NANOSTRING TOOL

Espressione genica e Tumor Inflammation Signature (TIS)

Estimated sample size: 300 samples approx.

For the analysis of gene expression on RNA and for the contextual identification of a Tumor Inflammation Signature (TIS) it is necessary to provide for the use of a panel that allows to simultaneously analyze the gene expression of a large number of target genes (min. 700) for the study of the expression of genes related to immune cells, the response to immunotherapy and the identification of tumor-specific antigens. The designated panel must be compatible with the Nanostring tool inside the structure.

- N. 13 TSO500 SEQUENCING KITS (T): PANEL COMPATIBLE WITH NEXTSEQTM 550 DX SYSTEM IN SEARCH MODE,

Next Generation Sequencing (NGS) on tissue samples

Estimated sample size: 300 samples approx.

The project involves genomic analysis on paraffin tissue samples (FFPE) from surgery or diagnostic biopsies, with the need to use an NGS panel that can guarantee complete genomic profiling through the identification of relevant DNA and RNA variants involved in NSCLC and SCLC lung cancer. In addition, it is essential to measure the immuno-oncology parameters available today, such as tumor mutation burden (TMB) and microsatellite instability (MSI). The chosen panel must be compatible with the sequencer present within the NextSeqTM 550 Dx (Illumina) system structure in search mode and evaluate the following classes of variants on DNA and RNA FFPE samples: single nucleotide variations (SNVs), insertions-deletions (indels), copy number variations (CNVs) and gene fusions. The panel should be based on hybrid-capture chemistry and built on at least 500 genes for the study of DNA variants and at least 55 genes for the study of RNA variants. Among the genes drawn in the panel must be present: AKT1, ALK, BRAF, DDR2, EGFR, ERBB2, FGFR1, FGFR3, KRAS, MAP2K1, MET, NRAS, PIK3CA, PTEN, RET, TP53.

- N. 3 KIT TSO500 (L): PANEL COMPATIBLE WITH THE NOVASEQ 6000 INSTRUMENT.

Estimated sample size: 150 samples approx.

As foreseen by the current projects, if the tissue is small and therefore not analyzable, the liquid biopsy (blood) on NGS method will be studied alternatively. In order therefore to make an analysis as comparable as possible between the two sources of genetic material (FFPE tissue vs. blood) it would be preferable to designate a panel of NGS on circulating tumor DNA samples (ctDNA) that also exists in the DNA version from FFPE tissue. The selected panel will evaluate the following classes of variants on ctDNA samples: single nucleotide variations (SNVs), insertions-deletions (indels), copy number variations (CNVs) and gene fusions. The panel should be based on hybrid-capture chemistry and built on at least 500 genes in order to achieve complete genomic profiling of the tumor. Among the genes drawn in the panel must be present: AKT1, ALK, BRAF, DDR2, EGFR, ERBB2, FGFR1, FGFR3, KRAS, MAP2K1, MET, NRAS, PIK3CA, PTEN, RET, TP53. In addition, it is essential to measure the immuno-oncology parameters available today, such as tumor mutation burden (TMB) and microsatellite instability (MSI).