Virtual Tissue Repository

3.1Obtain the necessary ethical and regulatoryapprovals and documentation relevant to this TO 3.1.1 Submit the VTR pilot Breast cancer genomic protocol and amendments to PDAC genomic protocol to a local IRB 3.1.2 Obtain IRB approval 3.1.3 Execute relevant Material Transfer Agreement(s) (MTA) if applicable 3.2 Document experience obtained through the VTR pilot 3.2.1 Complete a templated form provided by NCI 3.3Provide recommendations for the scaled SEER-linked VTR 3.3.1 Complete a questionnaire provided by NCI 3.4 Assess new BC subjects for the ongoing study of unusual survivaloutcomes in early stage BC The specific BC subjects will be provided by NCI. Currently 76 new BC subjects are eligible at the SEER Kentucky registry. The actual number may vary depending on the attrition rate across all participating registries. The subjects’ selection and matching criteria and details on subjects’ assessment are outlined in the Breast Cancer genomic protocol. For these subjects, the contractor shall: 3.4.1 Retrieve, de-identify, and submit to NCI via the VTR pilot portal all pathology reports for the subjects requested by NCI, if available at the registry or medical facilities within registry’s study catchment area 3.4.2 Determine if subject tissue stored at local pathology laboratories or off- site is available for research. The determination will be based on surgical pathology report availability, whether resection specimen is located in a laboratory within registry catchment area, and whether laboratory releases specimens for research, and other known factors that affect eligibility (such as neoadjuvant therapy). 3.4.3 Abstract relevant clinical data from medical records for subjects with available tissue using SEER*Abs software and the VTR coding manual (located on the VTR pilot portal). Note: Acceptance of data is subject to quality review by NCI, and corrections of data are to be made at no additional cost to the Government 3.5 Processing of biospecimens for the BCstudy. The specific BC subjects eligible for the genomic studies will be provided by NCI. Currently 91 BC subjects (new subjects and subjects from the previous VTR pilot TO) are estimated to be eligible for biospecimen processing at the SEER Kentucky registry. However, the actual number is expected to vary depending on the attrition rate across all registries. Details on biospecimen processing are outlined in the BC biospecimen processing manual (provided separately to the participating registries). 3.5.1 Request biospecimens from local pathology laboratories for subjects specified by NCI and track specimens in BSI from time of request until arrival in the NCI designated laboratory; 3.5.2 Pathologist review of BC subjects’ slides. A local pathologist, selected by the registry, will review the diagnostic slides to confirm histology and will select the most appropriate blocks with tumor and normal tissue for biospecimens processing as outlined in the BC Biospecimen Processing Manual. 3.5.3 Retrieval of formalin-fixed, paraphing embedded (FFPE) tissue blocks (2-3 blocks per subject) selected by a local pathologist in item3.5.2. 3.5.4 Biospecimen processing per BC genomic protocol and BC Biospecimen Processing Manual. Optimal amount of tissue per subject for the BC genomic studies is up to 4 H&E slides and 20 positively charged unstained slides prepared from normal and tumor tissue, with a minimum of 2 H&E slides and 10 positively charged unstained slides, as specified in the Biospecimen Processing Manual 3.5.5 For BC subjects for whom HER2 status is unknown, provide 2 additional positively charged unstained slides of 5 ìm tissue thickness. 3.5.6 Ship biospecimens for the BC genomic study to NCI designated laboratory. 3.5.7 If slides are lost or damaged during shipping or if an expert BC pathologist deems the slides to be inadequate, provide tissue slides from an additional block as specified in the Biospecimen Processing Manual. 3.5.8 The Contractor shall secure specimen pending destruction by collecting and storing the specimen for all subjects on their new subject’s manifest as well as for those requested through BSI. For details on specimen request, inventory intake and storage please refer to biospecimen processing manual. 3.6 Assess new PDAC subjects for the ongoing PDAC study. The specific subjects will be provided by NCI. Currently 3 new PDAC subjects are eligible at the SEER Kentucky registry. The actual number may vary depending on the attrition rate across all participating registries. These subjects are matched control 2 subjects who were not requested in the previous TO. These subjects are being requested because the matched control 1 subjects failed (for example, tissue was not available or was deemed to be not eligible per the Biospecimen Processing Manual). 3.6.1 Retrieve, de-identify, and submit to NCI all pathology reports for the subjects requested by NCI if available at the registry or medical facilities within registry’s study catchment area via the VTRPortal. 3.6.2 Determine if tissue stored at local pathology laboratories or off-site is available for research. The determination will be based on surgical pathology report availability, whether resection specimen is located in a laboratory within the registry’s catchment area, whether laboratory releases specimens for research, and other known factors that affect eligibility (such as neoadjuvant therapy). 3.6.3 Abstract relevant clinical data from medical records for subjects with available tissue using SEER*Abs software and the VTR coding manual (located on the VTR pilot portal). Note. Acceptance of data is subject to quality review by NCI, and corrections of data are to be made at no additional cost to the Government 3.7 Processing of biospecimen for the PDAC study. 3.7.1 The specific PDAC subjects eligible for the genomic studies will be provided by NCI. Currently 63 PDAC subjects are estimated to be eligible for biospeciemen processing at the SEER Kentucky registry. The actual number may vary depending on the attrition rate across all participating registries. Details on biospecimen processing are outlined in the attached PDAC Biospecimen Processing Manual. 3.7.2 Request biospecimens from local pathology laboratories for subjects specified by NCI and track specimens in BSI from time of request until arrival in the testing laboratory; 3.7.3 Pathologist’s review of PDAC subjects’ diagnostic slides. A local pathologist, selected by the registry, will review the diagnostic slides to confirm histology and will select the most appropriate blocks for biospecimen processing as outlined in the PDAC biospecimen processing manual. 3.7.4 Retrieval of formalin-fixed, paraffin-embedded (FFPE) tissue blocks (2-3 blocks per subject) selected by a local pathologist in item 3.7.2. 3.7.5 Biospecimen processing per PDAC genomic protocol and PDAC Biospecimen Processing Manual. Optimal amount of tissue per subject is up to 4 H&E slides and 20 positively charged unstained slides prepared from normal and tumor tissue, with a minimum of 2 H&E slides and 10 positively charged unstained slides. 3.7.6 Ship PDAC biospecimens to a central laboratory designated by NCI. 3.7.7 If slides are lost or damaged during shipping or if an expert PDAC pathologist deems the slides to be inadequate, provide tissue slides from an additional block(s) as specified in the Biospecimen ProcessingManual. 3.7.8 The Contractor shall secure specimen pending destruction by collecting and storing the specimen for all subjects on their new subject’s manifest as well as for those requested through BSI. For details on specimen request, inventory intake and storage please refer to biospecimen processing manual. 3.8 Sharing the data acquired through the VTR Pilot for research KCR agrees that controlled access to all de-identified data collected through this project will be provided to the research community to be used for biomedical research. NCI will make the genomic and clinical data, and digitally scanned H&E slides collected through this project available for research through the National Cancer Institute’s (NCI) Genomic Data Commons (GDC) and/or the National Library of Medicine’s (NLM) Database of Genotypes and Phenotypes (dbGAP). Providing data for research is consistent with Article H.23 “Sharing Research Data” of the base contract. Additionally, data sharing is mandated by the National Institute of Health’s (NIH) Genomic Data Sharing policy for all research funded in full or partially by NIH. 3.8.1 Execute relevant Institution Certification(s) for sharing and releaseof genomic data