PDMR SOPs
PDM Collection and Shipping
- SOP20101: Fresh Tumor Collection and Handling for Generation of Patient-Derived Models
- SOP20102: Blood Collection and Shipping for Germline DNA Sequencing
- SOP-PDM10107: Shipping and Handling of Fresh Autopsy/Post-Mortem Specimens (non-frozen) for Generation of Preclinical Models
- SOP-PDM10108: Shipping and Handling of Viably Cryopreserved Autopsy/Post-Mortem Specimens for Generation of Preclinical Models
Patient-Derived Xenografts (PDXs)
- SOP50101: Initial Tumor Implantation (Subcutaneous) and Monitoring
- SOP50102: PDX Implantation, Expansion and Cryopreservation (Subcutaneous)
- Determine Human: Mouse Content (2011, Alcoser et al.)
- SOP-M0001: Sectioning and Staining of PDX Tissue for Histopathologic Assessment
- SOP50103: Histopathological Assessment of Patient-Derived Xenografts
Patient-Derived Tumor Cultures (PDCs) and Cancer Associated Fibroblasts (CAFs)
- SOP30101: Recipes for Complete Media for Patient-Derived In Vitro and Organoid Cultures
- SOP30102: Preparation of Coated Flasks for Adherent Patient-Derived In Vitro Cultures
- SOP30103: Initial Culture, Sub-culture, and Cryopreservation of Adherent Patient-Derived Tumor Cultures (PDCs)
- SOP30104: Initial Culture, Sub-culture, and Cryopreservation of Suspension Patient-Derived Tumor Cultures (PDCs)
- SOP30105: Initial Culture and Sub-culture of Patient-Derived Cancer-Associated Fibroblasts (CAFs)
- SOP30108: Implantation of Patient-Derived in vitro Material (2D and 3D cell cultures) for Generation of Cell Line Xenografts (CLXs)
Patient-Derived Organoid Cultures (PDOrgs)
- SOP30101: Recipes for Complete Media for Patient-Derived In Vitro and Organoid Cultures
- SOP30108: Implantation of Patient-Derived in vitro Material (2D and 3D cell cultures) for Generation of Cell Line Xenografts (CLXs)
- SOP40102: Thawing and Initial Culture of Patient-Derived Organoid (PDOrg) Cultures
- SOP40103: Passaging and Sub-culture of Patient-Derived Organoid (PDOrg) Cultures
- SOP40104: Cryopreservation of Patient-Derived Organoid (PDOrg) Cultures
PDMR Genomics
- Host-mouse Reference Sequence — *.vcf file (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ)
- README file: Lists previously posted sequence files that should be removed from any subsequent analysis
- MCCRD-SOP0059: PDMR NextGen Sequence Filename and Versioning Structure
- MCCRD-SOP0002: Purification of Genomic DNA and Total RNA Tumor Tissue Using Qiagen AllPrep DNA/RNA Mini Kit
- MCCRD-SOP0053: Annotation of Variants from Whole Exome Assay with OncoKB
- MCCRD-SOP0005: SureSelectXT Automated Target Enrichment for Illumina Paired-End Sequencing Library
- MCCRD-SOP0006: Automated RNASeq Library Preparation using Illumina’s TruSeq RNA Access Library for Illumina Paired-End Sequencing
- MCCRD-SOP0007: Illumina Sequencing Library Quantitation using Droplet Digital PCR (ddPCR) Protocol
- MCCRD-SOP0008: Denaturing and Diluting Sequencing Library Pools and Cluster Generation Protocol
- MCCRD-SOP0009: Illumina Sequencing Library Pools on a HiSeq 2500
- MCCRD-SOP0009: Illumina Sample Sheet (CSV file)
- MCCRD_SOP0011: Whole Exome Sequencing Data Analysis Pipeline and Specifications
- MCCRD_SOP0012: RNASeq Transcriptome Data Analysis Pipeline and Specifications
- MCCRD-SOP: Generating Consensus VCF and MAF Files at the Model Level
- MCCRD-SOP0023: KAPA Hyper Low Input Whole Exome Library Construction
- MCCRD-SOP0057: Detection of Microsatellite Instability (MSI) Status from Whole Exome Sequencing Data
- MCCRD-SOP0058: Individual Ancestry Estimation from Whole Exome Sequencing Data
- MCCRD-SOP0063: Detection of Consensus Molecular Subtype (CMS) Classification of Colorectal Cancer from RNASeq Data
- MCCRD-SOP0064: Detection of Human Leukocyte Antigen (HLA) Typing from Whole Exome Sequencing Data