NIH, National Cancer Institute, Division of Cancer Treatment and Diagnosis (DCTD) NIH - National Institutes of Health National Cancer Institute DCTD - Division of Cancer Treatment and Diagnosis
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Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Center Network (CIMAC-CIDC Network)

Description

This compendium contains assay SOPs and assay analytical validation/performance reports contributed by the Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Center Network (CIMAC-CIDC Network; https://dctd.cancer.gov/ResearchNetworks/cimacs_cidc_network.htm). The Network's human material transfer agreement (HMTA), covering specimen and data transfers, is also available on the CIMAC-CIDC Network website at the link above. Note: (1) For the MIBI assay, the CIMAC analytical validation report can be found at Liu CC, et al. Lab Invest. 2022 Jul;102(7) 762-770 (https://www.nature.com/articles/s41374-022-00778-8) (2) For DNA-based TCRseq, CIMACs use Adaptive Immunosequencing. (3) For cfDNA assays, CIMACs collaborate with The Broad Institute.

Sources

  • CIMAC-CIDC Network

SOPs

Title Version (Release Date) Source
CIMAC Specimen Collection Umbrella CIMAC-CIDC Network
ATACseq: ATAC epigenome profiling Analytic Validation (Stanford) CIMAC-CIDC Network
ATACseq: inTAC-Seq Protocol (Stanford) CIMAC-CIDC Network
CITE-Seq: Analytical Performance (DFCI) CIMAC-CIDC Network
CyTOF Proteomics: Analytic Validation (Stanford) CIMAC-CIDC Network
CyTOF: CIMAC CyTOF Harmonized SOP/Approach CIMAC-CIDC Network
EVP: Extracellular vesicle and particles small RNA sequencing Analytical Validation (Mt Sinai) CIMAC-CIDC Network
Grand Serology ELISA: Analytical Validation (Mt Sinai) CIMAC-CIDC Network
Grand Serology ELISA: SOP (Mt Sinai) CIMAC-CIDC Network
MALDI Glycan Analytical Validation (Stanford) CIMAC-CIDC Network
Microbiome: 16S rRNA microbiome sequencing Analytical Validation (Mt Sinai) CIMAC-CIDC Network
Microbiome: 16S rRNA with MiSeq (Mt Sinai) CIMAC-CIDC Network
Microbiome: 16S V4 ribosomal RNA (rRNA) Sequencing Analytical Validation (MD Anderson) CIMAC-CIDC Network
Microbiome: 16S V4 Sequencing SOP (MD Anderson) CIMAC-CIDC Network
Microbiome: Human Fecal Sample Collection (Cryo) (Mt Sinai) CIMAC-CIDC Network
Microbiome: Human Fecal Sample Collection (DNA) (Mt Sinai) CIMAC-CIDC Network
Microbiome: Human Microbiome Sample Aliquoting (Mt Sinai) CIMAC-CIDC Network
Microbiome: Microbiome DNA Isolation (Mt Sinai) CIMAC-CIDC Network
MICSSS: Aperio AT2 DX Leica Biosystems Slide Scanner (Mt Sinai) CIMAC-CIDC Network
MICSSS: CIMAC IHC Slide Scanner SOP (Mt Sinai) CIMAC-CIDC Network
MICSSS: Digital Image Analysis of Whole Slide Images SOP (Mt Sinai) CIMAC-CIDC Network
MICSSS: Multiplex IHC Analytical Validation (Mt Sinai) CIMAC-CIDC Network
MICSSS: Multiplex Immunohistochemical Consecutive Staining on a Single Slide (MICSSS) SOP (Mt Sinai) CIMAC-CIDC Network
Multiplex Immunofluorescence (mIF): Panel Vectra 1 and Panel Vectra 2 SOP (MD Anderson) CIMAC-CIDC Network
Multiplex Immunofluorescence (mIF): Analytical Validation for Vectra 9C (MD Anderson) CIMAC-CIDC Network
Multiplex Immunofluorescence (mIF): Immunohistochemistry (IHC) Analytical Validation (DFCI) CIMAC-CIDC Network
Multiplex Immunofluorescence (mIF): Panel Vectra 9C SOP (MD Anderson) CIMAC-CIDC Network
Multiplex Immunofluorescence (mIF): Analytical Validation for Vectra Panels 1 and 2 (MD Anderson) CIMAC-CIDC Network
Multiplex Immunofluorescence (mIF): SOP (DFCI) CIMAC-CIDC Network
NanoString nCounter: Analytical Validation (MD Anderson) CIMAC-CIDC Network
NanoString nCounter: SOP (MD Anderson) CIMAC-CIDC Network
NULISA Analytical Performance (Stanford) CIMAC-CIDC Network
Olink: Analytical Validation (Mt Sinai) CIMAC-CIDC Network
Olink: Olink Assay using Proseek Multiplex Kit SOP (Mt Sinai) CIMAC-CIDC Network
RNAscope: Analytical Validation of RNAscope Assay for Immuno-oncology Biomarker Probes (MD Anderson) CIMAC-CIDC Network
RNAscope: RNAscope In Situ Hybridization Assay SOP (MD Anderson) CIMAC-CIDC Network
RNAseq: Extraction of RNA from FFPE Tissue Sections SOP (MD Anderson) CIMAC-CIDC Network
RNAseq: RiboGreen - Detection of RNA on the BioTek Synergy Microplate Reader SOP (MD Anderson) CIMAC-CIDC Network
RNAseq: RNA Extraction from Frozen Tissue via QIAamp RNeasy Mini Kit SOP (MD Anderson) CIMAC-CIDC Network
RNAseq: RNA Sequencing Analytical Validation (MDACC) CIMAC-CIDC Network
RNAseq: RNAseq library preparation SOP (MD Anderson) CIMAC-CIDC Network
scATACseq: Single-Cell ATAC-Sequencing Analytical Performance (DFCI) CIMAC-CIDC Network
scATACseq: Single-Cell ATAC Sequencing Analytical Validation (MD Anderson) CIMAC-CIDC Network
scRNAseq / scATACseq: Nuclei Isolation for Single Cell ATAC and RNA Sequencing (Mt Sinai) CIMAC-CIDC Network
scRNAseq: Single-Cell RNA sequencing Analytical Performance (Mt Sinai) CIMAC-CIDC Network
scRNAseq: Single-Cell RNA Sequencing with TCR Enrichment Analytical Validation (MDACC) CIMAC-CIDC Network
scTCRseq and bulk TCRseq: Single-cell and bulk RNA-based TCR sequencing Analytical Validation (DFCI) CIMAC-CIDC Network
scTCRseq: Single-Cell TCRseq Analytical Validation (Stanford) CIMAC-CIDC Network
scTCRseq: Standard Operating Procedure for Single Cell TCR Sequencing (sc-rhTCRseq1) (DFCI) CIMAC-CIDC Network
Singleplex IHC: Immunohistochemistry Analytical Validation (MDACC) CIMAC-CIDC Network
Singleplex IHC: CD3 Immunohistochemistry SOP (DFCI) CIMAC-CIDC Network
Singleplex IHC: Scoring of Chromogenic IHC CD4 (+) Tumor-Infiltrating Lymphocytes (TILs) SOP (DFCI) CIMAC-CIDC Network
Spatial transcriptomics: GeoMx Digital Spatial Profiler (DSP) nCounter Protein Assay SOP (MD Anderson) CIMAC-CIDC Network
Singleplex IHC: Singleplex Chromogenic IHC SOP (MD Anderson) CIMAC-CIDC Network
Spatial transcriptomics: NanoString GeoMx Digital Spatial Profiling Analytical Validation of Immuno-oncology Protein Targets (MD Anderson) CIMAC-CIDC Network
snRNAseq: Single Nucleus RNA Sequencing Analytical Performance (DFCI) CIMAC-CIDC Network
Spatial transcriptomics: SOP For Data Management Using the GeoMx DSP Analysis Software Suite (MD Anderson) CIMAC-CIDC Network
Spatial transcriptomics: SOP for Pathological Assessment and Region of Interest Selection using the NanoString GeoMx Digital Spatial Profiler (MD Anderson) CIMAC-CIDC Network
Spatial transcriptomics: Visium Spatial RNA Sequencing Analytical Performance (Mt Sinai) CIMAC-CIDC Network
TCRseq: Repertoire TCRseq using RNA Analytical Performance (DFCI) CIMAC-CIDC Network
WES: Agilent SureSelect Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library Protocol SOP (MD Anderson) CIMAC-CIDC Network
WES: CIMAC Library Preparation Using TWIST Kit SOP (MD Anderson) CIMAC-CIDC Network
WES: Extraction of DNA from FFPE Tissue Sections SOP (MD Anderson) CIMAC-CIDC Network
WES: Manual DNA Isolation from Frozen Tissue using 50 mL Tubes and the QIAamp DNA Mini Kit SOP (MD Anderson) CIMAC-CIDC Network
WES: PicoGreen - Detection of dsDNA on the BioTek Synergy Microplate Reader SOP (MD Anderson) CIMAC-CIDC Network
WES: Whole Exome Sequencing Analytical Validation (MD Anderson) CIMAC-CIDC Network
Olink Explore HT Analytical Performance (Mt Sinai) CIMAC-CIDC Network
Single Cell RNA Multi-Omics Sequencing with TCR & BCR Repertoire Enrichment (BD Rhapsody system) Analytical Validation (Stanford) CIMAC-CIDC Network
Download all SOP documents of selected versions [68]

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