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), which was established as part of the Cancer Moonshot Initiative. 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.

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
CyTOF Proteomics: Analytic Validation (Stanford) CIMAC-CIDC Network
CyTOF: CIMAC CyTOF Harmonized SOP/Approach CIMAC-CIDC Network
Grand Serology ELISA: Analytical Validation (Mt Sinai) CIMAC-CIDC Network
Grand Serology ELISA: SOP (Mt Sinai) CIMAC-CIDC Network
Microbiome: 16S rRNA microbiome sequencing Analytical Validation (Mt Sinai) CIMAC-CIDC Network
Microbiome: 16S V4 ribosomal RNA (rRNA) Sequencing Analytical Validation (MD Anderson) 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 Immunfluorescence (mIF): SOP (MD Anderson) CIMAC-CIDC Network
Multiplex Immunofluorescence (mIF): Analytical Validation for vectra 9C (MDACC) CIMAC-CIDC Network
Multiplex Immunofluorescence (mIF): SOP (DFCI) CIMAC-CIDC Network
Multiplex Immunofluorescence (mIF): Analytical Validation (MD Anderson) CIMAC-CIDC Network
NanoString nCounter: Analytical Validation (MD Anderson) CIMAC-CIDC Network
NanoString nCounter: SOP (MD Anderson) CIMAC-CIDC Network
Olink: Analytical Validation (Mt Sinai) CIMAC-CIDC Network
Olink: Olink Assay using Proseek Multiplex Kit SOP (Mt Sinai) 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: RNAseq library preparation SOP (MD Anderson) CIMAC-CIDC Network
scATACseq: Single-Cell ATAC Sequencing Analytical Validation (MD Anderson) CIMAC-CIDC Network
scRNAseq: Single-Cell RNA Sequencing with TCR Enrichment Analytical Validation (MDACC) CIMAC-CIDC Network
scRNAseq: Single-Cell RNA sequencing Analytical Performance (Mt Sinai) CIMAC-CIDC Network
scTCRseq and bulk TCRseq: Single-cell and bulk RNA-based TCR sequencing Analytical Validation (DFCI) CIMAC-CIDC Network
Singleplex IHC: CD3 Immunohistochemistry SOP (DFCI) CIMAC-CIDC Network
Singleplex IHC: Scoring of Chromogenic IH CD4 (+) Tumor-Infiltrating Lymphocytes (TILs) SOP (DFCI) CIMAC-CIDC Network
Singleplex IHC: Singleplex Chromogenic IHC SOP (MD Anderson) CIMAC-CIDC Network
Spatial transcriptomics: NanoString GeoMx Digital Spatial Profiling Analytical Validation of Immmuno-oncology Protein Targets (MDACC) 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
Download all SOP documents of selected versions [40]

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