Integrated CITI Platforms : Immunomonitoring/Discovery/Computational

RNA isolation from fresh tissue/PBMC

STAR alignment to reference genome, Pre/Post alignment QC collection, raw and normalized read counts over genes.

Add DNA fingerprinting to post-alignment QC report to ensure matching Tumor and Normal samples. Can be applied to WES/WGS.

Gene set enrichment analysis (GSEA) and pathway analysis and xCell Deconvolution (tumor samples only) for 64 Immune cell types. 

Includes standard Seurat pipeline, generating Integrated Seurat Object and automated cell typing.

Somatic or germline variant calling and annotation (SNV/INDELS), Allele Specific Copy Number calling, Microsatellite instability (MSI).

Standard Cell Ranger pipeline, Loupe objects per sample and per project, Pre/Post alignment QC metrics collection.

T-cell/Antibody Immune Repertoires Analysis. Data normalization, CDR3 identification, clonal dynamics, and repertoire features such as diversity and Shannon metrics. We will need to discuss metadata, comparison, and other parameters prior to analysis. For TCR Sequencing, please consult with Discovery Lab.

Differential gene expression as specified by users. Users are expected to provide metadata files according to provided templates.

Uploading genomics data we have processed/analyzed to SRA, dbGAP or GEO data repositories for publication.

Alignment to reference and Pre/Post alignment QC collection.

The HLA sequencing service permits investigators to characterize and identify HLA genotypes for research use only.

Data output uses CareDx's AlloSeq Assign software.

https://caredx.com/products-and-services/transplant-lab-products/hla-typing-solutions/alloseq-tx/

Deep (up to 800,000 cells)

Survey (up to 400,000 cells)

• Myeloid HLA-DR, CD16, CD80, CD86, CD206, PDL1, CD11b, CD56, CD19, CD14, CD163, CCR2, Vista CX3CR1, CD15, HIF1a, ARG, CD68, CD123, NFkb/p65, CD33, CD11c, CD3

• T cell Exhaustion CCR7, CD3, CD4, CD27, CD8, STAT3s727, CD45RO, CD45RA, Lag3, TIM-3,PD-1, CTLA4), TIGIT, Vista, TOX, pSTAT5y694, CD19, IRF4, BLIMP1, BATF

• T cells CCR7, CD3, CD4, CD27, CD8, CD25, RORgt, CD45RO, CD45RA, TBET, CD95, PD1, CD127, BCL2, EOMES, GATA3, IRF4, IFNg, pan TCRgd, FOXP3

Use Miltenyi Mouse Tissue Dissociation Kit

Single cell CITE-Seq (capture, library prep and sequencing)

CD45 PDL1 CD11c Anti-Mouse I-A/I-E CD25 Ly6G CCR2 CD8 CD11b CXCR2 CD4 PD1 F4/80 CD127

• PDL-1 PD1, CD33, HLA-DR, CD14, CD15, PDL1

• T cells CD8, CD4, PD1

• Vista CD33, HLA-DR, CD11b, CD14, CD15, Vista

• NK cells NK 1.1, CD3, DNAM-1, CD11b, CD27

• CD8: T_reg ratio CD3, CD4, CD25, Foxp3, CD73, PD-1, Lag3, Tim3, CD8

• Myeloid Lin, CD33, HLA-DR, CD11b, CD14, CD15, Lox1
• T_reg CD4, CD25, CD127

• https://www.olink.com/products/

• https://www.olink.com/products/

Pricing will vary depending on number of cases

Use Miltenyi Mouse Tissue Dissociation Kit

RNA isolation from fresh tissue/PBMC

Single cell CITE-Seq (capture, library prep and sequencing)

CD45 PDL1 CD11c Anti-Mouse I-A/I-E CD25 Ly6G CCR2 CD8 CD11b CXCR2 CD4 PD1 F4/80 CD127

• Myeloid Lin, CD33, HLA-DR, CD11b, CD14, CD15, Lox1
• T_reg CD4, CD25, CD127

• PDL-1 PD1, CD33, HLA-DR, CD14, CD15, PDL1

• T cells CD8, CD4, PD1

• Vista CD33, HLA-DR, CD11b, CD14, CD15, Vista

• NK cells NK 1.1, CD3, DNAM-1, CD11b, CD27

• CD8: T_reg ratio CD3, CD4, CD25, Foxp3, CD73, PD-1, Lag3, Tim3, CD8

• Myeloid HLA-DR, CD16, CD80, CD86, CD206, PDL1, CD11b, CD56, CD19, CD14, CD163, CCR2, Vista CX3CR1, CD15, HIF1a, ARG, CD68, CD123, NFkb/p65, CD33, CD11c, CD3

• T cells CCR7, CD3, CD4, CD27, CD8, CD25, RORgt, CD45RO, CD45RA, TBET, CD95, PD1, CD127, BCL2, EOMES, GATA3, IRF4, IFNg, pan TCRgd, FOXP3

• T cell Exhaustion CCR7, CD3, CD4, CD27, CD8, STAT3s727, CD45RO, CD45RA, Lag3, TIM-3,PD-1, CTLA4), TIGIT, Vista, TOX, pSTAT5y694, CD19, IRF4, BLIMP1, BATF

• https://www.olink.com/products/

• https://www.olink.com/products/

Pricing will vary depending on number of cases

The HLA sequencing service permits investigators to characterize and identify HLA genotypes for research use only.

Data output uses CareDx's AlloSeq Assign software.

https://caredx.com/products-and-services/transplant-lab-products/hla-typing-solutions/alloseq-tx/

Deep (up to 800,000 cells)

Survey (up to 400,000 cells)

STAR alignment to reference genome, Pre/Post alignment QC collection, raw and normalized read counts over genes.

Differential gene expression as specified by users. Users are expected to provide metadata files according to provided templates.

Gene set enrichment analysis (GSEA) and pathway analysis and xCell Deconvolution (tumor samples only) for 64 Immune cell types. 

Alignment to reference and Pre/Post alignment QC collection.

Add DNA fingerprinting to post-alignment QC report to ensure matching Tumor and Normal samples. Can be applied to WES/WGS.

Somatic or germline variant calling and annotation (SNV/INDELS), Allele Specific Copy Number calling, Microsatellite instability (MSI).

Standard Cell Ranger pipeline, Loupe objects per sample and per project, Pre/Post alignment QC metrics collection.

Includes standard Seurat pipeline, generating Integrated Seurat Object and automated cell typing.

T-cell/Antibody Immune Repertoires Analysis. Data normalization, CDR3 identification, clonal dynamics, and repertoire features such as diversity and Shannon metrics. We will need to discuss metadata, comparison, and other parameters prior to analysis. For TCR Sequencing, please consult with Discovery Lab.

Uploading genomics data we have processed/analyzed to SRA, dbGAP or GEO data repositories for publication.