Immune Profiling¶

OptiType (HLA Types)¶

{
    "hlaTypes": [
        {
            "pathology": "normal",
            "protocol": "DNA",
            "a1": "A*02:03",
            "a2": "A*11:01",
            "b1": "B*40:01",
            "b2": "B*38:02",
            "c1": "C*07:02",
            "c2": "C*07:02"
        }
    ]
}

Field	Type	Example	Description
a1	`string`	`"A*02:03"`
a2	`string`	`"A*11:01"`
b1	`string`	`"B*40:01"`
b2	`string`	`"B*38:02"`
c1	`string`	`"C*07:02"`
c2	`string`	`"C*07:02"`
pathology	`string`	`"normal"`	the disease state of this sample
protocol	`string`	`"DNA"`	the sequencing protocol used for ths sample

Cibersort (Immune Cell Types)¶

Cibersort publication

{
    "immuneCellTypes": {
        "cellType": "combined T cell",
        "kbCategory": "moderate",
        "score": 76,
        "percentile": 50
    }
}

Field	Type	Example
cellType (required)	`string`	`"combined T cell"`
kbCategory	`string`	`"moderate"`
percentile	`number`	`50`
score	`number`	`76`

Example cell type values are

B cells naive
B cells memory
Plasma cells
T cells CD8
T cells CD4 naive
T cells CD4 memory resting
T cells CD4 memory activated
T cells follicular helper
T cells regulatory (Tregs)
T cells gamma delta
NK cells resting
NK cells activated
Monocytes
Macrophages M0
Macrophages M1
Macrophages M2
Dendritic cells resting
Dendritic cells activated
Mast cells resting
Mast cells activated
Eosinophils
Neutrophils
T.cell.inflitration

Cibersort Images¶

Info

These will be passed to the report upload function via the images section of the JSON input

key: cibersort.cd8_positive_t-cell_scatter

cd8+ T-cell scatter plot

key: cibersort.combined_t-cell_scatter

combined T-cell scatter plot

MiXCR¶

Info

These will be passed to the report upload function via the images section of the JSON input

MiXCR Publication

key: mixcr.circos_trb_vj_gene_usage

mixcr circos

key: mixcr.dominance_vs_alpha_beta_t-cells_scatter

mixcr dominance