Table 1 Summary of methodology used by clinical TCR profiling studies
From: Sequence analysis of T-cell repertoires in health and disease
Disease | Patients | Controls/comparison | Sample | Platform | Sequencing depth | Diversity metric | References |
|---|---|---|---|---|---|---|---|
Hematological malignancy | Post-HSCT (n = 28) | Healthy donors | RNA from PBMCs | 454 (Roche) | Variable | Inverse Simpson's diversity index (1/Ds) | [34] |
Post-HSCT GI GVHD | Steroid refractory (n = 7) | Steroid responsive (n = 8) | DNA from PBMCs and GI biopsy | GA IIx or MiSeq (Illumina) | 103-106 | Bhattacharyya coefficient and Gini coefficient | [36] |
Post-HSCT pediatric neuroblastoma | Early T-cell infusion (n = 32) | Late T-cell infusion (n = 12) | DNA from PBMCs | ImmunoSeq (Illumina Platform) | Not reported | Number of clones and Vβ gene usage | [75] |
Ankylosing spondylitis | Post-HSCT (n = 1) | Pre-HSCT (n = 1; same patient) | RNA from PBMCs | 454 GS FLX (Roche) | Not reported | Number of clones and Vβ gene usage | [38] |
Rheumatoid arthritis | Recent onset (n = 6) | Established (n = 6) | RNA from synovium and PBMCs | 454 GS FLX Titanium (Roche) | >6 × 104 reads per sample | Frequency distribution | [40] |
CMV and EBV infection | Kidney transplant (n = 2) | EBV+/CMV+ donors (n = 5) | RNA from PBMCs | 454 GS FLX Titanium (Roche) | >104 reads per sample | Frequency distribution | [76] |
Recurrent HSV-2 Infection | Comparison of samples from various infection sites and times, and PBMCs in n = 1 individual | DNA from skin biopsy and PBMCs | HiSeq (Illumina) | Not reported | Frequency distribution | [77] | |
TALL | Post-treatment (n = 43) | Pre-treatment (n = 43) and healthy donors (n = 6) | DNA from bone marrow and PBMCs | HiSeq (Illumina) | Not reported | Frequency distribution | [41] |