Cohorts and sequencing characteristics
| Parameter . | Discovery cohort . | MS twin cohort . | Validation cohort . | ||||
|---|---|---|---|---|---|---|---|
| Name | COVID-19 | HD | MS | HD | MS | Control | MS |
| Data source | Data from Snyder et al. (2020) | Previously unpublished data | |||||
| Assay | immunoSEQ | immunoPETE | |||||
| Number of individuals | 607 | 229 | 1,336 | 35 | 35 | 51 | 59 |
| HLA | Imputed | Typed | Typed | Typed | Typed | Imputed | Imputed |
| Sequencing depth | 391,829 (182,941) | 564,815 (148,717) | 380,234 (171,527) | 670,874 (183,708) | 616,687 (209,577) | 42,759 (14,585) | 41,737 (12,769) |
| [Productive templates per sample] | [Input α β T cells per sequencing pool] | ||||||
| Age (yr) | 61 (18) | 52 (17) | 37 (9) | 40 (11) | 40 (11) | 45 (14) | 41 (10) |
| Sex (female) | 54.1% | 51.1% | 75.7% | 80.0% | 80.0% | 52.4% | 64.6% |
| Details of the HLA-A*02–positive subcohort | |||||||
| Number of HLA-A*02–positive individuals | 278 | 62 | 430 | 27 | 25 | ||
| Anti–VLA-4: untreated/treated | 248/73 | 33/2 | 17/8 | ||||
| IFNβ: treatment-naive/treated | 29/123 | 10/10 | |||||
| Anti-CD20: before/after treatment | 34/1 | 14/14 | |||||
| Vaccination: before/after | 5/5 | ||||||
| Parameter . | Discovery cohort . | MS twin cohort . | Validation cohort . | ||||
|---|---|---|---|---|---|---|---|
| Name | COVID-19 | HD | MS | HD | MS | Control | MS |
| Data source | Data from Snyder et al. (2020) | Previously unpublished data | |||||
| Assay | immunoSEQ | immunoPETE | |||||
| Number of individuals | 607 | 229 | 1,336 | 35 | 35 | 51 | 59 |
| HLA | Imputed | Typed | Typed | Typed | Typed | Imputed | Imputed |
| Sequencing depth | 391,829 (182,941) | 564,815 (148,717) | 380,234 (171,527) | 670,874 (183,708) | 616,687 (209,577) | 42,759 (14,585) | 41,737 (12,769) |
| [Productive templates per sample] | [Input α β T cells per sequencing pool] | ||||||
| Age (yr) | 61 (18) | 52 (17) | 37 (9) | 40 (11) | 40 (11) | 45 (14) | 41 (10) |
| Sex (female) | 54.1% | 51.1% | 75.7% | 80.0% | 80.0% | 52.4% | 64.6% |
| Details of the HLA-A*02–positive subcohort | |||||||
| Number of HLA-A*02–positive individuals | 278 | 62 | 430 | 27 | 25 | ||
| Anti–VLA-4: untreated/treated | 248/73 | 33/2 | 17/8 | ||||
| IFNβ: treatment-naive/treated | 29/123 | 10/10 | |||||
| Anti-CD20: before/after treatment | 34/1 | 14/14 | |||||
| Vaccination: before/after | 5/5 | ||||||
Given values are mean (SD) for scalar variables and n (%) for categorical variables.