Table 6.
Summary of sample outcomes for genotyping projects, by network and overall, T1DGC, July 4, 2009
| Asia-Pacific N (%) | European N (%) | North American N (%) | United Kingdom N (%) | Total N (%) | |
|---|---|---|---|---|---|
| 6K Genome scan (CIDR) | |||||
| N | 1338 | 4741 | 4813 | 631 | 11,523 |
| MIEs | 7 (0.5) | 32 (0.7) | 27 (0.6) | 2 (0.3) | 68 (0.6) |
| Failures | 8 (0.6) | 28 (0.6) | 65 (1.4) | 10 (1.6) | 111 (1.0) |
| Gender discrepancies | 2 (0.1) | 7 (0.1) | 2 (0.0) | 0 (0.0) | 11 (0.1) |
| Sample switches | 16 (1.2) | 12 (0.3) | 40 (0.8) | 0 (0.0) | 68 (0.6) |
| Replacements | 9 (0.7) | 66 (1.4) | 109 (2.3) | 13 (2.1) | 197 (1.7) |
| MHC fine mapping (The Wellcome Trust Sanger Institute) | |||||
| N | 782 | 1953 | 1373 | 484 | 4592 |
| MIEs | 4 (0.5) | 13 (0.7) | 17 (1.2) | 6 (1.2) | 40 (0.9) |
| Failures – OPA1 | 5 (0.6) | 15 (0.8) | 14 (1.0) | 4 (0.8) | 38 (0.8) |
| Failures – OPA2 | 6 (0.8) | 3 (0.2) | 9 (0.7) | 14 (2.9) | 32 (0.7) |
| Failures – microsatellites | 13 (1.6) | 38 (1.9) | 20 (1.5) | 12 (2.5) | 83 (1.8) |
| Gender discrepancies | 0 (0.0) | 0 (0.0) | 0 (0.0) | 2 (0.4) | 2 (0.0) |
| Sample switches | 4 (0.5) | 6 (0.3) | 6 (0.4) | 2 (0.4) | 18 (0.4) |
| Replacements | 18 (2.3) | 29 (1.5) | 39 (2.8) | 31 (6.4) | 117 (2.5) |
| Rapid response (The Broad Institute) | |||||
| N | 782 | 1953 | 1376 | 484 | 4595 |
| MIEs | 5 (0.6) | 13 (0.7) | 9 (0.7) | 8 (1.7) | 35 (0.8) |
| Failures – llumina | 19 (2.4) | 12 (0.6) | 53 (3.9) | 42 (8.7) | 126 (2.7) |
| Failures – Sequenom | 26 (3.3) | 55 (2.8) | 75 (5.5) | 25 (5.2) | 181 (3.9) |
| Gender discrepancies | 0 (0.0) | 0 (0.0) | 1 (0.1) | 2 (0.4) | 3 (0.1) |
| Sample switches | 2 (0.3) | 6 (0.3) | 8 (0.6) | 0 (0.0) | 16 (0.3) |