Table 1.
Genotype calls by GtTR using NA12878 Pacbio reference on targeted capture sequencing data compared with PCR sizing analysis
| Sample | Methoda | Target | Correlation | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| VNTR_8 | VNTR_32 | VNTR_57 | VNTR_86 | VNTR_87 | VNTR_93 | VNTR_109 | VNTR_112 | VNTR_120 | |||
| NA12877 | PCR | 12.5 | 21.8 | 12.1 | 2.0 | 7.0 | 2.0 | 16.0 | 3.4 | 2.0 | 0.9762 |
| Capture_Seq | 11.5 | 28.4 | 13.5 | 2.7 | 6.1 | 2.1 | 16.2 | 3.7 | 3.4 | ||
| 95% HPD interval | (10.2–12.8) | (18.8–38) | (11.9–15.2) | (2.07–3.33) | (5.43–6.7) | (1.76–2.52) | (14.4–18) | (3–4.35) | (2.41–4.38) | ||
| NA12878b | PCR | 12.0 | 9.5 | 11.6 | 2.0 | 7.5 | 2.0 | 16.0 | 3.4 | 2.0 | 0.9930 |
| Capture_Seq | 12.1 | 9.9 | 13.5 | 2.6 | 7.8 | 2.3 | 17.6 | 3.8 | 3.5 | ||
| 95% HPD interval | (10.9–13.3) | (5.5–14.7) | (12.1–15) | (2.12–3.14) | (7.1–8.41) | (1.97–2.69) | (16–19.2) | (3.19–4.35) | (2.64–4.36) | ||
| PacBio WGS c | 12.0 | 11.9 | 11.6 | 2.5 | 7.5 | 2.0 | 16.3 | 3.5 | 3.2 | ||
| NA12879 | PCR | 12.5 | 9.8 | 10.5 | 2.0 | 8.5 | 2.0 | 16.0 | 2.9 | 2.0 | 0.9738 |
| Capture_Seq | 12.6 | 11.7 | 14.4 | 2.6 | 8.2 | 2.0 | 16.3 | 3.2 | 3.0 | ||
| 95% HPD interval | (11.3–14) | (6–17.4) | (12.8–16) | (2.09–3.18) | (7.44–8.92) | (1.65–2.32) | (14.6–17.9) | (2.68–3.8) | (2.12–3.81) | ||
| NA12889 | PCR | 12.0 | 22.3 | 15.6 | 2.0 | 8.0 | 2.0 | 16.9 | 3.9 | 2.0 | 0.9871 |
| Capture_Seq | 11.1 | 27.0 | 20.3 | 2.2 | 7.7 | 2.2 | 21.3 | 4.1 | 3.4 | ||
| 95% HPD interval | (9.97–12.3) | (18.5–35.5) | (18.3–22.4) | (1.73–2.63) | (7.01–8.36) | (1.8–2.5) | (19.4–23.2) | (3.45–4.68) | (2.55–4.33) | ||
| NA12890 | PCR | 12.5 | 9.7 | 10.5 | 2.0 | 7.5 | 2.0 | 15.1 | 2.9 | 2.0 | 0.9853 |
| Capture_Seq | 13.5 | 10.3 | 11.6 | 2.2 | 7.2 | 2.2 | 13.4 | 3.1 | 3.0 | ||
| 95% HPD interval | (12.1–14.9) | (5.01–15.6) | (10.2–13) | (1.79–2.72) | (6.52–7.87) | (1.85–2.58) | (12–14.8) | (2.52–3.62) | (2.13–3.85) | ||
| NA12891 | PCR | 12.5 | 9.3 | 10.6 | 2.0 | 7.0 | 2.0 | 15.1 | 2.9 | 2.0 | 0.9882 |
| Capture_Seq | 11.7 | 10.4 | 12.1 | 2.6 | 6.8 | 2.1 | 16.2 | 3.1 | 3.5 | ||
| 95% HPD interval | (10.6–12.8) | (5.87–14.9) | (10.8–13.3) | (2.14–3.08) | (6.23–7.36) | (1.79–2.42) | (14.8–17.6) | (2.61–3.52) | (2.65–4.25) | ||
| NA12892 | PCR | 12.5 | 9.8 | 12.6 | 2.0 | 9.0 | 2.0 | 16.9 | 3.9 | 2.0 | 0.9833 |
| Capture_Seq | 11.0 | 8.8 | 12.9 | 3.0 | 8.4 | 2.3 | 18.3 | 4.0 | 3.4 | ||
| 95% HPD interval | (9.85–12.2) | (3.88–13.8) | (11.4–14.3) | (2.36–3.58) | (7.63–9.1) | (1.93–2.7) | (16.5–20.1) | (3.33–4.6) | (2.43–4.27) | ||
aValues for ‘PCR’ refers to the average number of repeats from the two alleles and the values for ‘Capture-Seq’ refers to the genotype estimates determined by the GtTR algorithm
bNA12878 sample is independent to the sample which was used as a reference sample for RCN analysis
cGenotype estimates from PacBio WGS on NA12878 sample included for comparison