Test

Keith T. Smith,\({}^{1}\) A. N. Other,\({}^{2}\) and Third Author\({}^{2,3}\)
\({}^{1}\)Affiliation 1
\({}^{2}\)Affiliation 2
\({}^{3}\)Affiliation 3

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Figure 1 Pollock 2014

Tables

\label{tab:2}Cross-validation accuracy. The percentage of correctly imputed two-field alleles is shown for each method at each HLA locus in each of four major populations from the cross-validation analysis with the multi-population reference panel. The number of individuals used for validation in each population at each HLA locus is also shown. *Method does not support this locus.
No. validation Method
Population HLA locus individuals HIBAG HLA*IMP:02 HLA*IMP:03 SNP2HLA
African-American / A 203 94.1 92.9 95.1 88.1
African B 235 88.3 85.1 90.0 77.4
C 203 93.3 92.4 94.6 79.8
DQA1 355 97.5 94.8 96.3 77.6
DQB1 531 85.2 82.8 86.0 63.0
DRB1 550 91.8 89.8 94.9 90.0
DRB3 338 * 95.6 99.0 *
DRB4 337 * 98.2 99.4 *
DRB5 342 99.1 99.4 99.6 *
Asian A 749 86.2 91.5 92.6 88.9
B 852 89.9 86.2 91.6 85.8
C 759 97.8 96.6 97.7 86.7
DPA1 452 99.3 99.1 99.3 91.5
DPB1 452 88.4 89.0 89.3 83.6
DQA1 487 96.6 96.1 97.4 84.8
DQB1 767 86.7 86.0 88.2 72.4
DRB1 845 87.8 86.8 91.2 88.4
DRB3 12 * 87.5 100.0 *
DRB4 11 * 100.0 100.0 *
DRB5 14 100.0 100.0 100.0 *
Europeans A 6,685 97.7 97.6 97.7 96.4
B 7,999 95.8 94.2 95.7 93.7
C 6,642 98.3 98.1 98.2 94.0
DPA1 5,615 99.7 99.7 99.9 97.5
DPB1 5,686 95.0 95.1 95.6 92.5
DQA1 5,899 99.3 98.8 99.3 91.4
DQB1 7,325 98.0 97.1 98.0 88.2
DRB1 7,918 94.1 93.6 95.0 94.2
DRB3 165 * 96.7 98.5 *
DRB4 197 * 97.5 99.2 *
DRB5 217 99.5 99.8 99.5 *
Latino A 217 91.5 92.4 92.4 89.4
B 350 78.3 73.6 78.9 70.7
C 220 96.1 94.5 96.4 90.2
DPB1 26 84.6 86.5 86.5 82.7
DQA1 42 100.0 98.8 98.8 84.5
DQB1 232 91.6 90.5 94.4 81.0
DRB1 339 83.9 82.2 88.8 84.4
DRB3 23 * 93.5 97.8 *
DRB4 11 * 100.0 100.0 *
DRB5 33 100.0 100.0 100.0 *
\label{tab:1}Summary of HLA reference panel. For each HLA locus the table displays: the number of individuals typed at two-fields in each dataset (CEU+58, GSK, YRI, 1000G, T1DGC, KC, PA, SW) and in total; the number of SNPs in the xMHC for the dataset formed by merging all individuals typed at that HLA locus; and the number of two-field alleles present in the dataset. MIM number – Mendelian Inheritance in Man number. HLA-DRB4 does not have a MIM number; the HUGO Gene Nomenclature Committee (HGNC) ID is given instead.
HLA locus A B C DQA1 DQB1 DRB1 DRB3 DRB4 DRB5 DPA1 DPB1
MIM number or HGNC ID 142800 142830 142840 146880 604305 142857 612735 HGNC:4952 604776 142880 142858
No. individuals in each dataset
CEU+58 890 1,490 836 61 1,017 1,122
GSK 379 1,365 398 302 498 1,191 158 182 265 112
YRI 23 23 23 23 22 18
1000G 927 927 926 925 927
T1DGC 5,192 5,192 5,192 5,192 5,192 5,192 5,192 5,190
KC 332 330 331 332 332 332
PA 443 439 449 450 450 448 452 441
SW 423 421 423 48 42 9 423 422
Total individuals 7,854 9,436 7,824 6,783 8,855 9,652 538 556 606 6,067 6,165
No. SNPs in merged dataset 1,672 1,672 1,672 1,357 1,162 1,162 2,254 2,253 2,291 2,193 2,097
No. two-field alleles 91 174 54 20 28 94 6 3 4 8 51
\label{tab:3}Imputation accuracy in T1DGC validation set. The percentage of correctly imputed two-field alleles is shown for each method at each HLA locus in the T1DGC validation set. Publicly available pre-trained models were used for HIBAG and MAGprediction. Two sets of results are presented for HLA*IMP:02 and HLA*IMP:03: the cross-validation analysis with the multi-population reference panel, and trained with all samples except T1DGC. The number of individuals available for validation at each HLA locus also shown. *Method does not support this locus.
HLA locus No. validation HIBAG MAGprediction HLA*IMP:02 HLA*IMP:03
individuals Pre-trained Pre-trained CV Excl. T1DGC CV Excl. T1DGC
A 5,192 95.2 41.2 97.4 95.5 97.5 96.6
B 5,192 91.5 46.6 93.3 91.5 95.1 93.8
C 5,192 97.2 56.2 98.3 97.1 98.4 97.7
DPA1 5,192 * * 99.7 98.3 99.8 98.8
DPB1 5,190 89.9 86.9 95.0 88.4 95.6 92.3
DQA1 5,192 98.4 * 98.8 98.2 99.4 98.8
DQB1 5,192 97.1 67.2 97.5 95.3 98.4 95.2
DRB1 5,192 88.8 37.6 93.6 90.1 95.3 93.7
Figure 1 Pollock 2014

References

  1. M. M. Pollock, T. J. Beechie, J. M. Wheaton, C. E. Jordan, N. Bouwes, N. Weber, C. Volk. Using Beaver Dams to Restore Incised Stream Ecosystems. BioScience 64, 279–290 Oxford University Press (OUP), 2014. Link

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