Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays

Lee, Charlie Wah Heng; Koh, Chee Wee; Chan, Yang Sun; Aw, Pauline Poh Kim; Loh, Kuan Hon; Han, Bing Ling; Thien, Pei Ling; Nai, Geraldine Yi Wen; Hibberd, Martin L.; Wong, Christopher W.; Sung, Wing-Kin

Of the experiments, two pairs of replicates (305_nasal and 305_cell_cond1) were amplified under the same optimal experimental conditions while each of the other pairs (305_cell_cond2, 305_cell_cond3, 305_cell_cond4, 305_cell_cond5) were amplified under different suboptimal experimental conditions (simulating experimental volatility). Compared with the available capillary sequences for sample 305, EvolSTAR had an average error rate of 0.0012% and 28 ambiguous calls per sample (338 in total). On the other hand, Nimblescan A CGT 547 246 CTG 558 237 GCT 957 367 GTC 2215 1407 TCG 1049 611 TGC 3015 2873 C AGT 2035 2712 ATG 1752 2400 GAT 382 341 GTA 159 134 TAG 360 377 TGA 165 129 G ACT 1474 1043 ATC 976 624 CAT 1639 1534 CTA 868 788 TAC 594 410 TCA 542 454 T ACG 432 529 AGC 562 636 CAG 623 841 CGA 1066 1616 GAC 1421 1878 GCA 1637 2841 Hybridization intensity reduction orders found in 25 028 true calls from two replicated hybridization experiments of patient sample 380. For each true call, for each strand, we rank the PM probe and its MM probes based on their hybridization intensities in decreasing order. We count the frequency of each hybridization intensity reduction order. 1 6002 6 5888 6 0 0 EvolSTAR 2 6002 6 5993 6 0 0 PBC 2 6002 6 5895 6 0 1 507 EvolSTAR 1 3921 8 3913 8 0 0 PBC 1 3921 8 3736 8 0 3 EvolSTAR 2 3921 8 3916 8 0 0 PBC 2 3921 8 3758 8 0 2 581 EvolSTAR 1 8574 10 8567 10 0 0 PBC 1 8574 10 8458 10 0 2 EvolSTAR 2 8574 10 8566 10 0 0 PBC 2 8574 10 8461 10 0 5 582 EvolSTAR 1 3057 4 3051 4 0 0 PBC 1 3057 4 2986 4 0 0 EvolSTAR 2 3057 4 3053 4 0 0 PBC 2 3057 4 3001 4 0 0 593 EvolSTAR 1 3054 3 3053 3 0 0 PBC 1 3054 3 3007 2 1 0 EvolSTAR 2 3054 3 3053 3 0 0 PBC 2 3054 3 2992 2 1 0 9 061 364 EvolSTAR 1 5129 5 5123 5 0 0 PBC 1 5129 5 5064 5 0 0 EvolSTAR 2 5129 5 5122 5 0 0 PBC 2 5129 5 5042 5 0 0 9 061 365 EvolSTAR 1 3000 3 2993 3 0 0 PBC 1 3000 3 2956 3 0 1 EvolSTAR 2 3000 3 2991 3 0 0 PBC 2 3000 3 2941 3 0 0 9 061 366 EvolSTAR 1 1683 3 1683 3 0 0 PBC 1 1683 3 1649 3 0 1 EvolSTAR 2 1683 3 1682 3 0 1 PBC 2 1683 3 1636 3 0 1 923 EvolSTAR 1 4373 5 4365 5 0 0 PBC 1 4373 5 4187 5 0 1 EvolSTAR 2 4373 5 4330 5 0 1 PBC 2 4373 5 3738 5 0 6 Types of calls and their frequencies generated by EvolSTAR and PBC in replicated microarray hybridizations of 14 patient samples. Partial or complete capillary sequences were generated for each sample and used to verify the calls made by EvolSTAR and PBC on each replicate. We then count the frequency of true-non-mutation, true-mutation, error and 'N' calls in each replicate.