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Table 1 Binning of probes into specific pathogen signature probe sets

From: Optimization and clinical validation of a pathogen detection microarray

  Pathogen Family Genome size (nt) Total tiling probes Top 20% AES* (a) GC content filter (b) Human genome filter (c) No. of filtered probes left (d = a - (b + c)) No. of predicted cross-hybridizing probes (HD ≤ 4 and MCM ≥ 18) (e) No. of probes in pathogen r-signature (d + e)
1 LCMV Arenaviridae 10,056 1,283 348 2 8 338 0 338
2 Hantaan Bunyaviridae 6,533 834 156 5 5 146 6 152
3 Sin Nombre Bunyaviridae 6,562 837 182 1 2 179 6 185
4 229E Coronaviridae 27,317 3,495 494 11 11 472 0 472
5 OC43 Coronaviridae 30,738 3,937 634 15 22 597 3 600
6 SARS Coronaviridae 29,711 3,805 575 8 2 565 1 566
7 Dengue serotype 1 Flaviviridae 10,717 1,370 230 2 8 220 8 228
8 Dengue serotype 2 Flaviviridae 10,722 1,370 241 0 9 232 11 243
9 Dengue serotype 3 Flaviviridae 10,707 1,370 230 0 4 226 13 239
10 Dengue serotype 4 Flaviviridae 10,649 1,361 229 1 7 221 3 224
11 Japanese encephalitis Flaviviridae 10,976 1,404 310 3 2 305 12 317
12 West Nile Flaviviridae 10,962 1,401 320 2 2 316 9 325
13 Yellow fever Flaviviridae 10,862 1,389 255 2 3 250 2 252
14 Hepatitis B Hepadnaviridae 3,215 409 147 14 0 133 0 133
15 Influenza A Orthomyxoviridae 12,561 1,582 510 1 15 494 0 494
16 Influenza B Orthomyxoviridae 14,452 1,822 665 5 18 642 2 644
17 Human papillomavirus type 10 Papillomaviridae 7,919 1,011 287 16 9 262 0 262
18 hMPV Paramyxoviridae 13,335 1,705 322 44 17 261 0 261
19 Newcastle disease Paramyxoviridae 15,186 1,943 329 0 2 327 3 330
20 Nipah Paramyxoviridae 18,246 2,335 389 12 5 372 0 372
21 Parainfluenza 1 Paramyxoviridae 15,600 1,995 330 8 13 309 2 311
22 Parainfluenza 2 Paramyxoviridae 15,646 2,002 333 10 2 321 0 321
23 Parainfluenza 3 Paramyxoviridae 15,462 1,979 409 28 23 358 3 361
24 RSV B Paramyxoviridae 15,225 1,948 383 28 4 351 4 355
25 Echovirus 1 Picornaviridae 7,397 945 238 1 10 227 22 249
26 Enterovirus A Picornaviridae 7,413 946 193 3 0 190 8 198
27 Enterovirus B Picornaviridae 7,389 944 179 0 4 175 22 197
28 Enterovirus C Picornaviridae 7,401 945 183 0 0 183 4 187
29 Enterovirus D Picornaviridae 7,390 944 155 0 3 152 8 160
30 Foot and mouth disease Picornaviridae 8,115 1,036 194 14 3 177 0 177
31 Hepatitis A Picornaviridae 7,478 955 163 1 6 156 0 156
32 Rhinovirus A (type 89) Picornaviridae 7,152 913 191 6 6 179 1 180
33 Rhinovirus B Picornaviridae 7,212 920 197 2 2 193 0 193
34 HIV 1 Retroviridae 9,181 1,174 191 4 0 187 0 187
35 Rubella Togaviridae 9,755 1,246 117 65 0 52 0 52
Total    419,242 53,555     9768   9921
  1. *AES scores for all tiling probes were ranked together and only those probes in the top 20th percentile were retained. Segment 7 of Influenza A was omitted during probe design.