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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.