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Table 2 Reproducibility of HPV type determination based on selected eWGS cut-offsa

From: Universal human papillomavirus typing by whole genome sequencing following target enrichment: evaluation of assay reproducibility and limit of detection

Copy Noc.

Expected HPV

Concordanceb

No. of reads ≥1000

Depth of coverage ≥20

Fraction of genome covered ≥0.5

All 3 cut-offs combined

625

6

4/4

4/4

4/4

4/4

 

11

4/4

4/4

4/4

4/4

 

16

4/4

4/4

4/4

4/4

 

18

4/4

4/4

4/4

4/4

 

31

4/4

4/4

4/4

4/4

 

33

4/4

4/4

4/4

4/4

 

45

4/4

4/4

4/4

4/4

 

52

4/4

4/4

4/4

4/4

 

58

4/4

4/4

4/4

4/4

125

6

2/4

0/4

4/4

0/4

 

11

4/4

4/4

4/4

4/4

 

16

4/4

2/4

4/4

2/4

 

18

4/4

4/4

4/4

4/4

 

31

4/4

2/4

4/4

2/4

 

33

4/4

4/4

4/4

4/4

 

45

4/4

4/4

4/4

4/4

 

52

4/4

4/4

4/4

4/4

 

58

4/4

4/4

4/4

4/4

25

6

0/4

0/4

0/4

0/4

 

11

0/4

0/4

2/4

0/4

 

16

0/4

0/4

1/4

0/4

 

18

0/4

0/4

3/4

0/4

 

31

0/4

0/4

4/4

0/4

 

33

0/4

0/4

2/4

0/4

 

45

0/4

0/4

4/4

0/4

 

52

0/4

0/4

4/4

0/4

 

58

0/4

0/4

4/4

0/4

  1. aSelected eWGS cut-offs are number of mapped reads ≥1000, average depth of coverage ≥20, and fraction of reference genome covered ≥0.5
  2. bLevel of agreement between eWGS call and expected HPV type in plasmid pool over 4 replicates (4/4 indicates 100% concordance)
  3. cData not shown for 5 and 1 HPV copy/reaction since eWGS did not meet any of the cut-off criteria for type determination
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BMC Genomics

ISSN: 1471-2164

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