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Table 1 Breakdown of times of principal steps for rapid diagnostic whole genome sequencing

From: A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases

Method

Sample

Site

DNA isolation, QC and shearing

PCR-free library prep

WGS library QC

SBS

Yield (GB)

% > Q30

Alignment

Variant calling

RUNES variant annotation

Provisional diagnosis

Total time

Published WGS50

Multiplea

Both

2:30

3:15

1:30

25:30

139

90

14:40

2:30

0:05

50:00

SBS18, GSNAP/GATK/noVQSR

5006-01

CMH

2:30

3:15

1:30

19:45

128

91

22:30

0:29

n.a.

49:59

WGS26, SBS18, and Dragen v1.2

UDT_173

Essex

2:30

3:02

1:30

17:58

106

92

0:15

0:15

0:34

0:04

26:08

WGS26, SBS18, and Dragen v1.2

UDT_103

Essex

2:30

3:05

1:30

18:25

130

90

0:19

0:22

0:31

0:05

26:47

WGS26, SBS18, and Dragen v1.2

NA12878

Essex

2:30

3:15

1:30

18:00

143

85b

0:19

0:22

0:33

n.a.

26:28

WGS26, SBS18, and Dragen v1.2

NA12878

CMH

2:30

3:15

1:30

18:36

65c

85b

0:10

0:11

0:35

n.a.

26:47

  1. GB, gigabases; Q, Phred-like quality score QC, quality control; SBS, 2 × 101 cycle sequencing-by-synthesis
  2. aReference 12
  3. bPrior to SBS18, after failing tiles were removed
  4. cSingle flowcell