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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