Table 1 Duration and metrics for the major steps in the diagnosis of genetic diseases by genome sequencing with rapid standard methods and a rapid, autonomous platform.

Primary (1°) and secondary (2°) analyses: Conversion of raw data from base call to FASTQ format, read alignment to the reference genomes, and variant calling. Tertiary (3°) analysis processing: Time to process variants and phenotypic features and make them available for manual interpretation in Opal interpretation software (Fabric Genomics) or to display a provisional, automated diagnosis(es) in MOON interpretation software (Diploid). Std., rapid standard methods; auto., rapid, autonomous platform; dev. delay, global developmental delay; PPHN, persistent pulmonary hypertension of the newborn; HIE, hypoxic ischemic encephalopathy; n.a., not applicable. Patients 263, 6124, and 3003 were retrospectively analyzed by the autonomous system. Patient 263 was analyzed two times by the autonomous system. Patients 6194, 290, 352, 362, 412, and 7072 were prospectively analyzed by both autonomous and standard diagnostic methods.

Use typeRetrospective patientsProspective patients
Subject ID2636124300361942903523623747052412
Age8 days14 years1 year5 days3 days7 weeks4 weeks2 days17 months3 days
Sex
Abbreviated
presentation
Neonatal
seizures
Rhabdo
myolysis
Dystonia,
dev. delay
Hypoglycemia,
seizures
Pulmonary
hemorrhage,
PPHN
Diabetic
ketoacidosis
Neonatal
seizures
HIE, anemiaPseudomonal
septic shock
Neonatal
seizures
MethodAuto.Auto.Auto.Auto.Auto.Std.Auto.Std.Auto.Std.Auto.Std.Auto.Std.Auto.Std.Auto.Std.
Number of
phenotypic
features
511151481422574103465111261243331
Molecular
diagnosis
Early infantile
epileptic
encephalopathy
7
Glycogen
storage
disease V
Dopa-
responsive
dystonia
NoneNoneNoneNonePermanent
neonatal
diabetes
mellitus
NoneNoneNoneNoneX-linked
agamma-
globulinemia 1
Benign familial
neonatal
seizures 1
Gene and
causative
variant(s)
KCNQ2
c.727C > G
PYGM
c.2262delA
c.1726C > T
TH
c.785C > G
c.541C > T
n.a.n.a.n.a.n.a.INS c.26C > Gn.a.n.a.n.a.n.a.BTK c.974 + 2
T > C
KCNQ2
c.1051C > G
Sample/Library
Prep (hours)
3:202:552:242:222:1023:542:1222:052:1315:422:3118:303:3010:104:3012:103:0523:50
NovaSeq
loading
(hours)
0:200:170:160:201:38*0:200:290:220:300:530:152:300:450:351:001:000:200:53
2 × 101 nt
sequencing
(hours)
15:3615:3115:3415:2715:2624:1315:2524:0815:2122:4415:1733:3615:1721:0715:1922:4615:5821:00
1° & 2° analysis
(hours)
1:031:020:590:591:073:051:001:571:012:301:022:301:022:301:092:251:242:24
3° analysis
processing
(hours)
0:060:050:070:050:060:150:080:140:060:150:050:1510:280:160:060:160:060:16
Total (hours)20:2519:5619:2019:1420:42*56:0319:2948:4619:1142:0419:1057:2131:0234:3822:0438:3720:5348:23

*Included time to thaw a second set of NovaSeq reagents.

†Included 10:20 hours of downtime due to data center relocation.