Table 1.

Examples of diagnoses facilitated by Whole Genome Sequencing (WGS).

Authors	Year	Gene	Disease	Type of Variation	Type of WGS	Ref.
Kloosterman et al.	2011	Multiple	Severe congenital abnormalities	De novo SV (chromothripsis)	SOLiD	[23]
Gilissen et al.	2014	SHANK3	Phelan-McDermid syndrome	De novo 66 kb deletion	Complete Genomics	[53]
Gilissen et al.	2014	VPS13B	Cohen syndrome	1.7 kb and 122 kb deletions	Complete Genomics	[53]
Gilissen et al.	2014	MECP2	Rett syndrome	De novo 0.6 kb deletion	Complete Genomics	[53]
Gilissen et al.	2014	IQSEC2	Intellectual disability	De novo 62 kb interspersed duplication	Complete Genomics	[53]
Gilissen et al.	2014	SMC1A	Cornelia de Lange syndrome	De novo 2.1 kb deletion	Complete Genomics	[53]
Gilissen et al.	2014	Multiple	16p11.2 deletion syndrome	De novo 611 kb deletion	Complete Genomics	[53]
Gilissen et al.	2014	STAG1	Intellectual Disability	De novo 382 kb deletion	Complete Genomics	[53]
van Kuilenburg et al.	2017	DPYD	DPDD	Large intragenic inversion	Illumina	[52]
Chiu et al.	2017	Multiple	Pulmonary alveolar proteinosis	425 kb deletion	Illumina	[63]
Borràs et al.	2017	PKD1	Polycystic kidney disease	Various, 18/19 probands	PacBio	[64]
Cretu Stancu et al.	2017	Multiple	Severe congenital abnormalities	De novo SV (chromothripsis)	ONT 1 + Illumina	[65]
Alfares et al.	2018	PHOX2B	Central hypoventilation syndrome	GCN (25) repeat expansion [+25]	Illumina	[54]
Alfares et al.	2018	TPM3	Nemaline myopathy 1	Large deletion	Illumina	[54]
Alfares et al.	2018	TSC2	Tuberous sclerosis type 2	De novo deep intronic SNV	Illumina	[54]
Lionel et al. 2	2018	GPR143	Ocular albinism	Deep intronic variant	Illumina	[55]
Lionel et al. 2	2018	OTC	Ornithine transcarbamylase deficiency	Deep intronic variant	Illumina	[55]
Ostrander et al.	2018	Multiple	Global developmental delay	Balanced inverted translocation	Illumina	[56]
Ostrander et al.	2018	CDKL5	Global developmental delay	De novo 63 kb tandem duplication	Illumina	[56]
Tavares et al.	2018	BBS1	Bardet-Biedl syndrome	Retrotransposon insertion	Illumina	[66]
Cowley et al.	2018	SYNGAP1	Epileptic encephalopathy	De novo 13 bp duplication	Illumina	[67]
Miao et al.	2018	G6PC	Glycogen storage disease type Ia	7.1 kb deletion	ONT 1	[68]
Merker et al.	2018	PRKAR1A	Carney complex	De novo 2184 bp deletion	PacBio	[69]
Sanchis-Juan et al.	2018	ARID1B	Coffin-Siris syndrome	De novo complex SV dupINVinvDEL	Illumina	[70]
Sanchis-Juan et al.	2018	HNRNPU	Seizures; Intellectual disability	De novo complex SV delINVdup	Illumina	[70]
Sanchis-Juan et al.	2018	CEP78	Cone-rod dystrophy; Hearing loss	complex homozygous SV delINVdel	Illumina	[70]
Sanchis-Juan et al.	2018	CDKL5	Birth asphyxia; Fetal distress	De novo complex SV dupINVdup	Illumina + ONT 1	[70]
Ishiura et al.	2018	SAMD12	BAFME 3	TTTCA and TTTTA repeat expansions	PacBio +ONT	[57]
Ishiura et al.	2018	TNRC6A	BAFME 3	TTTCA and TTTTA repeat expansions	PacBio + ONT	[57]
Ishiura et al.	2018	RAPGEF2	BAFME 3	TTTCA and TTTTA repeat expansions	PacBio + ONT	[57]
Mizuguchi et al.	2019	SAMD12	BAFME 3	4.6 kb intronic repeat insertion	PacBio	[71]

¹ Oxford Nanopore Tech. ² Lionel et al., reported 18 diagnoses by WGS; however, the majority was missed by exome panels since panels did not include the corresponding gene. The two deep intronic variants included in this table would not have been detected by exome sequencing approaches. ³ Benign adult familial myoclonic epilepsy.