Clinical applications of high-throughput genetic diagnosis in inherited retinal dystrophies: Present challenges and future directions

Table 1 List of retinal dystrophy causative and candidate genes identified in 2013-2014 and the strategy of identification

Gene	Retinal phenotype	Methodological approach
ABCD5	Recessive CRD, spastic parapesis, white matter disease	Homozygosity mapping combined with WES[25]
ADAMTS18	arRD early onset	Homozygosity mapping combined with WES[43]
ARLBP2	arRP	Homozygosity mapping combined with WES[44]
BBIP1	arBBS	WES[45]
C12orf65	Recessive optic atrophy, spastic paraplegia and neuropathy	Linkage mapping WES[46,47]
C21orf2	Recessive CRD	Homozygosity mapping combined with WES[25]
CSPP1	Recessive JS	WES[48-50]
DHX38	arRP (early onset with macular coloboma)	Homozygosity mapping combined with candidate gene approach[51]
DTHD1	Recessive LCA, myopathy	Homozygosity mapping combined with WES[25]
EMC1	arRP	Homozygosity mapping combined with WES[25]
GDF6	arRD	Candidate gene sequencing[52]
GPR125	arRP	Homozygosity mapping combined with WES[25]
HK1	adRP, nonspherocytic hemolytic anemia, and neuropathy	Linkage mapping and WES[53]
IFT27	arBBS	Homozygosity mapping combined with candidate gene approach[42]
IMPG1	Dominant MD	Linkage mapping
	Recessive MD	WES and candidate gene sequencing[54-56]
ITM2B	Dominant RD, dementia	WES combined with linkage mapping[57]
KIAA1549	arRP	Homozygosity mapping combined with WES[25]
KIZ	arRP, arCRD	WES[58]
LRIT3	arCSNB	WES[59]
MVK	arRP, recessive mevalonic aciduria	WES[60]
NEK2	arRP	WGS[6]
NR2F1	Dominant optic atrophy, intellectual disability	Deletion mapping
		WES and deletion mapping[61,62]
PCYT1A	arCRD with skeletal disease	WES and targeted candidate gene sequencing[63,64]
POC1B	Recessive CRD	WES[65]
PRPF4	adRP	Targeted capture NGS[41]
RAB28	arCRD	Homozygosity mapping combined with WES[66]
RDH11	arRP	WES[67]
SLC7A14		WES[68]
TUB	arRD with obesity	Homozygosity mapping combined with WES[69,70]
TTLL5	Recessive cone and CRD	WES[71]

ar: Autosomal recessive; ad: Autosomal dominant; CRD: Cone-rod dystrophy; RD: Retinal dystrophy; RP: Retinitis pigmentosa; BBS: Bardet-Biedl syndrome; JS: Joubert syndrome; LCA: Leber congenital amaurosis; MD: Macular dystrophy; CSNB: Congenital stationary night blindness; WES: Whole exome sequencing; WGS: Whole genome sequencing; NGS: Next generation sequencing.

Table 2 Possible genetic cause in undiagnosed patients after whole exome sequencing

Genetic variants	Technical restrains	Alternative approaches
MicroRNAs and lncRNAs	Not sequenced	Inclusion in the capture
Deep intronic	Not sequenced	RNASeq
		WGS
		Targeted re-sequencing
Variants in regulatory regions	Not sequenced	WGS
		Targeted re-sequencing
Large deletions	Mostly undetected	Detectable in homozygosis
		In heterozygosis can be detected in comparison with controls (if high coverage)
		WGS
		Targeted re-seq
CNVs	Mostly undetected	High coverage
		WGS
		Targeted re-seq
		CGH
Pathogenic trinucleotide repeats	Short reads not covering the whole expansion	Triple repeat based PCR
Structural chromosomal variants	Undetectable	FISH
		WGS
		Targeted Long PCR coupled to NGS
Aneuploidies	Undetectable	Conventional cytogenetics FISH
		WGS

lncRNAs: Long non-coding RNAs; CNVs: Copy number variants; RNASeq: RNA sequencing; WGS: Whole genome sequencing; CGH: Comparative genome hybrdization; PCR: Polymerase chain reaction; FISH: Fluorescent in situ hybridization; NGS: Next generation sequencing.

Table 3 List of prioritized candidates according to the clinical phenotype or X-linked pattern of inheritance

Main candidate gene	Disease
CNGB3, CNGA3	Achromatopsia
RHO	adRP
VMD2	Best disease
CYP4V2	Bietti crystalline dystrophy
RDS/PRPH2	Central areolar choroidal dystrophy
CHM	Choroideremia
LRPO5, FZD4, TSAPN12	Familiar exudative vitreoretinopathy
RDH5, RLBP1	Fundus albipunctatus
NR2E3	Goldman-Favre-Enhanced S-cone syndrome
CEP290	LCA
MFRP	Nanophthalmia
NDP	Norrie disease
SAG	Oguchi disease
RS1	Retinoschisis
RECQL4	Rothmund-Thompson syndrome
ABCA4, RDS/PRPH2	Stargardt disease
USH2A	Usher syndrome
VCN	Wagner syndrome
RPGR	XLCD, XLCRD
RPGR, RP2	XLRP, RP simplex

adRP: Autosomal dominant retinitis pigmentosa; LCA: Leber congenital amaurosis; XLCD: X-linked cone dystrophy; XLCRD: X-linked cone-rod dystrophy; XLRP: X-linked retinitis pigmentosa.