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

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.