Table 3.

Emerging methods and technologies for genome-wide diagnostic investigation of patients with suspected genetic disorders.

Method or technology	Added value over existing methods	Novel insights into genotype-phenotype relationships	Factors that are prohibitive for widespread, routine clinical application	Reference
Long-range sequencing	De novo assembly of haplotypes of several Mb in size, independent of the reference genome sequence	Haplotype reconstruction, identification of breakpoints that are not in unique DNA sequences, reconstruction of chromosomal rearrangements at nucleotide resolution	Costs per sample, not suitable for high-throughput application	[27]
Optical mapping of high molecular weight DNA	De novo assembly of all chromosomes of individual genomes, independent of the reference genome sequence	Identification of the structure of rearrangements, discrimination between direct and inverted tandem duplications and insertions with three breaks; identification of genes disrupted at breakpoints of rearrangements; discovery of ~60 Mb of non-redundant genome sequence that is absent in the GRCh38 reference sequence	Costs per sample, not suitable for high-throughput application	[28–30, 41]
Assessment of the pathogenic effects of CNVs other than by copy number changes of genes within the CNV	Interpretation of pathogenic effect of CNVs that disrupt or delete a TAD regulatory boundary	Identification of genes adjacent to CNVs that contribute to the clinical phenotype because their expression becomes influenced by novel, ectopic regulatory sequence elements	Software tools are available to identify adjacent genes that are associated with HPO terms matching the phenotype, but these await clinical validation	[42, 43]
Assessment of pathogenic effects of genes adjacent to breakpoints of de novo structural rearrangements by combining in silico analysis with transcriptome sequencing of lymphoblastoid cell lines	Identification of distorted expression of genes within ~1–2 Mb of breakpoints by determining overlaps of transcription starts, TADs, promoter capture Hi-C interactions and DNase hypersensitive sites	Prioritization of genes adjacent to breakpoints as candidate genes that contribute to the clinical phenotype	Laborious, requires dedicated software tools that are not commonly available	[4, 44]

CNV, copy number variant, HPO, human phenotype ontology (see http://hpo.jax.org/app/), TAD, topologically associated domain, Hi-C, method to study the three-dimensional organization of an entire genome by an unbiased identification of chromatin interaction.