Table 1.

Genetic testing options

Analysis ModalityPrimary ScopeAdvantagesDisadvantagesUses
Sanger sequencing• Identification of small variants (SNVs/INDELs) in a specific DNA region• Simple technical execution• Limited resolution (<1 kb) unsuitable for large structural variants• Confirmation of a specific suspected mutation in a gene
• High analytical accuracy (error rate 0.001%–1%)• Time- and cost-inefficient for analysis of large DNA segments• Confirmation of MPS-identified variants
• Fast and simple interpretation• Analysis of regions refractory to MPS analysis, such as repetitive regions
• No risk of secondary results
• Long reading lengths (approximately 800 bp)
Chromosomal microarrays• Identification of small chromosomal rearrangements/CNVs (≥200–400 kb)• Higher resolution than standard karyotyping (50–100 kb)• Cannot detect small mutations/CNVs• Patients with phenotype strongly suggestive of large rearrangements, such as multiple congenital anomalies and developmental diseases
• Genome-wide analysis• Limited ability to detect balanced chromosomal rearrangements, low-grade somatic mosaicism, and CNVs in pseudogenes and repetitive regions
Targeted MPS panels• Identification of small variants (SNVs/INDELs) within genes of interest for the clinical phenotype• Analysis of all genes possibly related to specific phenotypes• Error rate approximately 0.5%–2% (MPS)• Patients with phenotypes pointing to specific disorders and with low genetic heterogeneity
• Diagnostic yield up to 50% (depending on the patient phenotype and genes selection method)• Short reading length (generally 50–300 bp) (MPS)
• Restricted number of genes that minimizes risk of secondary findings and reduces analysis time• Limited reanalysis utility
• Reliability depends on challenging panel design
Exome sequencing• Identification of small variants (SNVs/INDELs) within coding regions of the genome• Analysis of all coding regions in the genome• Coverage per base is generally lower than with targeted panels• Patients undiagnosed with more specific methodologies
• Unbiased approach increases diagnostic sensitivity• Challenging and time-consuming interpretation (high number of candidate variants)• Screening of patients with undefined phenotype
• Cover almost all sites related to Mendelian diseases (approximately 85%)• Potential for detection of secondary findings• Patients with heterogeneous/unspecific phenotype
• Limited coverage in repetitive regions
• Limited reliability for INDELs
Genome sequencing• Identification of small variants (SNVs/INDELs) within coding and noncoding regions of the genome• Identification of deep splicing and intronic variants unidentifiable with other techniques• Maximizes results interpretation difficulty and time• Patients undiagnosed with other methodologies
• Better analytic performance than exome sequencing• Maximizes potential detection of secondary findings• Screening of patients with undefined phenotype
• Efficient CNV identification• Patients with heterogeneous/unspecific phenotype
• Extremely useful for reanalysis
  • SNV, single nucleotide variant; INDEL, insertion/deletion; MPS, massively parallel sequencing; CNV, copy number variation.