Table 2.

Overview of different sequencing techniques for polycystic kidney disease diagnosis.

Long-range PCR, Sanger sequencing and MLPA of PKD1 and PKD2	Custom capture next-generation sequencing of PKD gene-panel	Whole genome sequencing with analysis targeted to PKD gene-panel
Requires extensive laboratory preparation specific to PKD testing	Requires laboratory preparation specific to PKD testing	Able to ‘batch’ specimens with other disease-groups undergoing the same sequencing pathway
Specific to only targeted genes	Specific to only targeted genes	Analysis can be expanded to entire genome, with consent
Technical expertize required for long-range PCR and potential for amplification bias	Custom capture probes require redesigning when gene-panel requires updating	Flexibility to vary gene panel based on patient phenotype
Requires MLPA for detecting copy number variants and challenging to detect structural variants	Less robust for detecting copy number variants and challenging to detect structural variants	Able to detect both copy number and structural variants within same diagnostic test
Limited data storage challenges	Reduced data quantity reduces analysis and storage costs	Large data quantity increases analysis and storage costs
Able to detect some mosaicism of single nucleotide variants	Improved detection of low-frequency mosaic single nucleotide variants	Reduced coverage makes detection of mosaicism less robust

MLPA Multiplex Ligation-dependent Probe Amplification.