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 |
