Table 5.

Specific indications for alternative sequencing modalities in nephrology

Clinical Scenario	Alternative Testing Options
Large deletions or chromosomal rearrangements suspected (typically pediatric: CAKUT, multi-organ manifestations) or needed as a follow-up assessment to a negative test with suboptimal assessment of copy number variation (e.g., whole gene deletions of NPHP1) or to confirm large deletion found by WES or targeted NGS	SNP or chromosomal microarray Other options:  • Comparative genomic hybridization  • Whole genome sequencing  • Multiplex ligation probe amplification
ADTKD-MUC1 suspected (ADTKD phenotype but no mutations found in other ADTKD genes)	Variant-specific testing available without cost from the Broad Institute (contact ableyer@wakehealth.edu)
Single variant testing: An established familial pathogenic variant is known, and patient desires testing only for presence/absence of that variant	Sanger sequencing following PCR amplification of a small genomic region containing the variant location
Gold standarda for ADPKD	Sanger sequencing of long-range PCR amplicons designed to amplify only PKD1, PKD2, but not the duplicated regions (pseudogenes) homologous to PKD1
High suspicion for genetic etiology but no variant found	Consider testing for large deletions (above), and/or contacting testing facility to ask about sequencing quality for specific genes of interest

ADTKD, autosomal dominant tubulointerstitial kidney disease; ADPKD, autosomal dominant polycystic kidney disease; CAKUT, congenital anomalies of the kidney and urinary tract; NGS, next-generation sequencing; SNP, single nucleotide polymorphisms; WES, whole exome sequencing.

^aAs NGS-based methodologies improve, using paired-end sequencing, improved capture reagents, with or without preceding long-range PCR, the superiority of this approach is less apparent, and thus NGS-based panels are often used recently as first test for genetic diagnosis in ADPKD.