Autosomal Dominant Polycystic Kidney Disease via the PKD1 Gene

Autosomal dominant polycystic kidney disease (ADPKD) is a common inherited kidney disease with multisystem involvement. ADPKD is characterized by bilateral renal cysts accompanied by cysts in other organs including the liver, seminal vesicles, pancreas, and arachnoid membrane (Harris et al. 2011. PubMed ID: 20301424). Renal symptoms include hypertension, renal pain, and renal insufficiency. Nearly half of ADPKD patients have end-stage renal disease (ESRD) by age 60 years. The progressive growth of liver cysts is the most common extrarenal manifestation of ADPKD. The most important non-cystic manifestations of ADPKD are vascular and cardiac abnormalities including intracranial aneurysms, mitral valve prolapse, dilatation of the aortic root, dissection of the thoracic aorta, and abdominal wall hernias. The clinical spectrum of ADPKD is wide and substantial variability of disease severity can occur even within the same family.

Patients with ADPKD typically have onset of symptoms in adulthood. In some rare cases, however, patients with bi-allelic PKD1 variants may have clinical features similar to those of patients with autosomal recessive polycystic kidney disease (ARPKD) (Rossetti et al. 2009. PubMed ID: 19165178; Vujic et al. 2010. PubMed ID: 20558538; Audrézet et al. 2016. PubMed ID: 26139440). In these rare cases, symptoms may appear in early childhood or even in utero.

PKD1 and PKD2 are the two major causative genes for ADPKD (Rossetti et al. 2007. PubMed ID: 17582161; Audrézet et al. 2012. PubMed ID: 22508176). Accounting for a small fraction of ADPKD cases, GANAB and DNAJB11 are newly implicated in ADPKD (Porath et al. 2016. PubMed ID: 27259053; Cornec-Le Gall et al. 2018. PubMed ID: 29706351).

PKD1 (46 coding exons) encodes a member of the polycystin protein family, which plays an important role in renal tubular development. Genetic defects in PKD1 account for approximately 85% of genetically positive ADPKD cases and have been found across the whole coding region of the gene (Rossetti et al. 2007. PubMed ID: 17582161; Audrézet et al. 2012. PubMed ID: 22508176). In addition to missense substitutions and small in-frame changes, truncating changes (nonsense, canonical splice variants and frame-shifting small deletion/insertions) are the majority of PKD1 defects. Gross deletions have been also reported, but are relatively rare (<4% of pathogenic variants) (Ariyurek et al. 2004. PubMed ID: 14695542; Rossetti et al. 2007. PubMed ID: 17582161; Audrézet et al. 2012. PubMed ID: 22508176). Our internal data suggested gene conversions are rare (<0.5%) in PKD1.

The majority of PKD1 defects were found in single patients (Audrézet et al. 2012. PubMed ID: 22508176). De novo pathogenic variants account for about 10% of individuals with ADPKD in adulthood (Neumann et al. 2012. PubMed ID: 22367170).

In two large cohort studies, the overall pathogenic variant detection rate of PKD1 and PKD2 is about 89%, in which defects in PKD1 and PKD2 explain approximately 85% and 15% of genetically positive autosomal dominant polycystic kidney disease (ADPKD) cases, respectively (Rossetti et al. 2007. PubMed ID: 17582161; Audrézet et al. 2012. PubMed ID: 22508176). Large deletions and duplications in PKD1 and PKD2 are relatively rare (<4%) in ADPKD patients (Bataille et al. 2011. PubMed ID: 22008521; Audrézet et al. 2012. PubMed ID: 22508176).

Our sequencing method is expected to be nearly equal to the reported overall detection rate of PKD1 pathogenic variants in ADPKD due to the rarity of gross deletions in this gene. Copy number variants (CNVs) analysis for the homologous region (exons 1 to 33) of PKD1 via the multiplex ligation-dependent amplification (MLPA) assay, which can be ordered separately (Test #2058), can increase the detection rate of PKD1 pathogenic variants.

Since we primarily use Next Generation Sequencing (NGS) to test the PKD1 gene (see Testing Strategy section), gene conversions can be missed. However, our internal data suggested gene conversions are rare (<0.5%) in PKD1. These events have been found by long-range PCR based Sanger sequencing, but not by NGS only. Therefore, to increase detection rate (but by a very limited amount) of PKD1 pathogenic variants, Sanger sequencing for exons 1 to 33 (homologous regions) of PKD1 may be ordered.

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

DNA analysis of the PKD1 gene is complicated and challenging due to the presence of several PKD1 pseudogenes. There is high sequence similarity of exons 1 to 33 between PKD1 and its pseudogenes (Audrézet et al. 2012. PubMed ID: 22508176). We have validated Next Generation Sequencing (NGS) to reliably sequence these exons.

For the PKD1 gene, including exons 1 to 33 (homologous regions), we primarily use Next Generation Sequencing (NGS) (~96%) complimented with Sanger sequencing for low-coverage regions (~4%). For any pathogenic, likely pathogenic, and uncertain variants found in exons 1 to 33 (homologous regions) via NGS, we use long-range PCR based Sanger sequencing to confirm them. Therefore, this test provides full coverage of all coding exons of the PKD1 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Due to homologous sequence, gene conversion events in the PKD1 gene have been reported in the literature and found at PreventionGenetics. Our internal data suggested gene conversions are rare (<0.5%) in PKD1. These events have been found by long-range PCR based Sanger sequencing, but not by NGS only. Therefore, Sanger sequencing for exons 1 to 33 (homologous regions) of PKD1 may also be ordered.

Regarding copy number variants (CNVs) analysis, because of the paucity of CNVs and the complicated nature of sequence in PKD1, CNV analysis for this gene can be performed via the multiplex ligation-dependent amplification (MLPA) assay with limited increased sensitivity (compared to Next-Gen sequencing CNV analysis), and can be ordered separately (Test #2058).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).