Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome

Mark B. Consugar, Wai C. Wong, Patrick A. Lundquist, Sandro Rossetti, Vickie J. Kubly, Denise L. Walker, Laureano J. Rangel, Richard Aspinwall, W. Patrick Niaudet, Seza Özen, Albert David, Milen Velinov (+10 others)
2008 Kidney International  
Large DNA rearrangements account for about 8% of disease mutations and are more common in duplicated genomic regions, where they are difficult to detect. Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in either PKD1 or PKD2. PKD1 is located in an intrachromosomally duplicated region. A tuberous sclerosis gene, TSC2, lies immediately adjacent to PKD1 and large deletions can result in the PKD1/TSC2 contiguous gene deletion syndrome. To rapidly identify large
more » ... ents, a multiplex ligation-dependent probe amplification assay was developed employing base-pair differences between PKD1 and the six pseudogenes to generate PKD1-specific probes. All changes in a set of 25 previously defined deletions in PKD1, PKD2 and PKD1/TSC2 were detected by this assay and we also found 14 new mutations at these loci. About 4% of the ADPKD patients in the CRISP study were found to have gross rearrangements, and these accounted for about a third of base-pair mutation negative families. Sensitivity of the assay showed that about 40% of PKD1/TSC contiguous gene deletion syndrome families contained mosaic cases. Characterization of a family found to be mosaic for a PKD1 deletion is discussed here to illustrate family risk and donor selection considerations. Our assay improves detection levels and the reliability of molecular testing of patients with ADPKD. Autosomal dominant polycystic kidney disease (ADPKD) is a common cause of end-stage renal disease (ESRD) due to progressive cyst development and enlargement. 1 ADPKD is genetically heterogeneous with PKD1 (46 exons; 16p13.3) accounting for B85% of cases and PKD2 (15 exons; 4q21) B15%. 2-5 Immediately adjacent to PKD1 lies TSC2, the most common gene for tuberous sclerosis (TSC), a dominantly inherited disorder characterized by the development of benign hamartomas in multiple organs and often resulting in mental retardation/behavioral problems. 6 The majority of PKD1 (B40 kb, encoding exons 1-33) lies in a genomic region that is intrachromosomally, segmentally duplicated with six variously rearranged PKD1-like pseudogenes (PKD1P1-P6) located in 16p13.1. 2,7 As PKD1P1-P6 have 99% sequence similarity to PKD1, protocols utilizing the rare mismatches with PKD1 have been required to specifically amplify PKD1 for mutation analysis. 8 Base-pair screening strategies have identified mutations in B87% of ADPKD patients, including the well-characterized Consortium for Radiological Imaging Studies of PKD (CRISP) population. 5 The majority of mutations are predicted to truncate the protein, but a quarter are missense.
doi:10.1038/ki.2008.485 pmid:18818683 pmcid:PMC2756756 fatcat:x237mojls5cc7oa7wqqfcf2rle