Array comparative genomic hybridization (aCGH) analysis in Prader-Willi syndrome

Abstract

Prader-Willi syndrome (PWS) is due to loss of paternally expressed genes in the 15q11-q13 region generally from a paternal 15q11-q13 deletion. The proximal deletion breakpoint in the 15q11-q13 region occurs at one of two sites located within either of two large duplicons allowing for identification of two typical deletion subgroups. The larger type I (TI) deletion involving breakpoint 1 (BP1) is nearer to the centromere and located proximal to the microsatellite marker D15S1035, while the smaller type II (TII) deletion involves breakpoint 2 (BP2) and distal to D15S1035. Breakpoint 3 (BP3) is located at the distal end of the 15q11-q13 region and common to both typical deletion subgroups. Using high resolution aCGH, BP1 spanned a region from 18.683 to 20.220 Mb, BP2 from 20.812 to 21.357 Mb and BP3 from 25.941 to 27.286 Mb. The TI deletion ranged in size from 5.721 to 8.147 Mb (mean 6.583) and the type II deletion from 4.770 to 6.435 Mb (mean 5.330). A subset of the TI subjects showed larger deletions including the loss of at least three genes/transcripts (i.e., LOC283755, POTE5, OR4N4) in addition to the four genes between BP1 and BP2 (i.e., GCP5, CYFIP1, NIPA1, NIPA2). Interestingly, four PWS subjects had duplications of the 15q11 region in addition to the typical deletion. Furthermore, most PWS subjects had copy number variation (CNV) of 50 kb or larger in other chromosome regions; most common were deletions and duplications of 8p and 3q, previously recognized sites of CNV in the human genome.

Fig. 1

Typical type I and type II 15q deletion sizes and breakpoint assignments.

Fig. 2

Representative examples of chromosome 15 comparative genomic hybridization (CGH) of individuals with Prader–Willi syndrome and type I or type II deletions using the Agilent 244 K CGH microarrays.

Fig. 3

Comparative genomic hybridization (CGH) of individuals with Prader–Willi syndrome and 15q11 duplications and typical 15q deletions identified using Agilent 244K CGH microarrays showing areas with normal copy number, deletions and duplications.

Fig. 4

Human chromosome ideograms showing regions of copy number variation (deletion and/or duplication) observed in high resolution (244K) whole genome hybridization (aCGH) analysis of subjects with Prader–Willi syndrome (PWS). Deletions are shown on the left side of the chromosome ideogram and duplications on the right. Numbers indicate the frequency of copy number variants (CNVs) observed in PWS subjects studied. * Duplication of 15q11 observed in four PWS subjects in addition to the typical deletion.