Inter- and intrachromosomal rearrangements are both involved in the origin of 15q11-q13 deletions in Prader-Willi syndrome.

To the Editor: Prader-Willi syndrome (PWS) is due to an interstitial de novo deletion at 15q11-q13 in '70% of cases. The deletion spans a region of -4 Mb and invariably involves the paternally derived homologue (Robinson et al. 1991). For most patients the distal breakpoint appears to be located within a single YAC (Kuwano et al. 1992), whereas two consistent breakpoint hot spots have been identified on the proximal side; one (class I) lies in the region between the centromere and D15S541/ D15S542, and the other (class II) lies between D15S541/D15S542 and D15S543, with each accounting for approximately half of the deletions (Christian et al. 1995). The relatively high frequency of deletions, significant clustering of the breakpoints in PWS deletion patients, and the finding of a similar location for the breakpoints in small inv dup(15) has led to the hypothesis that small regions in proximal 15q may contain sequences leading to instability (Knoll et al. 1993; Huang et al. 1997). Recently, preliminary data for a low-copy repeat associated with a novel evolutionarily conserved gene family spanning the proximal and distal breakpoint regions has been reported (Ji et al. 1996). In order to analyze the mechanism underlying deletions in PWS, we genotyped 10 three-generation families of PWS-deletion patients, using microsatellite markers flanking the common deletion region. Each patient was known to be deleted for the interval from D1SS11 to GABRB3, by FISH and/or other molecular techniques. Peripheral blood samples were obtained, with appropriate informed consent, from the patient, both parents, and paternal grandparents. DNA was isolated by use of a QIAamp blood kit (Qiagen). We employed markers D15S541 and D15S542, both mapping to YAC A124A3, proximal to the deletion region, and markers D15S165 and D15S1048, both mapping distal to the common deletion region (Hudson et al. 1995). In addition, marker ATC3C11, mapping <1 Mb from the distal deletion breakpoint (S. L. Christian and D. H. Ledbetter, unpublished data), was used. PCR assays were performed as described elsewhere (Christian et al. 1995; Hudson et al. 1995). The results of the microsatellite analysis are shown in table 1, and examples of the analysis performed on two independent families are shown in figure 1. Three patients were deleted for the D15S541/D15S542 markers, thus being classified as class I-deletion patients. This finding was consistent with the known frequency of the class I breakpoints among PWS patients. The lack of a proximal marker on the deleted allele in these patients precluded assessment of the haplotype for the region comprising the deletion. Of the seven class II patients, five demonstrated a paternal recombination event between the markers flanking the common deletion region. The genetic distance between marker D15S541 and marker D15S165 has been estimated as 17.2 cM in males (Robinson and Lalande 1995). Marker D15S1048 maps 2 cM proximal to D15S165 (Hudson et al. 1995). Therefore, when the genetic distance between D15S541 and D15S165 in male meiosis is taken into account, the identification, in five of seven cases, of a different grandparental origin for the alleles flanking the deletion is significantly different from the expected frequency (X2 = 12.438, P = .0004). This finding is highly suggestive of an unequal crossover occurring in the paternal meio-