Soo-Jeong Kim¹, Jennifer L. Miller², Paul J. Kuipers², Jennifer Ruth German³, Arthur L Beaudet³, Trilochan Sahoo³ and Daniel J. Driscoll²  

Departments of Psychiatry¹ and Pediatrics, University of Florida College of Medicine, Gainesville²; Department of Molecular and Human Genetics³, Baylor College of Medicine, Houston, TX 

Introduction:  Prader-Willi syndrome (PWS) is a rare genetic disorder caused by the functional absence of paternally expressed genes within the chromosome 15q11q13 region via three main genetic mechanisms (i.e., deletion of paternally inherited genes, maternal uniparental disomy and imprinting defect).  The majority of deletions are classified into two types based upon size of the deleted segment and the breakpoints involved: 1) type 1 deletion extending from breakpoint 1 (BP1) to BP3 and 2) type 2 deletion from BP2 to BP3.  Recently another micro-deletion syndrome was identified just distal to the PWS region at 15q13.3 that causes a pattern of mental retardation, seizures and facial and digital dysmorphology (Sharp et al., 2008). 

Methods:  Our cohort of 63 PWS deletion patients was initially analyzed with Methylation-Specific Multiplex Ligation-dependent Probe Amplification (MS-MLPA), a recently developed method for detecting both copy numbers and DNA methylation status of genes within the 15q11q13 region, using a commercial kit (www.mrc-holland.com).  In addition, 24 subjects, including 7 with unique deletions as detected by MS-MLPA, were examined by a chromosome 15-specific targeted Chromosomal Microarray (CMA).  

Results:  In our deletion cohort 23 were type 1 (37%); 33 were type 2 (52%); and 7 were unique (11%) deletions.  The agreement rate between the MS-MLPA and CMA techniques was 100% in our subset (n=24) of subjects for identifying the deletion type.  However, CMA was able to more precisely map the breakpoints.  The distal breakpoint in 5 of the 7 unique deletions was located in the interval between ATP10A and OCA2 genes.  The remaining 2 subjects with unique deletions had much larger deletions (approximately 9 Mb) with the proximal breakpoint starting at BP2 and ending with a distal breakpoint at BP5.   

Clinical correlation of these 7 unique deletions found that: (1) the 4 subjects with an intact OCA2 gene did not have hypopigmentation; (2) the subject with a BP2 to ATP10A deletion had an above average birth weight, macrocephaly, normal sized hands and feet, and normal stature; (3) the subject with a distal breakpoint within the OCA2 gene (sparing exons 1 to 18) still had hypopigmentation; and (4) the 2 subjects with the larger BP2 to BP5 deletions only differed by approximately 250 Kb, but were significantly different in clinical presentation (e.g., time of acquisition of motor and speech skills, severity and lengths of failure to thrive in infancy, and academic performance and achievement).     

Conclusions:  We found that 11% of our deletion patients had unique deletions (i.e., neither type 1 nor type 2).  Genotype-phenotype correlations of these subjects provide insights into the possible roles of some of the genes in the PWS region, as well as in the more distal 15q13.3 region.  In particular, our 2 patients with large 9 Mb deletions extending to BP5 and including the CHRNA7 gene are very different clinically.  CHRNA7 has been suggested to be a candidate gene for mental retardation and seizures by several groups; however our data would suggest that the genetic region just distal to CHRNA7 may instead play a more important role in the 15q13.3 micro-deletion syndrome recently described by Sharp and colleagues (2008).

Edited: 02/09/2012