Comparative multiplex dosage analysis detects whole exon deletions at the phenylalanine hydroxylase locus

Abstract

For the PKU Special IssueWe have developed quantitative comparative multiplex dosage analysis to detect altered copy number of regions of the phenylalanine hydroxylase gene. Out of 41 alleles (4% of 1,010 PKU chromosomes) on which a mutation had not been characterized previously, this technique has highlighted two novel mutations: deletions of exon 5 and of exon 6 on a total of eight alleles. Restriction-enzyme digestion of genomic DNA and hybridization to an amplified segment of the phenylalanine hydroxylase (PAH) cDNA probe PAH247 established the size of the deletion in five individuals to be between 700 and 900 bases. We also report somatic mosaicism in the parent of an affected child previously shown to have a deletion spanning exons 5 and 6. Finally, we report a putative duplication of a region encompassing exon 6 in an affected individual. Hum Mutat 21:379-386,

Low proportion of whole exon deletions causing phenylketonuria in Denmark and Germany

“…MLPA identified the deletions of exons 5 and 6 previously detected by CMDA (Gable et al, 2003). However, the putative exon 6 duplication was not confirmed, and we assume that the reported duplication is the result of an artefact of CMDA analysis.…”

“…Also exon 6 duplications were suspected with CMDA in two patients (Gable et al, 2003). The value of this finding had remained unclear, as the duplication could not be verified by Southern blot (Gable et al, 2003). Likewise, MLPA analyses failed to confirm the putative exon 6 duplications (g-h, Table 1).…”

PAHdb 2003: What a locus-specific knowledgebase can do

“…Large deletions are rare in the PAH gene (see Gable et al [2003] in this issue of the Journal). Whether an allele actually affects phenotype, or whether the phenotype can be predicted from the genotype, remains an important general inquiry-no less so at the PAH locus.…”

“…They also help to delineate identity, either by descent or by state, of particular alleles (e.g., R408W [John et al, 1990;Byck et al, 1994]). Haplotype markers have also contributed to the discovery of large deletions in the PAH gene Gable et al, 2003]. …”

“…More frequently, multiple exons are affected. (For a literature review, see Gable et al [2003]). The relative frequency of large PAH gene deletions is apparently low (o1%) but this may reflect poor ascertainment.…”