PCR screening for 22q11.2 microdeletion: development of a new cost-effective diagnostic tool.
BACKGROUND
Del22q11.2 syndrome is the most frequent known chromosomal microdeletion syndrome. Previous studies suggest that a substantial number of patients with congenital heart disease have a 22q11 deletion. The molecular diagnosis of Del22q11.2 is usually made by fluorescence in situ hybridization, an expensive and not widely available technique. We developed an efficient and cost-effective PCR SNP assay designed for the screening of 22q11.2 deletion through consecutive homozygosity.


METHODS
Through the screening of dbSNP we have selected SNP markers located in the 22q11.2 microdeleted region. Population heterozygosities were determined in 213 normal individuals. Designed assays consisted of PCR amplification followed by restriction enzyme digestion. Fragments generated were visualized on agarose gel and genotyped.


RESULTS
Selected markers were: rs5748411, rs2238778, rs4819523 and rs4680. All selected markers were localized in the 22q11.2 deleted region. Allele and genotype frequencies of all selected markers were under Hardy-Weinberg equilibrium. Selected SNPs were not in linkage disequilibrium. Predicted assay specificity was estimated to be 92.86% in the Brazilian population.


CONCLUSIONS
The use of consecutive homozygosity in this SNP-based diagnostic test may be used as a cost-effective tool in reference molecular genetics laboratories.
Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), São Paulo University Medical School, São Paulo, Brazil.
L
L
Gioli-Pereira
A C
AC
Pereira
S M
SM
Mesquita
A A
AA
Lopes
J E
JE
Krieger
D000328:Adult; D002872:Chromosome Deletion; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics*; D005260:Female; D005820:Genetic Testing / Q000191:economics* / Q000379:methods*; D005838:Genotype; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D016133:Polymerase Chain Reaction / Q000191:economics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics