Multiplex dosage pyrophosphorolysis-activated polymerization: application to the detection of heterozygous deletions.
Large heterozygous chromosomal deletions and gene duplications are important classes of mutations that are generally missed by standard PCR amplification and sequencing. Multiplex dosage pyrophosphorolysis-activated polymerization (MD-PAP), a derivative of PAP, was utilized to detect these types of mutations. PAP is a method for nucleic acid amplification in which 3' blocked oligonucleotides (P*) are activated by pyrophosphorolysis when annealed to the target template and subsequently extended. A key advantage to this technology is that PAP reactions produce little or no primer-dimer or false priming. As a result of this enhanced specificity, MD-PAP is easy to optimize. Herein, we utilize MD-PAP to determine gene dosage of each exon of the human factor IX gene by comparison with one endogenous internal control from the ATM gene. Estimated dosage is proportional to the actual template copy number over a minimum dynamic range from 1 to 16 copies. A blinded analysis detected 100% of 43 heterozygous deletions of exons in the human factor IX gene.
Liu
Qiang
Q
City of Hope National Medical Center, Duarte, CA 91010-3000, USA.
Nguyen
Vu Q
VQ
Li
Xuemin
X
Sommer
Steve S
SS
D001260:Ataxia Telangiectasia / Q000235:genetics; D004252:DNA Mutational Analysis; D005091:Exons; D005164:Factor IX / Q000235:genetics; D017353:Gene Deletion; D018628:Gene Dosage; D006580:Genetic Carrier Screening / Q000379:methods*; D006579:Heterozygote; D006801:Humans; D008954:Models, Biological; D021141:Nucleic Acid Amplification Techniques; D009841:Oligonucleotides / Q000737:chemistry / Q000378:metabolism
D009841:Oligonucleotides; D005164:Factor IX