We developed a simple, cost-effective, and accurate JAK2 allele burden quantification method named alternately binding probe competitive PCR (ABC-PCR). ABC-PCR can be performed to quantify target JAK2 allele burdens in a single reaction. The throughput and running cost of ABC-PCR are markedly improved compared with those of allele-specific quantitative PCR (AS-qPCR). The quantification of samples with known JAK2 allele burdens revealed that ABC-PCR had a small assay-to-assay variation. The JAK2 allele burdens in the patients with myeloproliferative neoplasms measured by ABC-PCR and AS-qPCR showed a good fitting. ABC-PCR would be a powerful tool for quantifying target JAK2 allele burdens.
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