TaqMan real-time polymerase chain reaction for detection of SEC1-FUT2 hybrid alleles: Identification of novel hybrid allele

► A TaqMan assay to distinguish SEC1 and SEC1-FUT2 hybrid alleles was developed. ► Identification of a novel SEC1-FUT2 hybrid allele. ► Interlocus gene conversion is involved in rearrangement. ► The present TaqMan assay is a reliable and powerful method for the large scale association study.