TaqMan-based real-time polymerase chain reaction for detection of FUT2 copy number variations: identification of novel Alu-mediated deletion.
BACKGROUND
The human FUT2 locus, which encodes a secretor-type α(1,2)fucosyltransferase, is known to be highly polymorphic. In addition to many single-nucleotide polymorphisms, three recombination alleles with a deletion of complete or partial FUT2 coding region have been reported.


METHODS
To detect copy number variations (CNVs) of the FUT2 gene including three recombinant alleles by a high-throughput system, we developed a triplex TaqMan real-time polymerase chain reaction (PCR) method. The relative number of copies of two regions of the FUT2 gene, the 5' flanking (FUT2-5') and FUT2-promoter (Prom) regions, were determined by comparing the number of threshold cycles (Ct) to those of the albumin gene (ALB) as the internal control (ΔCt).


RESULTS
The mean 2(-ΔΔCt) values (FUT2-5'/ALB or Prom/ALB) obtained from 237 samples with known FUT2 copy numbers clearly differentiated two nonoverlapping intervals that corresponded to the one-copy-number samples ranging from 0.42 to 0.59 and two-copy-number samples ranging from 0.81 to 1.19; no FUT2-5' signal for recombination alleles was detected in homozygotes. Using this assay, we detected an individual in a Chinese population with a loss of one copy of the FUT2-5' region resulting from a novel Alu-mediated FUT2 deletion (approx. 4 kb).


CONCLUSIONS
The TaqMan real-time PCR method was able to detect the number of copies of FUT2 and distinguish different kinds of known CNVs. This system is robust, fast, and suitable for high-throughput analysis.
Soejima
Mikiko
M
Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Kurume, Japan.
Koda
Yoshiro
Y
D056915:DNA Copy Number Variations / Q000235:genetics*; D005647:Fucosyltransferases / Q000235:genetics*; D006023:Glycoproteins / Q000235:genetics; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods*; D012709:Serum Albumin / Q000235:genetics; D000075462:Serum Albumin, Human; D000097631:Galactoside 2-alpha-L-fucosyltransferase
D005647:Fucosyltransferases; D006023:Glycoproteins; D012709:Serum Albumin; D000075462:Serum Albumin, Human; D000097631:Galactoside 2-alpha-L-fucosyltransferase; C422455:ALB protein, human