VNTR polymorphism of the collagen type II, alpha 1 (COL2A1) gene detected by PCR.

The 3' side of the human type II collagen alpha 1 (COL2A1) gene contains a region consisting of a variable number of tandemly repeated short A + T-rich DNA sequences (VNTR). We amplified this region accurately by the polymerase chain reaction (PCR). Genomic DNA was purified from isolated buffy-coat cells, and thermostable Taq polymerase was used to amplify the target region. The amplification products were directly visualized after polyacrylamide gel electrophoresis. In this way, five alleles were distinguished in chromosomes from 33 unrelated Japanese, and named A, B, C, D, and E in decreasing order of length. The relative frequencies of the COL2A1 3' VNTR alleles A through E were 0.045, 0.075, 0.469, 0.015, and 0.393, respectively. Co-dominant segregation was observed in two informative families. The COLA2A1 3' VNTR locus was estimated to have a heterozygosity index of 62% and a polymorphic information content of 0.55.