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Detection of sequence variability of the collagen type II α 1 3′ variable number of tandem repeat
Author(s) -
van Meurs Joyce B. J.,
Arp Pascal P.,
Fang Yue,
Slagboom P. Eline,
Meulenbelt Ingrid,
van Leeuwen Johannes P. T. M.,
Pols Huibert A. P.,
Uitterlinden André G.
Publication year - 2000
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/1522-2683(200011)21:17<3571::aid-elps3571>3.0.co;2-3
Subject(s) - allele , genotyping , genetics , biology , heteroduplex , genotype , locus (genetics) , variable number tandem repeat , microsatellite , tandem repeat , gene , genome
The variable number of tandem repeat (VNTR) 3′ of the collagen type II (COL2A1) gene has been shown to be highly variable with a complex molecular structure. In a previous pilot experiment we observed discordance between methods to genotype this informative marker. To further investigate the extent and molecular nature of this discordance, we genotyped a random sample of 207 Caucasian individuals with two genotyping methods and sequenced new alleles. We compared single‐strand (SS) analysis, which is based on detection of size differences between the different alleles, and heteroduplex analysis (HA), which is sensitive to both size and sequence differences. Overall, 26% of discordance between the two methods was detected. Approximately two thirds of this discordance was caused by subdivision of SS‐alleles 13R1 and 14R2 into HA‐alleles 4A + 4B and 3B + 3C, respectively. Sequence analysis of the COL2A1‐VNTR alleles 4B and 3C showed that these alleles differed in sequence, but not in size, from already described SS‐alleles, which explains why they escape detection by SS. The 4B allele is a frequent allele in the population (14%) and is, therefore, important to distinguish in association studies. We conclude that HA is a reliable method when the described optimized electrophoretic conditions are used. HA is a sensitive genotyping method to document allelic diversity at this locus, which can distinguish more alleles compared to the SS method.