Internal sequence variations in the Ha-ras variable number tandem repeat rare and common alleles identified by minisatellite variant repeat polymerase chain reaction

Abstract

In this report, we describe the sequence allelotyping of the Ha-ras variable number tandem repeat (VNTR) region using a minisatellite variant repeat (MVR)-PCR approach. This method permits the rapid identification of internal sequence variations among the VNTR alleles, exploiting the presence of two polymorphic sites within the 28-bp repeat subunits that give rise to four distinct repeat types. Using MVR-PCR, 20 to 25 repeats at the 5' end of the VNTR can be sequenced rapidly and reliably. MVR typing of the common alleles a1, a2, a3, and a4 shows that the first six repeats at the 5' end of each allele constitutes an invariant region. Beginning with repeat 7, characteristic "signature" MVR patterns emerge for each common allele. The a1 and a2 common alleles were found to consist of specific repeat types 1, 2, and 3, whereas a3 and a4 contain an additional repeat type 4 not present in the smaller alleles. MVR typing of rare-length alleles indicates that they are comprised of disorganized sequences, although they usually bear a resemblance to one of the common alleles at the 5'-most end. These results suggest that the rare alleles may be generated from recombination or gene conversion-type events involving the common progenitor alleles. MVR typing could, therefore, improve the ascertainment of rare Ha-ras alleles and may provide molecular insights into the genesis of cancer-associated alleles.