We have enhanced the polymerase chain reaction (PCR) such that specific DNA sequences can be detected without opening the reaction tube. This enhancement requires the addition of ethidium bromide (EtBr) to a PCR. Since the fluorescence of EtBr increases in the presence of double-stranded (ds) DNA an increase in fluorescence in such a PCR indicates a positive amplification, which can be easily monitored externally. In fact, amplification can be continuously monitored in order to follow its progress. The ability to simultaneously amplify specific DNA sequences and detect the product of the amplification both simplifies and improves PCR and may facilitate its automation and more widespread use in the clinic or in other situations requiring high sample throughput.
The analysis of DNA for the presence of particular mutations or polymorphisms can be readily accomplished by differential hybridization with sequence-specific oligonucleotide probes. The in vitro DNA amplification technique, the polymerase chain reaction (PCR), has facilitated the use of these probes by greatly increasing the number of copies of target DNA in the sample prior to hybridization. In a conventional assay with immobilized PCR product and labeled oligonucleotide probes, each probe requires a separate hybridization. Here we describe a method by which one can simultaneously screen a sample for all known allelic variants at an amplified locus. In this format, the oligonucleotides are given homopolymer tails with terminal deoxyribonucleotidyltransferase, spotted onto a nylon membrane, and covalently bound by UV irradiation. Due to their long length, the tails are preferentially bound to the nylon, leaving the oligonucleotide probe free to hybridize. The target segment of the DNA sample to be tested is PCR-amplified with biotinylated primers and then hybridized to the membrane containing the immobilized oligonucleotides under stringent conditions. Hybridization is detected nonradioactively by binding of streptavidin-horseradish peroxidase to the biotinylated DNA, followed by a simple colorimetric reaction. This technique has been applied to HLA-DQA genotyping (six types) and to the detection of Mediterranean (3-thalassemia mutations (nine alleles).Differential hybridization with sequence-specific oligonucleotide probes has become a widely used technique for the detection of genetic mutations and polymorphisms (1)(2)(3)(4)(5). When hybridized under the appropriate conditions, these synthetic DNA probes (usually 15-20 bases in length) will anneal to their complementary target sequences in the sample DNA only if they are perfectly matched. In most cases, the destabilizing effect ofa single base-pair mismatch is sufficient to prevent the formation of a stable probe-target duplex (6). With an appropriate selection of oligonucleotide probes, the relevant genetic content of a DNA sample can be completely described.This very powerful method of DNA analysis has been greatly simplified by the in vitro DNA-amplification technique, the polymerase chain reaction (PCR) (7-9). The PCR can selectively increase the number of copies of a particular DNA segment in a sample by many orders of magnitude. As a result ofthis 106-to 108-fold amplification, more convenient assays and nonradioactive detection methods have become possible (10)(11)(12). These PCR-based assays are usually done by amplifying the target segment in the sample to be tested, fixing the amplified DNA onto a series of nylon membranes, and hybridizing each membrane with one of the labeled oligonucleotide probes under stringent hybridization conditions. However, each probe must still be individually hybridized to the amplified DNA and the process can easily become difficult in a system where many different mutations or polymorphisms occur.One approach t...
We present a genotyping method for simultaneously scoring 116,204 SNPs using oligonucleotide arrays. At call rates >99%, reproducibility is >99.97% and accuracy, as measured by inheritance in trios and concordance with the HapMap Project, is >99.7%. Average intermarker distance is 23.6 kb, and 92% of the genome is within 100 kb of a SNP marker. Average heterozygosity is 0.30, with 105,511 SNPs having minor allele frequencies >5%.
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