PCR-based markers

Morioka, Japan Rapid classification of partial waxy and waxy wheats was developed using PCR-based markers 267... 

Monti, J.R., Chilton, N.B., Qian, B.-Z. and Gasser, R.B. (1998) PCR-based differentiation of Necator americanus from Ancylostoma duodenale using specific markers in ITS-1 rDNA. Molecular and Cellular Probes 12, 71—78. 

Janke, C., Magiera, M. M., Rathfelder, N., Taxis, C., Reber, S., Maekawa, H., Moreno-Borchart, A., Doenges, G., Schwob, E., Schiebel, E., and Knop, M. (2004). A versatile toolbox for PCR-based tagging of yeast genes New fluorescent proteins, more markers, and promoter substitution cassettes. Yeast 21, 947-962. 

The discovery of new alternative splice forms of genes associated with disease has the exciting potential to lead to new rapid PCR-based diagnostic markers. The ability to extract such alternative splice forms together... 

Schmidt, H., Taniwaki, M. H., Vogel, R. F., and Niessen, L. (2004a). Utilization of AFLP markers for PCR-based identification of Aspergillus carbonarius and indication for its presence in green coffee samples. J. Appl. Microbiol. 97, 899-909. 

In order to increase the sensitivity of screening, so as to minimize the so-called window period during which serological markers will not detect the infectivity marker, methods of detecting nucleic acids from, for example, the virus particle have been developed. Hepatitis C virus nucleic acid testing is obligatory in Europe, the USA, and Japan, and in many countries nucleic acid testing for other viruses has also been implemented. There is nevertheless no doubt that in future PCR-based methods will further increase the safety of blood and blood products. 

Both FISH and PCR-based detection of LOH can be achieved successfully in FFPE samples, and each method has its own limitations. FISH will show a false-negative result in the event of uniparental disomy (i.e., when cancer cells have lost one chromosome in the presence of duplication of another chromosomal allele). The PCR-based LOH analysis can detect the Ip loss in this situation. However, for optimal performance, the PCR-LOH analysis requires normal cells (isolated from normal tissue or blood) and must rely on amplification of several markers located in the same region because some of the microsatellite loci will be non-informative. 

A DNA marker is simply a uniquely identifiable segment of DNA. There are several different types of markers, usually ranging in size from one to 300-400 nucleotide bases in size. Markers can be thought of as landmarks, and a set of markers whose relative positions (or order) within a genome are known comprises a map. Markers can be categorized in several ways. Some markers are polymorphic, and others are not (monomorphic). Detection of markers may be either PCR based or hybridization based. Some markers lie in a sequence of DNA that is expressed some do not, or their expression status may be unknown. 

A third type of polymorphism is due to tandem repeats of short sequences that can be detected by PCR-based analysis. These are known variously as microsatellites, short tandem repeats (STRs), STR polymorphisms (STRPs), or short sequence length polymorphisms (SSLPs). These repeat sequences usually consist of two, three, or four nucleotides and are plentiful in most organisms. All PCR-converted STR markers (those for which a pair of oligonucleotides flanking the polymorphic site suitable for PCR amplification of the locus has been designed) are considered to be STSs. The advent of PCR-based analysis quickly made microsatellites the markers of choice for mapping. 

Many studies show that the use of PCR-based molecular methods to amplify PSA-mRNA as molecular marker offer a sensitive assay for the detection of extraprostatic PSA synthesizing cells suitable for monitoring and detection of micrometastases and circulating tumor cells originated from prostatic carcinoma. The use of PSA as a molecular target proved to be more sensitive than the amplification of other prostate-specific tissue markers like prostate-specific membrane antigen (PSMA) or human glandular kallikrien (a member of the kallikrien family of serine proteases with trypsin like activity). 

Cytokeratins are a complex family vith more than 20 isotypes consists of keratinlike proteins with a molecular weight of 40-68 kDa and are the most important markers for epithelial structures and epithelial differentiation. Cytokeratins 9-20 are type I intermediate filaments whereas cytokeratins 1-8 are type II. Specific antibodies to different cytokeratins are widely used in immunohistochemistry to detect the cytokeratin expression and tumor differentiation as the cytokeratin profile remains usually constant after malignant transformation. Another approach for the detection of cytokeratin expression is the detection of their complementary mRNA using RT-PCR-based molecular methods. 

GARLAND, S., LEWIN, L., BLAKENEY, A., REINKE, R., HENRY, R., PCR-based molecular markers for the fragrance gene in rice (Oryza sativa L.), Theor. Appl. Genet., 2000,101, 364-371. 

Fujii, T., Nakashima, K., Hayashi, N. (2005). Random ampUfledpolymorphic DNA-PCR based cloning of markers to identify the beer-spoilage strains of Lactobacillus brevis, Pediococcus damnosus, Lactobacillus collinoides and Lactobacillus coryniformis. Journal of Applied... 

DQAl). This marker looked at a genetic marker that had originally been tested at the protein level at the DNA level. This type of marker looked at DNA-sequence-based differences. This became the first PCR based tested to be used forensically. Other sequence-based tests were developed but they did not provide the same level of identification produced by RFLP based testing. Using the available sequence based tests only allowed individualization in the 100s to 100,000s. 

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