VNTR analysis

Galvin, P., Sadusky, D., McGregor, D. and Cross, T. (1995). Population genetics of Atlantic cod using amplified single locus minisatellite VNTR analysis. Journal of Fish Biology 47(suppl. A), 200-208. 

A 21-year-old woman was abducted when she went to the local convenience store. Her body was found the next morning in a wooded area behind the store. The autopsy revealed that she had been sexually assaulted and strangled. Crime scene investigators were able to collect a semen sample from vaginal fluid as well as tissue samples from underneath the victim s fingernails. DNA samples were obtained from three suspects besides the victim. A variable number of tandem repeats (VNTR) analysis was performed on the DNA samples from the evidence collected, the victim, and the suspect, and the results were compared. 

Multiple-Locus Variable Numbers of Tandem Repeat (VNTR) Analysis... 

For some bacterial strains, sequencing of 16S rRNA or real-time PCR with specific primers cannot provide all the information needed. Especially if infectious pathways have to be followed, subtyping with VNTR is the method of choice. For several bacterial species, VNTR (and STR) analysis methods are described that can be used. In Figure 1.20 DNA profiles received by VNTR analysis of Francisella strains are shown. The method can also be used to determine whether reference strains are pure or contain a mixture of two or more substrains (Bystrom et al., 2005). 

RFLP analysis by the Southern blot procedure and detection with probe specific for each VNTR are the basis of DNA fingerprinting. Using just four DNA probes, paternity can be excluded with a cumulative probability of 99.9% (J2). 

Answer C. VNTR sequences are amplified using a PCR and analyzed by gel electrophoresis. Although RPLP analysis could potentiaDy be used for this purpose, it is not the method of choice. 

The analysis of the predictive role of TS polymorphisms may be more complex if the 6-bp deletion/insertion (del/ins) polymorphism in the 3 UTR is added for consideration. The 6-bp deletion allele may cause mRNA instability and reduce intratumoral TS mRNA levels (32). The improved study design on the pharmacogenetic effect of TS polymorphisms should include a global evaluation of the combined VNTR, G/C, and 6-bp del/ins polymorphisms (33). The same global analysis applies to other genes, especially when the functional polymorphism is unclear. Haplotypes may be more informative than individual genotypes. Haplotype tag SNPs (htSNPs) based on the international HapMap project may represent the next wave of pharmacogenomic studies. 

Forensic analysis of DNA samples DNA fingerprinting by means of PCR has revolutionized the analysis of evidence from crime scenes. DNA isolated from a single human hair, a tiny spot of blood, or a sample of semen is sufficient to determine whether the sample comes from a specific individual. The DNA markers analyzed for such fingerprinting are most commonly short tandem repeat polymorphisms (STRs). These are very similar to the VNTRs described previously (see p. 455), but are smaller in size. [Note Verification of paternity uses the same techniques.]... 

The VNTRs or minisatellites of the human genome may be repeated 100 times or more in different persons. Many VNTRs, numbering in the thousands, are well characterized. Restriction fragment analysis will produce different size fragments proportional to the number of repeats in the VNTR. Where the identification of traits has been slowed for lack of a sufficient number of suitable genetic markers, the use of VNTRs should alleviate this constraint.(24)... 

In conclusion, these results further open the door to the creation of numerous minisatellite probes to survey for VNTR loci. Such probes can be used not only for restriction fragment length polymorphism (RFLP) analyses of the many biological applications outlined in the introduction, but they can also be employed to screen cloned libraries with the ultimate goal of determining the sequences flanking VNTR loci. The latter information provides perhaps the most accurate and rapid means of utilizing the variation at such loci via the PCR analysis of alternate alleles. 

In the mid-1980s, these techniques were replaced by direct analysis of the DNA polymorphisms. The first of such techniques, developed by Alec Jeffries utilized multilocus DNA probes. This technique is known as the restriction fragment length polymorphism (RFLP) testing. RFLP techniques are based on variable number of tandem repeats (VNTR), which are sequences of 10 to 60 bp (base pairs) of length, that lie adjacent to each other in the same chromosomal orientation (minisatellites). 

RFLP analysis of VNTRs 1980s-1990s — +-H-+ Labor intensive... 

DNA typing methods used in engraftment analysis are smnmarized m Table 41-5. These methods have evolved like those used for identity testing in general. Initial methods relied on Southern blotting to detect RFLPs or VNTRs. These labor-intensive hybridization assays have been largely replaced by PCR-based methods. 

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