Question

Compare the historical technique of VNTR analysis to that of STR analysis in relation to discriminatory ability and data quality. write approx 700 words

Answer 1

SHORT TANDEM REPEAT (STR) ANALYSIS:

STR analysis is helpful in comparision of different samples of DNA with respect to specific loci. A short tandem can be described as a microsatellite which comprises of 2-13 nucleotides that are repeated several times in a row on the DNA strand. Short tandem repeat analysis is helpful in identifying and calculating the precise number of repeating units by attaching probes to the desired short tandem sequences followed by polymerase chain reaction to determine the length of the STR.

It is having a vital role in forensic science where polymorphic STR regions of nuclear DNA are used for generation of DNA profile which is used for differentiation of DNA samples (as the length of STR is highly variable from person to person) thus helping in conviction of culprits.

Discrimination ability and Data quality of STR analysis:

STR analysis, as the name suggests, employ short sequence of 3-5 (4 bases are most commonly used) repeated bases. But it should be remembered that 5 to 20% of persons share same STR sequence, the advantage of STR analysis comes with the fact that, it statistically measures (using product rule of probabilities) how many times the STR is repeated, measuring many STR loci simultaneously at the same time and how far does the loci are located from each other which is peson specific. Multiple copies of STR sequence are generated by using polymerase chain reaction which are later segregated and identified using capillary electrophoresis or gel electrophoresis.

For DNA profiling various systems are used in different countries Ex. Combined DNA Index system (US national database) where 13 core loci is used, on the other hand European countries uses DNA-17 loci system.

STR analysis is more helpful in discrimination between non related individuals than related individuals. Mitochondrial DNA from hair shaft can be used to create a DNA profile which helps in identification of maternal relatives, and hence used for finding lost children, parents etc. But having said all these, STR analysis, sometimes lead to aberration matches with a probability of 1 x 10¹⁸ It has poor discrimination ability in the case of monozygotic twins.

Data quality may also be altered due to degradation of nuclear DNA sample even before collection as in the case of Blood and Semen. It is also affected due to cross contamination of the sample with foreign cells that are in the vicinity of the cell during collection, or due to introduction of leftover DNA fragments from previous test may also lead to false matching. For person who are closely related full DNA profiles are carried out to discriminate the samples rather than subset sampling. To increase the ruggedness of STR analysis, several control samples are to be collected and fed into the test, to have an exact correlation of the results

VARIABLE NUMBER TANDEM REPEATS (VNTR) ANALYSIS:

VNTR analysis is a helpful tool in biology (for detection of different strains of microorganisms), genetics (for determination of relationship of the offspring to the parent) and forensic science (for DNA fingerprinting and culprit identification using blood, semen, hair samples etc). Like STR analysis, VNTR analysis also determine the variation in length of loci, utilises Polymerase chain reaction (PCR) to create multiple copies of DNA and gel electrophoresis for determination of size of DNA, but it emphasizes the variable number tandem repeat which is a short nucleotide sequence on many chromosomes whose variability is considered to be inherited allele, thus forming the basis for determination of relationship or identification of the samples.

Discriminatory ability and Data quality in VNTR analysis:

VNTR analysis utilises PCR, Restriction fragment length polymorphism (RFLP) to map the genes. DNA fingerprinting and gene database systems are probed to know whether the samples are genetically related or not. Gel electrophoresis (alternatively SoutherN blotting technique can also be used) generates a specific band pattern which is characteristic to a particular person. This is can be tested with VNTR markers, for more sensitive data establishment. The chances for two non related individuals producing the same pattern is very low

The repeating nucleotide bases used in VNTR analysis is 10-100, and it also requires relatively a larger sample for better discrimination or proper interpretation. The interpretation is also a bit complex in VNTR analysis when compared to STR. Hence VNTR is more used for knowing the parental linkage, or gene mapping whereas STR is more helpful in crime investigation as the sample required is very less and interpretation is easy.