Protocol:Checking for maternal DNS contamination by variable number tandem repeat (VNTR) analysis

Checking for maternal DNA contamination by Variable number tandem repeat (VNTR) analysis

principle

PCR can also be used to check for maternal contamination in the fetal DNA sample by variable tandem repeat (VNTR) polymorphism analysis, using the procedure of gap-PCR. The reagents and method of this non fluorecent PCR is detailed in the gap-PCR protocol. The method uses simple technology in the form of agarose gels and ethidium bromide staining, the disadvantages are that the low resolution of agarose gel electrophoresis means that only VNTRS with a repeat size of 30 nucleotides or above are useful. Also this non fluorescent method is not as sensitive as the fluorescent STR method in identifying small amounts of contamination.

method

The primer sequences required for the analysis of the Apo B, IgJh, Col2A1 and D4S95 VNTR polymorphisms are detailed in Table 7.3. An informative test is when both parents have two different size alleles and the fetus can clearly be seen to have inherited one of the maternal and one of the paternal alleles. If a faint positive signal for the second maternal allele is seen in the fetal DNA (which shows three bands in total) this indicates maternal DNA contamination.

'''Table 7.3. '''Primers used to check for maternal contamination by VNTR analysis.

All except the IgJh primers use the standard PCR buffer. The IgJh primers requires a (NH4)2SO4buffer as detailed in the methods in chapter 5.