[SNP-specific mismatched PCR for embryonic DNA detection using blood from pregnant mothers]

Although prenatal diagnoses are performed using amniotic fluid cells, chorionic villus, or cord blood, these methods are hazardous for pregnant woman and the fetus. To determine a procedure for safe prenatal diagnosis, we have developed a sensitive method to analyze SNPs and we evaluated the possibility to detect fetal DNA in the maternal blood.

GeneScan analysis was performed by using mismatched specific primers for 5 SNP types and fluorescein amidite (FAM) labeled primers, and Real-time PCR analysis was also performed by using mismatched specific primers for the same SNP type and probes labeled with FAM and black hole quencher. DNA from healthy volunteers' blood was used for a primary examination to establish procedures, and DNA from 200 microl of blood from pregnant women, their partners and children were used for detection of fetal DNA and/or typing and selection of SNPs.

To evaluate the sensitivity of this method, mixing tests of DNA containing a SNP nucleotide and its counterpart indicated the sensitivities were 10(-1)-10(-3) for GeneScan analysis and 10(-1)-10(-4) for Real-time PCR analysis. Fetal DNA (rs3769393-A and G) was detected in blood from pregnant women (GG-type mother: 2 out of 2, AA-type mother: 1 out of 2) only at 18 and/or 28 gestation weeks by Real-time PCR analysis. However, 4 SNPs measured by Real-time PCR analysis and 5 SNPs examined by GeneScan analysis were not detected in all women in different gestation periods.

We established a SNP detection method using GeneScan and Real-time PCR analysis. The latter detected fetal DNA in 200 microl of blood in only some pregnant women. We speculate that using a large amount of DNA from nucleated erythrocytes in 20 ml of blood will improve the detection rate of fetal DNA.