Polymerase chain reaction amplification specificity: Incidence of allele dropout using different DNA preparation methods for heterozygous single cells

Purpose: The purpose was to evaluate methods of DNA preparation in a single cell to determine the ability to amplify and correctly diagnose a targeted gene.Methods: One- or two-cell lymphoblasts (n=100/group), heterozygous for the normal and 4-base pair insertion on exon 11 of the -hexosaminidase A gene, were collected and prepared under the following conditions: (1) freeze-thaw liquid nitrogen, then boiling (LN₂); (2) potassium hydroxide/dithiothreitol, heated to 65°C, followed by acid neutralization (KOH); (3) boiling only (BI); and (4) water only (H₂O). Cells were analyzed by polymerase chain reaction using nested primers.Results: The total number of cells amplifying [in brackets] and the cells with amplification for both alleles (heterozygous), the normal allele, or the mutant allele were as follows, respectively: LN₂ [38], 11, 16, 11; KOH [97], 91, 5, 1; BI [41], 17, 13, 11; and H₂O [85], 41, 16, 28. With two cells per reaction tube the results were as follows: LN₂ [85], 53, 14, 18; and KOH [97], 96, 1, 0.Conclusions: KOH lysis was significantly greater than with all other methods (P<0.006) and should be used for single cells. This study also demonstrates the importance of using heterozygous cells to determine the ability to amplify both alleles as a method of quality control for single-cell analysis.Presented at the 42nd annual meeting of the Society for Gynecologic Investigation, Chicago, Illinois, March 15–18, 1995 and at the 5th Annual Meeting of the International Working Group on Preimplantation Genetics, Hamburg, Germany, June 28, 1995.