Finding a Needle in a Haystack: Detection and Quantification of Rare Mutant Alleles Are Coming of Age

Abstract

Detecting rare mutant alleles in the background of wild-type DNA sequences and quantifying a specific DNA sequence in a clinical sample are two of the most challenging problems in DNA diagnostics. Successful approaches can expect important applications. For example, prenatal diagnosis of genetic disorders can be accomplished by invasive procedures such as amniocentesis, chorionic villus sampling, or fetal blood sampling, or by labor-intensive methods such as fetal cell enrichment from maternal circulation (1). If one can detect the mutant allele in the small number of fetal cells found in the maternal circulation, prenatal diagnosis of many devastating genetic disorders can be done with a simple blood test that poses minimal risk to the mother or the fetus. Other applications of the ability to find “a needle in the haystack” include cancer marker detection for early diagnosis or detection of relapse (2), and detection of specific alleles in pooled population samples (3). Similarly, the ability to quantify the amount of a specific DNA species present in clinical samples can help define the viral load in HIV-positive patients (4), determine minimal residual disease in patients with leukemia (5)(6), and monitor specific gene expression (7). In this issue of the journal, a …