Beyond simple pooling for HIV screening

Estimating the prevalence of infectious agents using pooled samples: biometrical considerations

Pooled testing of units is a common approach in the prevalence estimation of infectious agents, which leads to a reduction of total costs of diagnostic testing. We examine how the pool size affects the statistical properties of the prevalence estimator r. Exact formulae are used to determine bias and precision of r. It is shown that with moderate pool sizes the (upward) bias of r is negligible. If there is no diagnostic error, the random error of r increases slightly with higher pool sizes, whereas if sensitivity and specificity are lower than 1, pooling may markedly decrease the random error of r. Another reason why pooling may be beneficial (and even indispensable) is that it greatly reduces the huge bias that can result if the assumed values of the sensitivity and specificity of the diagnostic test are not equal to the true values. The numerical calculations show that, in case of prevalence rates of up to 5% and total sample sizes of n > or = 500, pool sizes of about 10 to 20 are generally satisfactory from a statistical view-point. The methodological advantages and disadvantages of more complicated pooling strategies involving repeated testing of units are discussed.

Analysis of multistage pooling studies of biological specimens for estimating disease incidence and prevalence

The testing of pooled samples of biological specimens for the purpose of estimating disease prevalence may be more cost effective than testing individual samples, particularly if the prevalence of disease is low. Multistage pooling studies involve testing pools and then sequentially subdividing and testing the positive pools. A simple estimator of disease prevalence and its variance are derived for general multistage pooling studies and are shown to be natural generalizations of Thompson's (1962) original estimators for single-stage pooling studies. The reduction in variance associated with each additional stage is calibrated. The results are extended to estimating disease incidence rates. The methods are used to estimate HIV incidence rates from a prevalence study of early HIV infection using a PCR assay for HIV RNA.

Mass allele detection (MAD) of rare 5-HT1A structural variants with allele-specific amplification and electrochemiluminescent detection

A strategy is described that exploits allele-specific amplification (ASA-PCR) and electrochemiluminescence (ECL) detection technology to rapidly and cheaply screen large numbers of DNAs arranged in pooled matrices in order to identify individual nucleotide sequence variants. To demonstrate this strategy, a large genomic DNA collection was screened for two nucleotide variants in the 5-HT1A serotonin receptor gene and individual heterozygotes were identified. Conversion of two SSCP variants to allele-specific PCR polymorphisms was accomplished, and PCR product capture and ECL detection were enabled by the covalent addition of biotin to allele-specific PCR primers and ruthenium to the nonspecific PCR primer. A two-level DNA pooling strategy was used to reduce the number of individual PCR reactions required. Pooling experiments established that ASA-PCR with ECL detection is sufficiently sensitive to reproducibly detect a single specific allele in the presence of a 40-fold excess of genomic DNA from individuals negative for the specific allele. The detection sensitivity of the ECL device and the design of the pooled DNA arrays reduced the number of PCRs required to detect the rare individuals with the variant sequences by approximately 90%. This strategy is called mass allele detection (MAD).