A major focus of our research has dealt with biophysical chemistry of nucleic acid hybridization and branch migration as well as DNA-interacting proteins. In recent work related to single cell analyses, we have developed a single molecule-based molecular haplotyping system. The system begins with simultaneous PCR across two heterozygous polymorphic sites on single template molecules isolated by an oil-water emulsion. The method relies on linking PCR in the emulsion to connect the two PCR products, capping and allele-specific PCR readouts.

Human PON1 haplotypes were determined in a large cohort to demonstrate haplotype-phenotype association. PON1 is essential for the detoxification of organophosphates. As part of the birth cohort study in the Mount Sinai Children's Environmental Health Center, we have examined human variation in activation and detoxification of organophosphates. We have found that not only do neonates have four-fold lower levels of PON1 than adults, but that those levels vary more widely with common promoter polymorphisms in neonates than in adults. Thus certain neonates have up to 10-fold less protection than adults. Low maternal PON1 together with maternal exposure to a commonly used organophosphate had a significant effect on birth outcome in the cohort.

In additional current work related to individual genetic variation, we are developing high-throughput methods for measuring mRNA allelic imbalance in human dendritic cells challenged with viruses in the Technology Development Component (TDC) of the Center for Investigating Viral Immunity and Antagonism (CIVIA) and in the Program for Research in Immune Modeling and Experimentation (PRIME). These studies complement the transcriptome approaches in CIVIA and PRIME and enable the discovery of new human variation evident only in the context of viral challenge. In addition, we have developed new technology allowing measurement of transcription from single human dendritic cells and from individual chromosomes within these single cells. Such variation may be important in identification of susceptible individuals and in the development of vaccines.