Technology development in service of patients
Every program in the lab pairs a measurement we are building with a question that could not be answered without it. Most of our questions come from the clinic, where a small number of cells that survive treatment decide a patient's outcome.
Single-cell and cell-free genomics technologies
The lab invented primary template-directed amplification (PTA), a method for amplifying the genome of a single cell. PTA gives a more complete and more uniform representation of the original genome than previous whole-genome amplification methods, which lets us call roughly 90% of small variants in a cell with high precision. It is now used across sample types, from low-input and ancient DNA to eukaryotic cells to single microbes.
We have since paired PTA with full-length transcript capture so that genomic variants and transcript abundance can be measured in the same cell, and we are developing sparse methylation marking to add regional DNA methylation to that readout. In parallel, we build wet-lab and computational methods to detect mutations, methylation changes, and microbial nucleic acids in cell-free DNA.
How PTA works. In MDA, exponential amplification from the first primed sites over-represents random loci; in PTA, exonuclease-resistant terminators keep amplification quasi-linear from the original template, giving far more uniform coverage. From Gonzalez-Pena et al., PNAS 2021.
Leukemia clonal evolution and treatment resistance
Most children with leukemia are cured with standard therapy, yet some relapse and do poorly. In most of those patients the cancer is not uniformly resistant. Instead, a very small fraction of malignant cells harbor or acquire resistance to many different agents, and those cells drive an incurable disease.
Using the single-cell methods we develop, we isolate and sequence rare persistent leukemia cells from patients across diagnosis, treatment, and relapse to define the mechanisms of resistance and the mutational processes, such as APOBEC-driven mutagenesis, that fuel evolution. The goal is a set of biomarkers and single-cell assays that flag relapse before it is clinically visible and guide each child to the most effective, least toxic treatment. Related projects examine acute myeloid leukemia and the infectious and environmental exposures that may contribute to leukemia development.
Single-cell whole-genome phylogeny of one patient's leukemia before (blue) and after (pink) treatment, with per-cell mutations, copy-number changes, and surface markers. From Pang et al., bioRxiv 2025 (v2).
Genetic and epigenetic mosaicism in human tissues
Each of us develops from a single cell into tens of trillions, acquiring somatic mutations with nearly every division and with exposure to the environment as we age. This enormous within-tissue genomic diversity is present in everyone, but little is known about how it contributes to disease, or why only a tiny number of mutated cells ever progress to malignancy.
We apply the lab's paired genome-and-epigenome methods to the same single cells from normal and diseased human tissues, including neurons and hematopoietic cells, to learn how specific genetic and epigenetic features interact to produce abnormal phenotypes. Recent work with collaborators has mapped somatic mutations in human neurons and shown that intermediate-heteroplasmy mitochondrial DNA mutations are a source of functional heterogeneity among primary cells.
Stereo-EEG electrodes mapped onto a pediatric patient's brain. After the electrodes are removed, we sequence the genome of single neuronal nuclei from their tips. Collaboration with Gerald Grant, Duke Neurosurgery.
Infectious disease diagnostics
Children receiving cancer therapy are at high risk of bloodstream infection, and bacterial sepsis remains a leading cause of death worldwide. Current culture-based diagnosis is slow and often negative, so treatment is empiric.
With collaborators at St. Jude Children's Research Hospital, we have shown that sequencing microbial cell-free DNA in plasma can predict bloodstream infection in children with cancer, in some cases days before the clinical diagnosis. We are also developing rapid, inexpensive approaches to sepsis diagnosis, including cataloguing volatile organic compounds in blood that are specific to bacterial bloodstream infection as the basis for an electronic-nose point-of-care test developed with IBM Research.
Single-microbe genomics
Most microbes cannot be cultured, and metagenomic assemblies blur the differences between closely related strains. Adapting PTA to single bacterial cells (scMicrobe PTA), in collaboration with the DOE Joint Genome Institute, recovers near-complete genomes from individual cells without culture.
We are applying this to strain-level questions in microbial communities and to the genetics of antimicrobial resistance in clinical isolates, where a single resistant cell can matter.
Methicillin-resistant Staphylococcus aureus, colorized scanning electron micrograph. Image: NIAID (CC BY 2.0).
Methods that leave the building
We build technologies so that they can be used, and we measure success partly by how far they travel. PTA is now a commercial product used by academic and industry groups worldwide, it is licensed for preimplantation genetic testing in IVF clinics, and paired single-cell genome and transcriptome sequencing of residual leukemia cells, an approach developed here, is offered as a service to other researchers. Chuck Gawad co-founded BioSkryb Genomics to carry that work out of the lab and serves as its scientific founder; Stanford's conflict-of-interest office reviews the relationship. Milestones are posted on the news page.
Interested in collaborating?
We are always excited to work with new scientists. Email Chuck Gawad with a short description of the question you want to answer.