Skip to content

Immunology, Retrovirology and Cure Core

The Immunology, Retrovirology and Cure Core provides advanced tools and training for evaluating humoral and cellular responses to HIV infection.

The assays, reagents, technology, and education offered by the Core support CFAR research involved with the prevention, detection, and treatment of HIV infection and AIDS. Most Core services are used by investigators to help quantify immune responses in plasma, serum, secretions, or cells from HIV-infected patients or lentivirus-infected nonhuman primates. The types and levels of support available from Core faculty are flexible—from quick telephone or email troubleshooting consultations to intensive group trainings on specific technologies; from simple cytometry experiments using one to three colors to cutting-edge experiments using up to 18 colors; and from rapid immune analysis of a few samples for a pilot assessment or hypothesis generation to longer-term collaborations involving joint study design and execution. Services are accessible through our four subcores:

Cellular Immunity and Flow Cytometry Subcore

The mission of the flow cytometry subcore is to support all phases of experimental studies using flow cytometry including experimental design, staining panel design, laboratory procedures, collection of samples on the instrument, analysis of data and interpretation of results.

Read more

Humoral Immunity Subcore

Antibody and antigen testing; recombinant protein and antibody production; viral and cell line culture; neutralization assays.

Read more

Mucosal Immunity and Non-Human Primate Immunology Subcore

Advice in study design and testing of vaccines and therapies in SIV and SHIV monkey models for AIDS and analysis of humoral, cellular, and innate immune responses in the blood and mucosal compartments of nonhuman primates.

Read more

Quantitative RNAseq and High Content Data Analysis Subcore

Read more

6-color Naica droplet digital PCR (dPCR) system

UW/Fred Hutch CFAR Immunology Core has used CFAR Administrative Supplement funding to purchase a 6-color Naica droplet digital PCR (dPCR) system. The system provides absolute counts of target copies using up to 6 fluorescent dyes and no standard curve is required.

Workflow: Primers, probes and template are combined with PCR master-mix and transferred to a chip. Partitioning and thermal-cycling, take place in the Geode instrument and the chip is transferred to the Prism instrument for scanning and imaging. Raw data can be viewed and analyzed in the provided Crystal Miner analysis software.

Applications: ddPCR is the ideal technology to quantify nucleic acids with high precision; applications include rare event detection, whole genome amplification and copy number variation. In the Hladik lab, this instrument will allow the team to accurately measure intact HIV proviral reservoirs, get the most HIV-related information from each sample by highly multiplexing, and recover samples after analysis for subsequent sequencing. Multi-color-detection also allows combination of reference assays with assays of interest in the same ddPCR reaction (increasing normalization accuracy), testing of multiple mutational variants in the same reaction, and conservation of limited sample material (e.g., blood from infants or mucosal specimens).

Use: The equipment is now available for use in the Center for Reproductive Sciences in the UW SLU Campus (850 Republican St), building S, room 220. The accompanying analysis software (Crystal Miner) can be installed on a separate PC for post-run analysis outside the lab. The Hladik group has extensive experience running routine ddPCR assays, using ddPCR equipment creatively to design and optimize specialized assays, as well as analyze and visualize raw results using R or excel.

Interested CFAR users will either contract with us to design and run assays for them (clinical scientists), or we will train them to use the equipment, with ongoing technical and assay design assistance (laboratory scientists).

interested parties should contact Florian Hladik at

Genome Sequence Analysis
We provide researchers consultation access to Core scientists with leading edge expertise in all current nucleic acid sequencing methodologies, including Sanger, Illumina, PacBio, and Oxford Nanopore platforms. We also provide legacy support for the 454/pyrosequencing platform. Consulting on HIV genome sequence analysis includes bioinformatic pipeline development, high-performance computing power, and interpretive support from Core staff.
Retrovirology and Molecular Data Science Core Consulting
Our scientists offer consulting to investigators on the experimental design, optimal specimen acquisition, collection and processing, experimental aspects of clinical trial development, data processing and data interpretation, focusing on experiments that acquire molecular sequence data. Areas of expertise include virologic assays, nucleic acid sequence analysis (see below), phylogenetics, molecular epidemiology, viral integration site analysis, and more.
Introduction to Flow Cytometry Workshop

Keith Jerome, MD, PhD
Core Co-Director

Florian Hladik, PhD
Core Co-Director

Mucosal Immunity and Non-Human Primate Immunology Subcore Director
Email: fhladik at

Stephen De Rosa, MD
Cellular Immunity and Flow Cytometry Subcore Director
Email: sderosa at
Telephone: 206-667-1681

Noah Sather, PhD
Core Associate Director
Humoral Immunity Subcore Director
Email: noah.sather at

Deborah Fuller, PhD
Non-Human Primate Immunology Subcore Director
Email: fullerdh at

Sandra Dross, PhD
Non-Human Primate Immunology Subcore Co-Director
Email: sdross at

Michael Gale, PhD
Quantitative RNAseq and High Content Data Analysis Subcore Director
Email: mgale at