The goal of the Retrovirology and Molecular Data Science (RMDS) core is to help researchers perform optimized viral analysis experiments and analyze data from state-of-the-art genomics and database technologies, in support of HIV and related research. To inquire about any of the services listed below, send email to firstname.lastname@example.org, and Core staff will route your request appropriately.
As new technologies of likely general use are identified this resource works with other center investigators to acquire and deploy those techniques. The tools include computational tools and also their associated laboratory protocols and techniques.
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.
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.
The UW Primary Infection Clinic (PIC) and specimen repository were established in 1992. The PIC has specimens from 833 individuals and enrolled 394 subjects in primary and early HIV infection into longitudinal studies of the pathogenesis, clinical epidemiology, and management of primary HIV-1 infection. The PIC specimen repository is currently composed of over 120,000 blood product specimens, focusing on heavy sampling of subjects during the acute phase of HIV infection and continued sampling at 6-12 month intervals, often over many years of follow up.
Bringing computational tools to bench scientists risks their misuse and data misinterpretation without basic training in the concepts and methods that underlie these tools. Responsibility for data management and analysis often falls on graduate students and postdoctoral fellows, who must familiarize themselves with software tools, or even programming languages, without the benefit of formal training or peer or supervisor mentorship.
Our labs offer advanced virologic assays on a fee-for-service basis, subsidized in part by the CFAR. Assays available include the quantitative viral outgrowth assay (QVOA) and tat-induced limiting diultion assay (TILDA) for measuring HIV reservoirs; the oligonucleotide ligation assay (OLA) for drug resistance; Illumina-based screening for HIV co-receptor tropism (CCR5 vs. CXCR4); and multiple approaches to HIV integration site (IS) determination. Some assays are available under CLIA-certified conditions.
The Core resource allows researchers to gain access to specialized expertise that is not ordinarily expected in individual laboratories nor is often accessible through more common shared resources or services. In its most general form all aspects related to the use of any molecular assay that frequently requires non-trivial computational or mathematical expertise; although the services are not limited to the computational component. The core’s expertise includes the laboratory protocols needed to generate the data sets; sequences of DNA or RNA (or RNA subcomponents like polysomes) from host cells (including T Cells) or viruses, and includes both high dimension and also low dimensional assays. We can support consulting, training and technology development and also hands on data analysis or laboratory work when the effort is modest.
1. Short-term and longer term consulting - An email help-desk is staffed for users to submit questions, request meetings to discuss specific analysis strategies, and solicit advice on experiment design and novel research studies. For longer term projects that may not require sustained effort but can benefit from longer term lower level of effort team members can be assigned to assist in supervising your staff who can then implement the plan.
2. Hands on support for laboratory components, data processing and analysis - Staffing is provided for short term projects in the areas of microarray, high-throughput DNA sequencing, genomics, & proteomics data, and for combining data with public bioinformatics resources, including expertise specific to viral sequence analysis (described below), analysis of DNA and RNA sequences of host cells, microbiome, and other assays. We can also provide longer term more intensive support to move a manuscript or specific project past a milestone (like a manuscript acceptance) whenever handing it off is impractical (e.g., whenever the effort at one time depends on understanding of previous steps or decision choices) especially when multiple CFAR investigators are involved. This “hands on” component of the resource is the highest priority of the core.
3. Technology Development and Acquisition -- As new technologies of likely general use are identified this resource works with other center investigators or shared resources to acquire and deploy those techniques, including companion laboratory and computational components; examples include T Cell sequencing, ribosome or polysome profiling, and others. The Core steering committee meets frequently to discuss the potential impact of new technology acquisition. Researchers with ideas should send an email to the helpdesk (email@example.com) with a description. Whenever new technologies are developed the group begins with a pilot to understand the feasibility and potential expense of providing the service to CFAR. The investigators who are requesting it and will benefit from it are asked to contribute to the pilot, by providing resources such as their own time, or physical materials (specimens) used in the pilot. Pilots are undertaken whenever the steering committee feels that it is worth the price compared to other activities that will be eliminated.
4. Development, maintenance, support and access to software: A key aspect of the Core is to provide access to computational tools (some web-based, others standalone) required to interpret sequence data, including phylogenic analysis, classification/clustering, processing RNA- or DNA- sequence data. A current list of software & some algorithms: http://indra.mullins.microbiol.washington.edu/ https://github.com/fredhutchio/ https://github.com/fredhutchio/argo-navis
To receive services, users should send a brief email to firstname.lastname@example.org that includes a few sentences describing, briefly, the nature of your questions and your contact information. Core leaders will use this description to assign your request to an appropriate staff member who will contact you for follow-up. Most often you will be contacted by a staff member the same day as the request. Follow-up may include a one-on-one meeting, or possibly email or phone exchanges if that is adequate.