High-Throughput HLA-Typing: on Raw, Unpurified Cord Blood Samples

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DESCRIPTION (provided by applicant): Abstract. The Unmet Opportunity: Accurate, simple, inexpensive, high throughput HLA-Typing, as the Companion Genetic Test to support a national-scale program of stem cell therapy. It has become clear that the 50-100mls of blood, readily obtained at birth from the umbilical cord (UCB) can become an abundant, relatively-inexpensive source of pluripotent mesenchymal stem cells to be used in the treatment of lymphoid cancers, the thalassemias and more recently, as the potential source for a much larger range of potential stem cell therapies. As ongoing research reveals the full pallet of cord blood stem cell therapies (diabetes, neurological disease, cardiovascular disease, trauma, etc) it could be feasible to scale-up the collection and processing of UCB stem cells to a level that would approximate the birth cohort (@12,000/day in the US). However, to support even 10% of that accrual rate, substantial enhancement of UCB sample processing and sample analysis will be required. In this R21, we focus on the scale-up of the Companion Genetic Test required for such allogenic UCB stem cell therapy: HLA-Typing of both the processed UCB stem cell samples and the patient population who would benefit from them. The Solution: Inexpensive Microarrays for HLA-Typing of raw stem cells from fresh umbilical cord blood, or better, from UCB collected and shipped dry on Guthrie Cards. We will optimize & validate a simple & inexpensive suite of microarray technologies for HLA-Typing, which we have already shown in Preliminary Results, to work on raw, completely-unpurified adult blood and on matched raw samples collected & shipped dry on Guthrie Cards. Of special importance to this R21, is access to highly-validated (raw) UCB specimens from the NHLBI-funded COBLT study, the seminal UCB c0nsortium (see Letter of Support). High resolution HLA-typing has already been obtained, by COBLT, on those UCB samples, using "gold-standard" genotyping technologies. In this R21, we will focus on HLA-A, HLA-B and DRB1 genes, which are known to have the strongest associations with UCB therapeutic outcome and HLA-C & DQB1 for which there are preliminary data to suggest a role in optimized UCBT outcomes. Of special logistical importance will be our demonstration that such "Raw Sample HLA-Typing" can be optimized to work on dried enriched UCB samples, collected and shipped on Guthrie cards, via a novel recovery approach where we "just add water" to produce a sample ready for analysis. Validation of this set of coupled microarray technologies, in support of UCB-based stem cell therapy, will be supported by 4 Specific Aims: SA1. Yrs 1,2. Manufacture low-cost HLA-Chips [HLA-A, HLA-B, HLA-C, DRB1 & DQB1]. SA2. Yr-1. Optimize HLA-Typing with 480 raw, enriched UCB samples. SA3. Yr-2. Optimize HLA-Typing on 480 raw, enriched UCB specimens: dry on Guthrie Cards. SA4. Yr-2. Automated, HLA-Typing of raw, enriched UCB samples: fresh & dried. Relation to a Follow-on R33. In this R21, we will demonstrate that 5uL of enriched UCB can be pipetted to a Guthrie Card, mailed dry, then fed-into our high throughput HLA-Typing workflow by "just adding water". In a follow-on R33, we will leverage this R21 validation as the basis for a much larger, prospective validation with a NHLBI-affiliated group such as the Cord Blood Working Group of the World Marrow Donor Association. Although ambitious, that idea is feasible: given that one of this R21 Team (BK) was previously Chairman of the International Committee of The NMDP. In that R33, the current SOPs for collection, processing & HLA-Typing would continue unaltered: but, in parallel, 5uL of each enriched UCB sample would be transferred to a Guthrie Card at point of processing, anonymized, mailed internationally to GenUSA for high throughput HLA-Typing, on a scaled-up version of the system developed in the R21. That "Raw Guthrie Card" HLA-Typing would then be compared, in terms of accuracy & cost, to that obtained by current methods of HLA-Typing on purified DNA.