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A Novel Real-Time PCR Assay for Detection of HLA-A*31:01 in Individuals Being Considered for Carbamazepine Therapy
- David S. Krause, Kathleen Davis, Daniel Dowd, David J. Robbins
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- Journal:
- CNS Spectrums / Volume 26 / Issue 2 / April 2021
- Published online by Cambridge University Press:
- 10 May 2021, pp. 154-155
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Background
Carbamazepine, an anticonvulsant also used as a mood stabilizer and for trigeminal neuralgia, is associated with serious, sometimes fatal cutaneous adverse drug reactions, including Stevens Johnson Syndrome and toxic epidermal necrolysis1. Current literature demonstrates a genetic predisposition linked to specific class I and II human leukocyte antigen (HLA) types in various ethnic populations2. HLA-A*31:01 is one such HLA type, and is routinely identified by the tag SNP rs1061235. However, rs1061235 has poor specificity for HLA*31:01 due to interference of HLA-A*33 types3. We investigated the false positive rate in our population and developed a novel real-time PCR assay that distinguishes HLA-A*31:01 from other HLA-A types including HLA-A*33.
Methods120 unique samples were tested in triplicate during the validation of this assay and were sent to a reference lab for HLA next generation sequencing (NGS) typing, including 89 in-house samples and 31 Coriell samples with documented HLA typing results. The results from our real-time PCR assay were compared to the HLA typing results. HLA typing results were also compared to the tag SNP rs1061235 results to calculate the false positive rate.
ResultsThere was 100% concordance between our real-time PCR results and expected results based on HLA typing. 89 sample results for tag SNP rs1061235 were compared to HLA typing results. 75/89 samples had a rs1061235 variant, but 31/75 (41%) samples did not have the HLA-A*31:01 type, thus defining the false positive rate of the tag SNP for our population. We theorized there would be a small subset of rare HLA-A types that would interfere with the assay and we tested the three types available to us. We confirmed that 3 of the HLA types (HLA-A*31:04, 31:12, and 31:16) result falsely positive due to sequence homology with 31:01. There is no known literature indicating whether these rare HLA-A*31 subtypes are associated with cutaneous adverse reactions. These 3 HLA types and the other suspected interfering HLA types have limited frequency data sets and are expected to occur rarely in our patient population; we expect these HLA types make up less than 0.003% of the our population. Our assay specificity for the validation is >99%.
ConclusionsOur custom real-time PCR assay for detection of HLA-A*31:01 is significantly more specific than the commonly used tag SNP rs1061235. Clinicians considering carbamazepine therapy for their patients will have a better understanding of cutaneous adverse reaction risk and can make improved personalized treatment decisions. This quick, cost effective assay allows more patients in need of carbamazepine treatment to benefit from its use.
FundingGenomind, Inc.
4235 The Use of Checklists Throughout the Lifecourse of a Clinical Research Study: The Rockefeller University Checklist Suite
- Donna Brassil, Roger Vaughan, Arlene Hurley, Kathleen Dowd, Richard Hutt, Barry S. Coller
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- Journal:
- Journal of Clinical and Translational Science / Volume 4 / Issue s1 / June 2020
- Published online by Cambridge University Press:
- 29 July 2020, p. 69
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OBJECTIVES/GOALS: We have developed a comprehensive Translational Research Navigation Program to guide investigators all the way from protocol development through study closure. As the program evolved, we initially developed organizational tools and then restructured them into a series of checklists to ensure that critical elements were not excluded or duplicated. METHODS/STUDY POPULATION: A series of checklists to assure that all research elements, including regulatory, scientific, and institutional, are addressed from protocol inception through study closure were developed by clinical research coordinators/navigators. The checklists are periodically updated and modified to reflect changing local and national regulations and policies. The first tool became the “Protocol Development Checklist” and then additional tools were developed and modified into a suite of navigation checklists that include “Protocol Implementation Checklist,” “Protocol Conduct Checklist,” and “Protocol Completion Checklist.” RESULTS/ANTICIPATED RESULTS: The checklists have been incorporated into the Translational Research Navigation Program and have enhanced the organization and quality of protocols throughout their lifespan. For example, implementation of the Protocol Development Checklist resulted in a reduction in time to IRB approval (currently 10 days), and implementation of the Protocol Implementation Checklist has impacted the time from IRB approval to study start-up. The Protocol Conduct Checklist has aided investigators in being better prepared and more organized for study conduct activities and the Protocol Closure Checklist has assured timely protocol closure and regulatory compliance, including reporting to ClinicalTrials.gov. DISCUSSION/SIGNIFICANCE OF IMPACT: Protocol checklists are powerful tools to enhance thoroughness, organization, and quality of the clinical research process. The Rockefeller University protocol checklists are available to the CTSA and Scientific Communities. CONFLICT OF INTEREST DESCRIPTION: NA.