Subgrouping Chronic Fatigue Syndrome Patients by Genetic and Immune Profiling
Abstract
We have a cohort of 200 untreated CFS cases and 400 matched controls that will undergo two novel tests (CyTOF-phosphoflow and HLA Typing through a breakthrough method discovered at Stanford) in order to help enhance our understanding of CFS and contribute to the elucidation of the pathogenesis of the disease. For CyTOF testing, we are exploring the immune responses by a novel flow cytometer that detects individual cell traits with time-of-flight mass spectrometry (CyTOF). We have completed the CyTOF phenotyping, phospho-flow panel, and gating schemes for testing. Also, the flow cytometry preparation robotics for CyTOF was optimized and antibodies were conjugated. The testing is ongoing and we hope to continue testing as permitted. For HLA typing testing, we are determining the human leukocyte antigens (HLA) types using a novel method that combines long-range polymerase chain reaction (PCR) with very high-throughput, multiplexed Illumina paired-end sequencing of genes permitting direct haplotyping. We have identified the DNA PAXgene tubes that will be used for testing. Also, we have identified the best possible conditions to amplify all the HLA gene of interest, namely for the class I genes HLA-A, -B, -C and for the class II genes: HLA DQA, DQB, DRB DPA and DPB. Lastly, we achieved the goal of robust and highly reproducible amplification of each In summary, for CyTOF testing we finalized the Phospho-CyTOF panel and have begun testing samples. To date we have tested 54 samples. These samples will continue to be tested for Year 2. The data is being received; no analysis has been done yet. The data will be analyzed by our statistical team. For HLA typing testing, all the DNA PAXgenes have been identified and separated into different batches. To date, two plates have been run and are currently being analyzed. To date we have tested 180 samples Year 1 has allowed us to ready the logistics and to begin CyTOF and HLA Typing testing.
Document Details
- Document Type
- Technical Report
- Publication Date
- Oct 01, 2013
- Accession Number
- ADA586003
Entities
People
- Holden Maecker
- Ian Valencia
- Jose Montoya
- Michael Mindrinos
- Rosemary Fernandez
Organizations
- Stanford University