Analysis of MHC class I as one of the host factors responsible for severe dengue infection by means of a portable sequencer
Project/Area Number |
18K16170
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Research Category |
Grant-in-Aid for Early-Career Scientists
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Allocation Type | Multi-year Fund |
Review Section |
Basic Section 54030:Infectious disease medicine-related
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Research Institution | The University of Tokyo |
Principal Investigator |
Runtuwene Lucky 東京大学, 大学院新領域創成科学研究科, 特任助教 (40793782)
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Project Period (FY) |
2018-04-01 – 2020-03-31
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Project Status |
Completed (Fiscal Year 2019)
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Budget Amount *help |
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2019: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2018: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
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Keywords | MinION / Dengue virus / Dengue hemorrhagic fever / Dengue fever / MHC class I / Dengue / Portable sequencer |
Outline of Final Research Achievements |
Since 2018, we have collected 23 samples from Manado, Indonesia. Previously we have reported on 2019, that these samples were collected from hospitalized patients that were positive for dengue fever. We were able to sequence their HLA-A, HLA-B, and HLA-C genes and had analyzed the HLA type using a bioinformatics pipeline called Athlon. Continuing on this project, in 2019 we have performed Illumina sequencing to validate the MinION results. Using the available data from 23 samples, we found that the results obtained from MinION+Athlon and Illumina have 36.5% difference. We conclude that MinION is still not good for HLA typing and we were not able to determine the HLA correlated to dengue severity. One of the reasons is because of the high error rate of the v9.4 flowcell. Therefore, using the new v10.3 flowcell that has lower error rate available in 2020, we will re-sequence and re-analyze the samples.
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Academic Significance and Societal Importance of the Research Achievements |
We think that MinION may have advantage over Illumina because the pipeline is able to detect MHC up to three fields which is more specific. Furthermore, with its relatively cheap investment overhead, MHC class I detection can be very valuable in developing countries, but it will still need refining.
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Report
(3 results)
Research Products
(4 results)