The investigation of single molecule sequencing to characterise HLA genes for clinical use in allogeneic transplantation

Linh Truong

doi:10.26182/ccc6-fb97

The investigation of single molecule sequencing to characterise HLA genes for clinical use in allogeneic transplantation

Linh Truong

UWA Medical School

Research output: Thesis › Doctoral Thesis

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Abstract

Experiments presented in this thesis reveal the possibility of producing phase-defined HLA genotypes through the use of multiplexed amplification and nanopore sequencing. We present a breakthrough that provides prospective HLA allele-level typing during solid organ allocation. We encountered challenges throughout the development of HLA nanopore sequencing, specifically in the generation of large datasets. A novel data analysis pipeline was built to utilise cloud resources. When analysing HLA genes on a larger scale, important SNPs and extended haplotypes became more apparent. Finally, future research based on the findings in this thesis should focus on HLA haplotypic associations or MHC block matching.

Original language	English
Qualification	Doctor of Philosophy
Awarding Institution	The University of Western Australia
Supervisors/Advisors	D'Orsogna, Lloyd, Supervisor Martinez, Olga, Supervisor Tilanus, Marcel G.J., Supervisor, External person De Santis, Dianne, Supervisor Groeneweg, Mathijs, Supervisor, External person
Thesis sponsors	Australian Government Research Training Program
Award date	9 Nov 2023
DOIs	https://doi.org/10.26182/ccc6-fb97
Publication status	Unpublished - 2022

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10.26182/ccc6-fb97

THESIS - DOCTOR OF PHILOSOPHY - TRUONG Linh - 2022
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Report from the extended HLA-DPA1 ~ promoter ~ HLA-DPB1 haplotype of the 18th international HLA and immunogenetics workshop
Truong, L., Matern, B. M., El-Lagta, N., Mobegi, F. M., Askar, M., Ogret, Y., Oguz, F. S., Kwok, J., D'Orsogna, L., Martinez, P., Petersdorf, E., Tilanus, M. G. J. & De Santis, D., Dec 2023, In: Hla. 102, 6, p. 690-706 17 p.
Research output: Contribution to journal › Article › peer-review

Open Access
3 Link opens in a new tab Citations (Scopus)
Nanopore sequencing data analysis using Microsoft Azure cloud computing service
Truong, L., Ayora, F., D'Orsogna, L., Martinez, P. & De Santis, D., Dec 2022, In: PLoS One. 17, 12, 15 p., e0278609.
Research output: Contribution to journal › Article › peer-review

Open Access
9 Link opens in a new tab Citations (Scopus)
A novel multiplexed 11 locus HLA full gene amplification assay using next generation sequencing
Truong, L., Matern, B., D'Orsogna, L., Martinez, P., Tilanus, M. G. J. & De Santis, D., 1 Feb 2020, In: Hla. 95, 2, p. 104-116 13 p.
Research output: Contribution to journal › Article › peer-review
12 Link opens in a new tab Citations (Scopus)

Cite this

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title = "The investigation of single molecule sequencing to characterise HLA genes for clinical use in allogeneic transplantation",

abstract = "Experiments presented in this thesis reveal the possibility of producing phase-defined HLA genotypes through the use of multiplexed amplification and nanopore sequencing. We present a breakthrough that provides prospective HLA allele-level typing during solid organ allocation. We encountered challenges throughout the development of HLA nanopore sequencing, specifically in the generation of large datasets. A novel data analysis pipeline was built to utilise cloud resources. When analysing HLA genes on a larger scale, important SNPs and extended haplotypes became more apparent. Finally, future research based on the findings in this thesis should focus on HLA haplotypic associations or MHC block matching.",

keywords = "HLA typing, Transplantation, Nanopore sequencing, Cloud computing, Haplotype matching, Block matching",

author = "Linh Truong",

year = "2022",

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language = "English",

school = "The University of Western Australia",

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AB - Experiments presented in this thesis reveal the possibility of producing phase-defined HLA genotypes through the use of multiplexed amplification and nanopore sequencing. We present a breakthrough that provides prospective HLA allele-level typing during solid organ allocation. We encountered challenges throughout the development of HLA nanopore sequencing, specifically in the generation of large datasets. A novel data analysis pipeline was built to utilise cloud resources. When analysing HLA genes on a larger scale, important SNPs and extended haplotypes became more apparent. Finally, future research based on the findings in this thesis should focus on HLA haplotypic associations or MHC block matching.

KW - HLA typing

KW - Transplantation

KW - Nanopore sequencing

KW - Cloud computing

KW - Haplotype matching

KW - Block matching

U2 - 10.26182/ccc6-fb97

DO - 10.26182/ccc6-fb97

M3 - Doctoral Thesis

ER -

The investigation of single molecule sequencing to characterise HLA genes for clinical use in allogeneic transplantation

Abstract

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Research output

Report from the extended HLA-DPA1 ~ promoter ~ HLA-DPB1 haplotype of the 18th international HLA and immunogenetics workshop

Nanopore sequencing data analysis using Microsoft Azure cloud computing service

A novel multiplexed 11 locus HLA full gene amplification assay using next generation sequencing

Cite this