Assessing the feasibility to implement NGS-based HLA typing for diagnostic purposes
Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
The Human Leukocyte Antingen (HLA) genes encode for the Major Histocompatibillity Complex (MHC) and are know to be highly polymorphic. The HLA genes consist of more than 220 genes and are well studied; due to their high importance in for example organ and stem cell transplantations. HLA polymorphism between a donor and a recipient to achieve a successful transplantation. Sequence-specific oligonucleotie (SSO), Sequence-specific priming (SSP) and Sequenced-based typing (SBT) are PCR-based HLA typing methods that have been used for several years. However, these methods have limitations in terms of resolution and ambiguities. Next Generation Sequencing (NGS) technologies have the ability to overcome these limitations and the demand of an NGS-based HLA typing approach is increasing. This project aims to assess the feasibility and to implement NGS-based HLA typing for diagnostic purposes. A market analysis is performed to understand the market demand and the limitations with today's technologies. hree NGS platforms (Illumina MiSeq system, PacBio RS II and Ion Torrent PGM 314) are compared in two different benchmarks. Next, we practically implement an HLA typing approach by the Illumina MiSeq sequencing technology. In conclusion, the Illumina MiSeq system is today the most suitable platform for HLA typing and provides reagent kits for low and high throughput HLA typing.
Place, publisher, year, edition, pages
massively parallel sequencing, HLA, diagnostics, next generation sequencing, target product profile benchmark, HLA typing, transplantation
Engineering and Technology
IdentifiersURN: urn:nbn:se:kth:diva-173606OAI: oai:DiVA.org:kth-173606DiVA: diva2:853824