title: Next generation sequencing with a semi-conductor technology (Ion Torrent PGM™) for HLA typing: overall workflow performance and debate.
abstract: Current high resolution HLA typing technologies produce ambiguous results, and it is often necessary to perform additionnal tests to resolve these ambiguities. Next generation sequencing is a promising technology, which can overcome this problem. It is going to usher a new strategy to determine HLA compatibility between donor and recipient. It can lead to non ambiguous results by analysing the full amplified sequence of HLA genes and by eliminating heterozygote phase ambiguities. Instead, as many new techniques, we can face several problems, such as analysis difficulties because of incomplete HLA sequences in the database or errors related to the sequencing instrumentation. Moreover, the clinical relevance of analysing non coding regions of HLA genes is not well understood, but raise questions about the interest of getting HLA full sequence to understand drugs side effects or pathogenesis of infectious or auto-immune diseases. Our objective in this article is to present a commercial workflow for HLA typing by NGS, on Ion Torrent PGM™ sequencer, and to focus attention about pitfalls encountered during the analysis.
authors: Laboratoire de génétique moléculaire et d'histocompatibilité, Pôle de pathologie biologie, CHRU Morvan, Brest, France.
authors: Virginie
authors: V
authors: Moalic-Allain
authors: Laboratoire de génétique moléculaire et d'histocompatibilité, Pôle de pathologie biologie, CHRU Morvan, Brest, France.
authors: Bernard
authors: B
authors: Mercier
authors: Laboratoire de génétique moléculaire et d'histocompatibilité, Pôle de pathologie biologie, CHRU Morvan, Brest, France.
authors: Paul
authors: P
authors: Gueguen
authors: Laboratoire de génétique moléculaire et d'histocompatibilité, Pôle de pathologie biologie, CHRU Morvan, Brest, France.
authors: Claude
authors: C
authors: Ferec
mesh_terms: D003951:Diagnostic Errors / Q000706:statistics & numerical data; D003955:Diagnostic Tests, Routine / Q000295:instrumentation / Q000379:methods; D005602:France; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation* / Q000379:methods; D006650:Histocompatibility Testing / Q000295:instrumentation* / Q000379:methods*; D006801:Humans; D015203:Reproducibility of Results; D012666:Semiconductors; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000295:instrumentation* / Q000379:methods; D057188:Workflow
keywords: HLA genes; Ion Torrent PGM™ sequencer; next generation sequencing