TypeLoader2: Automated submission of novel HLA and killer‐cell immunoglobulin‐like receptor alleles in full length

Abstract

The Immuno Polymorphism Database (IPD) databases provide global, curated repositories for information regarding polymorphisms of genes of the immune system, thereby generating immense value for the research and clinical communities. The advent of high‐throughput genotyping in immunogenetics has led to dramatically growing numbers of heretofore unknown HLA and lately also killer‐cell immunoglobulin‐like receptor (KIR) alleles, which are to be curated and deposited in the IPD‐IMGT/HLA and IPD‐KIR databases, respectively. It is highly desirable that these novel alleles are characterised and submitted in full length, and that known alleles are extended to cover the complete gene sequence. However, the manual annotation and submission of sequences to European Molecular Biology Laboratory's European Nucleotide Archive and the IPD‐IMGT/HLA and IPD‐KIR databases is time‐consuming and error‐prone. Here, we report the substantial extension of the HLA allele submission tool TypeLoader, which now also supports the annotation and submission of KIR alleles. To enable a more widespread use of this tool, we have made it available as a stand‐alone application that can easily be installed on standard Windows or Linux computers. Furthermore, an internal SQLite database was added to store a wide range of metadata about each allele. This allows TypeLoader2 to be used as a lab's central information platform for the annotation, curation and submission of full‐length HLA and KIR allele sequences. The software is freely available from GitHub ( https://github.com/DKMS-LSL/typeloader ). We hope that the increased convenience and scope of TypeLoader2 will foster the submission of more full‐length sequences to the IPD‐IMGT/HLA and IPD‐KIR databases, ultimately promoting the use of full‐length sequencing for genotyping both HLA and KIR.

HLA‐E diversity unfolded: Identification and characterization of 170 novel HLA‐E alleles

“…Besides the targeted novel alleles, the full‐length sequences of all partner alleles were analyzed to identify additional variations. Finally, all approved sequences were submitted to IPD‐IMGT/HLA using TypeLoader2 20 . If two identical sequences from different samples were available, the second sequence was submitted as confirmatory sequence.…”

Immunogenetics in stem cell donor registry work: The DKMS example (Part 2)

“…In order to facilitate the submission process for novel alleles, we developed TypeLoader2. This software tool supports the automated bulk submission of whole‐gene HLA, MIC and KIR sequences (Schöne et al, ; Surendranath et al, ). TypeLoader2 runs on Windows and Linux and is freely available at https://github.com/DKMS-LSL/typeloader.…”