TypeLoader: A fast and efficient automated workflow for the annotation and submission of novel full-length HLA alleles

HLA : Immune Response Genetics
V SurendranathV Lange

Abstract

Recent years have seen a rapid increase in the discovery of novel allelic variants of the human leukocyte antigen (HLA) genes. Commonly, only the exons encoding the peptide binding domains of novel HLA alleles are submitted. As a result, the IPD-IMGT/HLA Database lacks sequence information outside those regions for the majority of known alleles. This has implications for the application of the new sequencing technologies, which deliver sequence data often covering the complete gene. As these technologies simplify the characterization of the complete gene regions, it is desirable for novel alleles to be submitted as full-length sequences to the database. However, the manual annotation of full-length alleles and the generation of specific formats required by the sequence repositories is prone to error and time consuming. We have developed TypeLoader to address both these facets. With only the full-length sequence as a starting point, Typeloader performs automatic sequence annotation and subsequently handles all steps involved in preparing the specific formats for submission with very little manual intervention. TypeLoader is routinely used at the DKMS Life Science Lab and has aided in the successful submission of more than 900 no...Continue Reading

References

Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Apr 2, 2010·Tissue Antigens·S G E MarshJ Trowsdale
Jun 2, 2012·Tissue Antigens·H Erlich
Nov 30, 2012·Nucleic Acids Research·Dennis A BensonEric W Sayers
Jan 28, 2014·BMC Genomics·Vinzenz LangeAlexander H Schmidt
Feb 6, 2014·PloS One·Alexander H SchmidtGerhard Ehninger
Jan 1, 2013·Human Heredity·Jean-Marie Tiercy, Frans Claas
Nov 22, 2014·Nucleic Acids Research·James RobinsonSteven G E Marsh
Nov 19, 2015·Nucleic Acids Research·Jun MashimaToshihisa Takagi
Nov 29, 2015·Nucleic Acids Research·Richard GibsonGuy Cochrane
Aug 6, 2016·Bioinformatics and Biology Insights·Steffen KlasbergLudovic Mallet

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Citations

Feb 9, 2020·International Journal of Immunogenetics·Alexander H SchmidtJohannes Schetelig
Nov 10, 2020·Frontiers in Immunology·David RoeMartin Maiers

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