Seq2HLA
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Application data |
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| Created by | Sebastian Boegel, Martin Löwer, Michael Schäfer, Thomas Bukur, Jos de Graaf, Valesca Boisguerin, Özlem Türeci, Mustafa Diken, John C Castle and Ugur Sahin |
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| Biological application domain(s) | Transcriptomics, Mapping |
| Principal bioinformatics method(s) | Read mapping, Genetic variation analysis |
| Technology | Illumina |
| Created at | TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg
University Medical Center of the Johannes Gutenberg University Mainz, III. Medical Department Ganymed Pharmaceuticals AG, Freiligrathstrasse 12, 55131 Mainz |
| Maintained? | Yes |
| Input format(s) | FASTQ |
| Output format(s) | sam, .txt, console (browser) - output |
| Programming language(s) | Python, R |
| Operating system(s) | Unix, Mac OS X |
Summary: seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.
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Description
The major histocompatibility complex (MHC) molecules display peptide antigens that are derived from intracellular (class I) and extracellular (class II) proteins on the surface of vertebrate nucleated cells. The human MHC, called the Human Leukocyte Antigen is highly polymorphic and polygenic. Next generation sequencing (NGS) is a novel platform that enables rapid generation of billions of short nucleic acid sequence reads. Several studies described the use of NGS in high-throughput HLA genotyping utilizing genomic DNA or cDNA, e.g. Lank et al. 2012. All of these techniques utilize specialized NGS protocols including primer design to amplify only MHC class I alleles and amplicon sequencing with long reads (>=150 nucleotides) using Roche/454 GS FLX or Illumina GAIIx. In contrast, gene expression profiling in patient samples using “whole transcriptome” sequencing (RNA-Seq profiling) typically utilizes much shorter reads. Seq2HLA is an algorithm to utilize the sequence content of RNA-Seq reads to determine both HLA type and expression. It uses standard RNA-Seq reads and requires no change to lab protocols, adding a new dimension for HLA typing and biomarker studies
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