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seq2HLA specifications

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Unique identifier OMICS_02152
Name seq2HLA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some RNA-Seq sequence reads.
Input format FASTQ
Output data The most likely HLA class I and class II types, a P-value for each call, and the expression of each class.
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages Python, R
Computer skills Advanced
Version 2.2
Stability Stable
Maintained Yes

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Publication for seq2HLA

seq2HLA citations

 (10)
library_books

HLA and proteasome expression body map

2018
BMC Med Genomics
PMCID: 5872580
PMID: 29587858
DOI: 10.1186/s12920-018-0354-x

[…] the reference does not reflect the polymorphic nature of the hla system, precluding accurate hla typing [] and thus expression determination. to account for this, we developed the algorithm ‘seq2hla’ [] that takes bulk rna-seq raw data as input and outputs the most probable 4-digit hla class i and ii types [] and locus-specific expression., here, we extended seq2hla to determine the hla […]

library_books

Immunopharmacogenomics towards personalized cancer immunotherapy targeting neoantigens

2018
Cancer Sci
PMCID: 5834780
PMID: 29288513
DOI: 10.1111/cas.13498

[…] to obtain hla allele information from genome‐wide sequencing data (whole‐exome, whole‐genome, and rna sequencing data), including optitype, polysolver, phlat, hlareporter, hlaforest, hlaminer, and seq2hla. we have tested 961 whole‐exome data from the 1000 genomes project to evaluate the accuracy of these programs. among these algorithms, optitype showed the highest accuracy of 97.2% for hla […]

library_books

Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer

2018
BMC Cancer
PMCID: 5778667
PMID: 29357823
DOI: 10.1186/s12885-017-3825-0

[…] substitution). in the case of frameshift mutations, all downstream peptides generated up to a stop codon were considered potential neoantigens., hla typing was performed using a consensus of seq2hla [] and optitype [] across the samples for each patient (additional file )., class i mhc binding predictions were performed for peptides of length 8–11 using netmhcpan 2.8 [] with default […]

library_books

Computational Pipeline for the PGV 001 Neoantigen Vaccine Trial

2018
Front Immunol
PMCID: 5778604
PMID: 29403468
DOI: 10.3389/fimmu.2017.01807

[…] the patient’s hla type. this can be determined computationally from exome or bulk rna sequencing or validated externally using hla-specific amplicon sequencing (). the pgv pipeline currently uses seq2hla () for hla typing from tumor rna while also using amplicon sequencing of normal dna for validation. across 10 patients, the two methods have only disagreed on a single allele, […]

library_books

Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune control Mechanisms of HIV 1 Infected Elite Controllers

2017
PMCID: 5828548
PMID: 29269040
DOI: 10.1016/j.ebiom.2017.11.031

[…] the variant discovery. finally, variant discovery was performed by unifiedgenotyper module. the module used bayesian genotype likelihood model to call the variants. hla-typing was performed using seq2hla_ver2.2 ()., the search tool for the retrieval of interacting genes/proteins (string) (http://string.embl.de/) was used to identify known and predicted interactions among the differential […]

library_books

A genomic perspective on HLA evolution

2017
Immunogenetics
PMCID: 5748415
PMID: 28687858
DOI: 10.1007/s00251-017-1017-3

[…] ; melé et al. )., a promising approach is to use of an index with thousands of hla sequences reported in databases such as ipd-imgt/hla, instead of relying on a single reference genome. for example, seq2hla is a pipeline proposed by boegel et al. () which uses a form of in silico genotyping to both infer the genotypes at hla genes as well as estimate the expression of each hla allele at a locus. […]


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seq2HLA institution(s)
TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Mainz, Germany; University Medical Center of the Johannes Gutenberg University Mainz, III, Medical Department, Mainz, Germany; Ganymed Pharmaceuticals AG, Mainz, Germany

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