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OptiType specifications

Information


Unique identifier OMICS_05461
Name OptiType
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline András Szolek <>

Publication for OptiType

OptiType citations

 (15)
library_books

Population level distribution and putative immunogenicity of cancer neoepitopes

2018
PMCID: 5899330
PMID: 29653567
DOI: 10.1186/s12885-018-4325-6

[…] its coordinates from the vcf file and the cds in the hg19 gene transfer format file [], and translating this sequence into amino acids. each patient’s hla type was determined from fastq files using optitype (v1.3.1) [], and the binding affinity of all predicted tumor and normal epitopes was predicted with netmhcpan (v2.8) [] for each epitope and patient-specific hla allele combination. […]

call_split

A pilot study of durvalumab and tremelimumab and immunogenomic dynamics in metastatic breast cancer

2018
PMCID: 5922371
PMID: 29721177
DOI: 10.18632/oncotarget.24867
call_split See protocol

[…] ≥10%, (v) variant frequency in normal of <2%, and (vi) fisher p value of <0.05., using whole-exome sequence data of the germline dnas, hla class i genotypes of each patient were determined by optitype algorithm []. subsequently, neoantigens for each hla allele were predicted from non-synonymous mutations identified through the whole exome sequence data of 14 tumor samples. all 8- […]

library_books

Increased RNA Editing May Provide a Source for Autoantigens in Systemic Lupus Erythematosus

2018
PMCID: 5905401
PMID: 29617672
DOI: 10.1016/j.celrep.2018.03.036

[…] the peptide sequence for the analyses and find recoding, he and pre-known sites filtered for snps and hla genes were annotated using wannovar (, ). hla alleles for each sample were derived using optitype (). for each sample, recoding sites (detected by the he analysis) inside peptides that have at least one window (see ) with strong affinity to the sample-predicted hla alleles were selected […]

library_books

Immunopharmacogenomics towards personalized cancer immunotherapy targeting neoantigens

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

[…] which can bind to hla molecules. several tools have been developed 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 […]

library_books

Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer

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

[…] 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 arguments […]

call_split

Effective screening of T cells recognizing neoantigens and construction of T cell receptor engineered T cells

2018
PMCID: 5834292
PMID: 29541393
DOI: 10.18632/oncotarget.24232
call_split See protocol

[…] variant depth of ≥4, (iv) variant frequency in tumor of ≥10%, (v) variant frequency in normal of <2%, and (vi) fisher p value of <0.05. hla class i genotypes of the tumor were determined by optitype algorithm using whole-exome sequence data of normal dnas []. potential neoantigens were predicted for each non-synonymous mutation by testing all 8- to 11-mer peptides harboring the amino […]


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OptiType institution(s)
Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen, Institute of Medical Genetics and Applied Genomics, University of Tübingen, and CeGaT GmbH, Tübingen, Germany

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