A HLA genotyping algorithm based on integer linear programming, capable of producing accurate predictions from NGS data not specifically enriched for the HLA cluster. OptiType significantly outperformed previously published in silico approaches with an overall accuracy of 97% enabling its use in a broad range of applications.
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Determines human leukocyte antigen (HLA) matching at epitope level in alloantibody responses. HLAMatchmaker utilizes an algorithm where each HLA antigen is considered as a string of amino acid configurations in antibody-accessible positions. This program can be used as a quantitative tool to define the degree of a mismatch such as mismatched eplets of triplets.
A software for HLA class I and II predictions from next-generation shotgun (NGS) sequence read data that supports direct read alignment and targeted assembly of sequence reads. This approach circumvents the additional time and cost of generating HLA-specific data and capitalizes on the increasing accessibility and affordability of massively parallel sequencing.
Applies assembly, allele identification and allelic pair inference to short read sequences, and applied it to data from Illumina platforms. In 15 data sets with adequate coverage for HLA-A, -B, -C, -DRB1 and -DQB1 genes, ATHLATES correctly reported 74 out of 75 allelic pairs with an overall concordance rate of 99% compared with conventional typing.
A NGS data analysis pipeline allowing user to make HLA alleles genotyping quickly and efficiently. HLATyphon supports all cDNA template of HLA locus A, B, C, DPA1, DPB1, DQA1, DQB1 and DRB1 in IMGT/HLA database. Currently the internal HLA allele reference sequences of HLATyphon were from IMGT/HLA database release 3.17.0 including 12,010 alleles.
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Discover our proposed protocols.
They are easy to use or edit to meet your needs.
They are easy to use or edit to meet your needs.
A pilot study of durvalumab and tremelimumab and immunogenomic dynamics in metastatic breast cancer
Tools (3):
BWA, Picard, OptiType
Topics (5):
WES analysis, RNA-seq analysis, Homo sapiens, Breast Neoplasms, Breast Diseases
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures
Tools (4):
OptiType, cBioPortal, SAMtools, SnpEff
Topics (9):
WES analysis, RNA-seq analysis, Homo sapiens, Urogenital Neoplasms, Urologic Diseases, Kidney Diseases, Neoplasms, Glandular and Epithelial, Urologic Neoplasms, Neoplasms
Integrated analysis of somatic mutations and immune microenvironment of multiple regions in breast cancers
Tools (6):
FASTX-Toolkit, BWA, Picard, ANNOVAR, OptiType, RefGene
Topics (3):
WES analysis, RNA-seq analysis, Homo sapiens
Effective screening of T cells recognizing neoantigens and construction of T cell receptor engineered T cells
Tools (3):
BWA, Picard, OptiType
Topics (12):
WES analysis, RNA-seq analysis, Homo sapiens, Head and Neck Neoplasms, Esophageal Diseases, Gastrointestinal Neoplasms, Digestive System Neoplasms, Neoplasms, Ovarian Diseases, Genital Diseases, Female, Ovarian Neoplasms, Endocrine Gland Neoplasms
Increased RNA Editing May Provide a Source for Autoantigens in Systemic Lupus Erythematosus
Tools (5):
STAR, REDItools, DESeq, wANNOVAR, OptiType
Topics (1):
RNA-seq analysis