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.
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Allows to discover and genotype sequence variants in large populations using pangenome graphs. Graphtyper is a population-scale genotype caller. The software locally realigns sequence reads from a genomic region to a pangenome graph, and concomitantly genotypes sequence variants in all individuals. Using variation-aware realignment, it is capable of characterization of the region’s variation with no Mendelian errors and no falsely reported additional sequence variants around the indel.
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 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.
Permits to screen raw Illumina high-throughput sequencing (HTS) data for sample swaps for datasets where the Human Leukocyte Antigen (HLA) loci are covered. HLA-MA is based on the HLA typing result of the state-of-the-art method OptiType. It uses information from small but genetically highly variable regions and thus complements approaches that rely on genome or exon-wide variant profiles. The tool takes a relatively short time and can be run before or in parallel with the usual downstream processing.
Enables human leukocyte antigen (HLA) imputation with different population specific reference panels. HLA-IMPUTER is a web server that implements the HIBAG algorithm. The software provides a function "Impute" allowing HLA allele imputation in four steps, where the user can choose between the Han Chinese panel or any other panels based on different populations from HIBAG. It also permits association analysis either directly or from HLA alleles inputted by the user.
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.
A tool for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles, followed by de novo assembly of the gene-specific short reads. Accurate HLA typing from NGS data holds much promise for applications in clinical laboratories and biomedical research. Preliminary analysis on both public and local datasets indicates a great potential for broad application of this method.
Allows users to perform human leukocyte antigen (HLA) typing and neoepitope forecasting using whole genome sequencing (WGS) and RNA-seq data. NeoepitopePred is a web-based workflow that leans on somatic missense mutations and gene fusions to determine putatives epitopes. This application was used for the investigation of the neoepitope landscape of more than 20 subtypes of pediatric cancer.
An algorithm for HLA type inference from next-generation sequencing data. HLA-PRG outperforms existing methods by a wide margin and for the first time consistently achieves the accuracy of gold-standard reference methods with one error across 158 alleles tested. HLA-PRG will enable researchers to augment population-scale whole-genome sequencing data with reliable HLA type information and contribute to characterizing HLA signals in important medical phenotypes.
A tool algorithm named to discover the most probable pair of HLA alleles at four-digit resolution or higher, via a unique integration of a candidate allele selection and a likelihood scoring. PHLAT significantly leverages the accuracy and flexibility of high resolution HLA typing based on genome-wide sequencing data. It may benefit both basic and applied research in immunology and related fields as well as numerous clinical applications.
An efficient and accurate human leucocyte antigen (HLA) typing method using high-throughput sequencing data without the need of primer design for HLA loci. In the first step of the HLA-VBSeq pipeline, read sequences are aligned to the reference genomic sequences of the registered HLA allelles in the IMGT/HLA database, in which multiple hits are allowed. Then, HLA-VBSeq optimizes both read alignments to the HLA allele sequences and relative quantities of reads on HLA alleles simultaneously under a statistical framework by variational Bayesian inference. Our approach considers all the possible alignments of reads to HLA allele sequences, and calculates the marginal likelihood of data from gapped alignments of reads to the reference sequences, in which deletions and insertions as well as SNP sites are naturally considered. It does not assume any prior knowledge about HLA allele frequencies, and hence HLA-VBSeq is broadly applicable to human samples obtained from a genetically diverse population.
Assists users to analyze human leukocyte antigen (HLA) genes from whole genome sequence data. ALPHLARD is an algorithm that collects reads potentially generated from HLA genes and is able to determine a pair of HLA types for each of HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes at 6-digit resolution. Moreover, it includes features for detecting rare germline variants not stored in HLA databases and call somatic mutations from paired normal and tumor sequence data.
Predicts HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest uses BioPerl to read in FASTA files. Alignments use Bowtie, although any alignment tool can be used to generate SAM alignments for use as input to HLAforest.
Performs alignment of reads to human leukocyte antigen (HLA) sequences from the international ImMunoGeneTics project (IMGT)/HLA database. HLAscan is an alignment-based multi-step HLA typing method considering read distribution. It outperforms the established next generation sequencing (NGS)-based methods but also may complement sequencing-based typing methods when dealing with high-depth (average 90×) short sequence reads. This method could be generally applied for variant calling in highly polymorphic regions.
Allows human leucocyte antigen (HLA) haplotype frequency estimation. Hapl-o-Mat preprocesses the input genotype data, resolves genotyping ambiguities, translates alleles to a uniform resolution per locus and then computes the most likely set of haplotypes including their frequencies via the expectation-maximization (EM) algorithm. The software handles large-scale HLA genotype data. Its accuracy and performance were demonstrated on the basis of artificial and real genotype data.
Provides functions for association analysis, zygosity tests, and interaction tests between HLA alleles and diseases. PyHLA is a Python package which implements several methods for HLA association analysis, to fill the gap. It is a tailor-made, easy to use, and flexible tool designed specifically for the association analysis of the HLA types imputed from genome-wide genotyping and NGS data. This method is applicable to small and large sample sizes and can finish the analysis in a timely manner on a personal computer with different platforms. PyHLA is designed for case-control studies and is currently unable to analyze family-base datasets.
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.
Assists for the assignment of human leukocyte antigen (HLA) type. Assign can accomplish base calling, edit sequences, import sequence data and compare sample consensus sequences via a HLA / international ImMunoGenTics (IMGT) database of alleles. This software contains sequence quality control analysis and genotyping to ease high-throughput sequencing-based typing (SBT). Analysis of Phred quality values are done to deliver results for a sample and a sequencing run.
Allows users to analyze a sequencing data. SAF is a program that assists researchers in working on typing Human Leukocyte Antigen (HLA) loci in tissue transplantation, particularly in bone marrow transplantation.
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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
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
Integrated analysis of somatic mutations and immune microenvironment of multiple regions in breast cancers
Tools (5):
FASTX-Toolkit, BWA, Picard, ANNOVAR, OptiType
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