4.7 Article

Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data

Related references

Note: Only part of the references are listed.
Article Oncology

HLA-A*03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study

Vivek Naranbhai et al.

Summary: This study aimed to determine the effect of HLA-A*03 as a biomarker for predicting response to immunotherapy. The results showed that the HLA-A*03 gene was associated with reduced overall survival after immunotherapy and this effect was observed across different types of immunotherapy agents and tumor types.

LANCET ONCOLOGY (2022)

Article Biochemical Research Methods

Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools

Jian Yi et al.

Summary: HLA typing is crucial for cancer immunotherapy, and this study found that OptiType demonstrated the highest accuracy in HLA-Ia typing from WES data, potentially providing a superior performance for its clinical application.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Biochemical Research Methods

In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales

Jieming Chen et al.

Summary: Immunogenetic variation in humans is crucial for research and clinical diagnosis, with the HLA system and KIR receptors playing critical roles. Recent algorithm evaluations show promising accuracy in computationally inferring HLA alleles and KIR haplotypes, indicating their potential use in clinical and high-throughput research settings.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Oncology

Benchmarking HLA genotyping and clarifying HLA impact on survival in tumor immunotherapy

Xiangyong Li et al.

Summary: HLA genotyping has a critical role in cancer immunotherapy, but generating reliable results remains challenging. The study presents a 'Gun-Bullet' model to clarify the survival impact of HLA alleles. Different HLA genotyping tools show specific error patterns, and ensemble calling from top-3 tools is superior.

MOLECULAR ONCOLOGY (2021)

Article Genetics & Heredity

Low immunogenicity of common cancer hot spot mutations resulting in false immunogenic selection signals

Arne Claeys et al.

Summary: Cancer is mainly driven by somatic mutations that provide cellular fitness advantage, with the immune system responding to novel neoantigens generated by driver mutations. It has been shown that HLA affinity predictions can be easily misinterpreted when studying immunogenic selection processes.

PLOS GENETICS (2021)

Article Cell Biology

Systematic comparative study of computational methods for HLA typing from next-generation sequencing

Yuechun Yu et al.

Summary: The HLA system plays a crucial role in transplantation and immunotherapy, but HLA typing remains challenging. New algorithms and software tools have been developed, yet there is a lack of systematic comparative studies. Research compared eight HLA typing software tools across different scenarios, assisting researchers in selecting the most appropriate tool for specific datasets.
Article Immunology

A New Human Leukocyte Antigen Typing Algorithm Combined With Currently Available Genotyping Tools Based on Next-Generation Sequencing Data and Guidelines to Select the Most Likely Human Leukocyte Antigen Genotype

Miseon Lee et al.

Summary: This study compared the accuracy of eight HLA genotyping tools and created a new algorithm combining the results of multiple tools to improve the accuracy of HLA genotyping. The results showed that when at least six tools provided consistent calls, the accuracy and precision of the HLA genotypes were high.

FRONTIERS IN IMMUNOLOGY (2021)

Article Biochemical Research Methods

arcasHLA: high-resolution HLA typing from RNAseq

Rose Orenbuch et al.

BIOINFORMATICS (2020)

Article Biochemistry & Molecular Biology

Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools

Faviel F. Gonzalez-Galarza et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemical Research Methods

HLA*LA-HLA typing from linearly projected graph alignments

Alexander T. Dilthey et al.

BIOINFORMATICS (2019)

Article Oncology

RNA Sequencing of the NCI-60: Integration into CellMiner and CellMiner CDB

William C. Reinhold et al.

CANCER RESEARCH (2019)

Review Hematology

Bioinformatics Strategies, Challenges, and Opportunities for Next Generation Sequencing-Based HLA Genotyping

Steffen Klasberg et al.

TRANSFUSION MEDICINE AND HEMOTHERAPY (2019)

Article Multidisciplinary Sciences

MHC-II neoantigens shape tumour immunity and response to immunotherapy

Elise Alspach et al.

NATURE (2019)

Article Genetics & Heredity

Lack of detectable neoantigen depletion signals in the untreated cancer genome

Jimmy Van den Eynden et al.

NATURE GENETICS (2019)

Review Oncology

Biological Consequences of MHC-II Expression by Tumor Cells in Cancer

Margaret L. Axelrod et al.

CLINICAL CANCER RESEARCH (2019)

Article Biochemical Research Methods

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios

Maria Luisa Matey-Hernandez et al.

BMC BIOINFORMATICS (2018)

Article Biochemical Research Methods

Mosdepth: quick coverage calculation for genomes and exomes

Brent S. Pedersen et al.

BIOINFORMATICS (2018)

Article Biotechnology & Applied Microbiology

Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery

Heewook Lee et al.

GENOME BIOLOGY (2018)

Article Genetics & Heredity

HLA-HD: An accurate HLA typing algorithm for next-generation sequencing data

Shuji Kawaguchi et al.

HUMAN MUTATION (2017)

Article Multidisciplinary Sciences

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA

Chao Xie et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Multidisciplinary Sciences

Alignment of 1000 Genomes Project reads to reference assembly GRCh38

Xiangqun Zheng-Bradley et al.

GigaScience (2017)

Article Biochemistry & Molecular Biology

Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab

Nadeem Riaz et al.

Article Biochemical Research Methods

HLAscan: genotyping of the HLA region using next-generation sequencing data

Sojeong Ka et al.

BMC BIOINFORMATICS (2017)

Article Biotechnology & Applied Microbiology

HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data

Naoki Nariai et al.

BMC GENOMICS (2015)

Article Biochemistry & Molecular Biology

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

Michael S. Rooney et al.

Article Biochemistry & Molecular Biology

Development of a high-resolution NGS-based HLA-typing and analysis pipeline

Michael Wittig et al.

NUCLEIC ACIDS RESEARCH (2015)

Review Multidisciplinary Sciences

Neoantigens in cancer immunotherapy

Ton N. Schumacher et al.

SCIENCE (2015)

Article Genetics & Heredity

HLAreporter: a tool for HLA typing from next generation sequencing data

Yazhi Huang et al.

GENOME MEDICINE (2015)

Article Biochemical Research Methods

OptiType: precision HLA typing from next-generation sequencing data

Andras Szolek et al.

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads

Yu Bai et al.

BMC GENOMICS (2014)

Article Multidisciplinary Sciences

HLA Diversity in the 1000 Genomes Dataset

Pierre-Antoine Gourraud et al.

PLOS ONE (2014)

Article Multidisciplinary Sciences

Transcriptome and genome sequencing uncovers functional variation in humans

Tuuli Lappalainen et al.

NATURE (2013)

Article Biochemistry & Molecular Biology

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing

Chang Liu et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens

Xiaoming Jia et al.

PLOS ONE (2013)

Article Multidisciplinary Sciences

HLA Haplotyping from RNA-seq Data Using Hierarchical Read Weighting

Hyunsung John Kim et al.

PLOS ONE (2013)

Review Multidisciplinary Sciences

Cancer Genome Landscapes

Bert Vogelstein et al.

SCIENCE (2013)

Article Genetics & Heredity

HLA typing from RNA-Seq sequence reads

Sebastian Boegel et al.

GENOME MEDICINE (2012)

Article Genetics & Heredity

Derivation of HLA types from shotgun sequence datasets

Rene L. Warren et al.

GENOME MEDICINE (2012)

Article Medicine, Research & Experimental

HLA class I and II genotype of the NCI-60 cell lines

S Adams et al.

JOURNAL OF TRANSLATIONAL MEDICINE (2005)

Article Immunology

Primary antitumor immune response mediated by CD4+ T cells

A Corthay et al.

IMMUNITY (2005)