Unique Molecular Identifier-Based High-Resolution HLA Typing and Transcript Quantitation Using Long-Read Sequencing

High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells

(2021) Chang Liu et al.   HUMAN IMMUNOLOGY

Bias in RNA-seq Library Preparation: Current Challenges and Solutions

(2021) Huajuan Shi et al.   Biomed Research International

Next-generation sequencing and clinical histocompatibility testing

(2021) Caleb Cornaby et al.   HUMAN IMMUNOLOGY

Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci

(2020) Maria Gutierrez-Arcelus et al.   NATURE GENETICS

scHLAcount: allele-specific HLA expression from single-cell gene expression data

(2020) Charlotte A Darby et al.   BIOINFORMATICS

The Shared Epitope Phenomenon – A potential impediment to virtual crossmatch accuracy

(2020) Cynthia Garcia‐Sanchez et al.   CLINICAL TRANSPLANTATION

A long road/read to rapid high-resolution HLA typing: The nanopore perspective

(2020) Chang Liu   HUMAN IMMUNOLOGY

NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline

(2020) Yifei Xu et al.   NUCLEIC ACIDS RESEARCH

Rapid high‐resolution HLA genotyping by MinION Oxford nanopore sequencing for deceased donor organ allocation

(2020) Dianne De Santis et al.   HLA

Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing

(2020) Timothy L. Mosbruger et al.   HUMAN IMMUNOLOGY

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

(2020) Yelena Levin et al.   Jove-Journal of Visualized Experiments

Complete nucleotide sequence characterization of DRB5 alleles reveals a homogeneous allele group that is distinct from other DRB genes

(2019) Konstantinos Barsakis et al.   HUMAN IMMUNOLOGY

Development of data-driven models for the flow cytometric crossmatch

(2019) Eric T. Weimer et al.   HUMAN IMMUNOLOGY

Using Nanopore Whole-Transcriptome Sequencing for Human Leukocyte Antigen Genotyping and Correlating Donor Human Leukocyte Antigen Expression with Flow Cytometric Crossmatch Results

(2019) Maureen C. Montgomery et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing

(2018) Chang Liu et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

(2018) Ryan R. Wick et al.   PLoS Computational Biology

Performance Characteristics and Validation of Next-Generation Sequencing for Human Leucocyte Antigen Typing

(2016) Eric T. Weimer et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations

(2016) Ruqin Kou et al.   PLoS One

Variable HLA expression on deceased donor lymphocytes: Not all crossmatches are created equal

(2015) Jessica L. Badders et al.   HUMAN IMMUNOLOGY

High HLA-DP Expression and Graft-versus-Host Disease

(2015) Effie W. Petersdorf et al.   NEW ENGLAND JOURNAL OF MEDICINE

High-allelic variability in HLA-C mRNA expression: association with HLA-extended haplotypes

(2014) F Bettens et al.   GENES AND IMMUNITY

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

(2012) Simon M Lank et al.   BMC GENOMICS

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing

(2010) C. Lind et al.   HUMAN IMMUNOLOGY

Reassessing the role of HLA-DRB3 T-cell responses: Evidence for significant expression and complementary antigen presentation

(2009) Rosa Faner et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS