A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

Type 1 Diabetes Risk in African-Ancestry Participants and Utility of an Ancestry-Specific Genetic Risk Score

(2019) Suna Onengut-Gumuscu et al.   DIABETES CARE

Clinical use of current polygenic risk scores may exacerbate health disparities

(2019) Alicia R. Martin et al.   NATURE GENETICS

Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population

(2019) Jun Hirata et al.   NATURE GENETICS

HLA*LA—HLA typing from linearly projected graph alignments

(2019) Alexander T Dilthey et al.   BIOINFORMATICS

Polygenic Prediction of Weight and Obesity Trajectories from Birth to Adulthood

(2019) Amit V. Khera et al.   CELL

Polygenic Risk Scores Expand to Obesity

(2019) Ali Torkamani et al.   CELL

Fine-Scale Inference of Ancestry Segments Without Prior Knowledge of Admixing Groups

(2019) Michael Salter-Townshend et al.   GENETICS

Structural topology defines protective CD8+ T cell epitopes in the HIV proteome

(2019) Gaurav D. Gaiha et al.   SCIENCE

The psoriasis risk allele HLA-Cw0602 shows evidence of association with chronic or recurrent streptococcal tonsillitis

(2018) Karita Haapasalo et al.   INFECTION AND IMMUNITY

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

(2018) Yukinori Okada et al.   Nature Communications

Human Leukocyte Antigen-A, B, C, DRB1, and DQB1 Allele and Haplotype Frequencies in a Subset of 237 Donors in the South African Bone Marrow Registry

(2018) Mqondisi Tshabalala et al.   Journal of Immunology Research

Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations

(2018) Amit V. Khera et al.   NATURE GENETICS

6-Locus HLA allele and haplotype frequencies in a population of 1075 Russians from Karelia

(2018) Yvonne Hagenlocher et al.   HUMAN IMMUNOLOGY

Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles

(2018) Frauke Degenhardt et al.   HUMAN MOLECULAR GENETICS

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel

(2017) Mario Mitt et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A genomic perspective on HLA evolution

(2017) Diogo Meyer et al.   IMMUNOGENETICS

The HLA-B landscape of Africa: Signatures of pathogen-driven selection and molecular identification of candidate alleles to malaria protection

(2017) Alicia Sanchez-Mazas et al.   MOLECULAR ECOLOGY

Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control

(2017) István Bartha et al.   PLoS Computational Biology

Contribution of a Non-classical HLA Gene, HLA-DOA , to the Risk of Rheumatoid Arthritis

(2016) Yukinori Okada et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): An integrated case-control analysis pipeline

(2016) Derek J. Pappas et al.   HUMAN IMMUNOLOGY

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs

(2016) Alexander T. Dilthey et al.   PLoS Computational Biology

Strong Selection at MHC in Mexicans since Admixture

(2016) Quan Zhou et al.   PLoS Genetics

Genome-wide association study identifies HLA 8.1 ancestral haplotype alleles as major genetic risk factors for myositis phenotypes

(2015) F W Miller et al.   GENES AND IMMUNITY

Construction of a population-specific HLA imputation reference panel and its application to Graves' disease risk in Japanese

(2015) Yukinori Okada et al.   NATURE GENETICS

Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risk

(2015) Xinli Hu et al.   NATURE GENETICS

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases

(2015) Tobias L Lenz et al.   NATURE GENETICS

Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load

(2015) Paul J. McLaren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting Structure of Haplotypes and Local Ancestry

(2014) Y. Guan   GENETICS

Host-Specific Adaptation of HIV-1 Subtype B in the Japanese Population

(2014) T. Chikata et al.   JOURNAL OF VIROLOGY

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

HLA Diversity in the 1000 Genomes Dataset

(2014) Pierre-Antoine Gourraud et al.   PLoS One

RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference

(2013) Brian K. Maples et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation

(2013) Bogdan Pasaniuc et al.   BIOINFORMATICS

HIBAG—HLA genotype imputation with attribute bagging

(2013) X Zheng et al.   PHARMACOGENOMICS JOURNAL

Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens

(2013) Xiaoming Jia et al.   PLoS One

Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls

(2013) Paul J. McLaren et al.   PLoS Pathogens

Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans

(2012) Paul J. McLaren et al.   HUMAN MOLECULAR GENETICS

HIV Control through a Single Nucleotide on the HLA-B Locus

(2012) H. N. Kloverpris et al.   JOURNAL OF VIROLOGY

Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis

(2012) Soumya Raychaudhuri et al.   NATURE GENETICS

A Fast, Powerful Method for Detecting Identity by Descent

(2011) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

HLA*IMP—an integrated framework for imputing classical HLA alleles from SNP genotypes

(2011) Alexander T. Dilthey et al.   BIOINFORMATICS

Possession of HLA Class II DRB1*1303 Associates with Reduced Viral Loads in Chronic HIV-1 Clade C and B Infection

(2011) Boris Julg et al.   JOURNAL OF INFECTIOUS DISEASES

HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control

(2011) H. N. Kloverpris et al.   JOURNAL OF VIROLOGY

Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility

(2011) David M Evans et al.   NATURE GENETICS

Immunogenetics of Spontaneous Control of HIV

(2010) Mary Carrington et al.   Annual Review of Medicine

The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation

(2010)   SCIENCE

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition

(2009) Julia K. Archbold et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Genetic Structure of Europeans: A View from the North–East

(2009) Mari Nelis et al.   PLoS One

Long-Range LD Can Confound Genome Scans in Admixed Populations

(2008) Alkes L. Price et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project

(2008) Roger Horton et al.   IMMUNOGENETICS