A genomic perspective on HLA evolution

Sequence and Phylogenetic Analysis of the Untranslated Promoter Regions forHLAClass I Genes

(2017) Veron Ramsuran et al.   JOURNAL OF IMMUNOLOGY

HLA-G variability and haplotypes detected by massively parallel sequencing procedures in the geographicaly distinct population samples of Brazil and Cyprus

(2017) Erick C. Castelli et al.   MOLECULAR IMMUNOLOGY

Defining KIR and HLA Class I Genotypes at Highest Resolution via High-Throughput Sequencing

(2016) Paul J. Norman et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Evaluation of computational programs to predict HLA genotypes from genomic sequencing data

(2016) Denis C. Bauer et al.   BRIEFINGS IN BIOINFORMATICS

Next-Generation Sequencing of the HLA locus: Methods and impacts on HLA typing, population genetics and disease association studies

(2016) Raphael Carapito et al.   HUMAN IMMUNOLOGY

HLA-F coding and regulatory segments variability determined by massively parallel sequencing procedures in a Brazilian population sample

(2016) Thálitta Hetamaro Ayala Lima et al.   HUMAN IMMUNOLOGY

Elucidating the origin of HLA-B*73 allelic lineage: Did modern humans benefit by archaic introgression?

(2016) Yoshiki Yasukochi et al.   IMMUNOGENETICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease

(2016) Fusheng Zhou et al.   NATURE GENETICS

HLA class II sequence variants influence tuberculosis risk in populations of European ancestry

(2016) Gardar Sveinbjornsson et al.   NATURE GENETICS

Detection of human adaptation during the past 2000 years

(2016) Yair Field et al.   SCIENCE

A time transect of exomes from a Native American population before and after European contact

(2016) John Lindo et al.   Nature Communications

Understanding of HLA-conferred susceptibility to chronic hepatitis B infection requires HLA genotyping-based association analysis

(2016) Nao Nishida et al.   Scientific Reports

Strong Selection at MHC in Mexicans since Admixture

(2016) Quan Zhou et al.   PLoS Genetics

Ancestry variation and footprints of natural selection along the genome in Latin American populations

(2016) Lian Deng et al.   Scientific Reports

Pemphigus is associated withKIR3DL2expression levels and provides evidence that KIR3DL2 may bind HLA-A3 and A11 in vivo

(2015) Danillo G. Augusto et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

KIR and HLA under pressure: evidences of coevolution across worldwide populations

(2015) Danillo G. Augusto et al.   HUMAN GENETICS

HLA-E coding and 3′ untranslated region variability determined by next-generation sequencing in two West-African population samples

(2015) Erick C. Castelli et al.   HUMAN IMMUNOLOGY

Epigenetic regulation of differentialHLA-Aallelic expression levels

(2015) Veron Ramsuran et al.   HUMAN MOLECULAR GENETICS

HLA supertype variation across populations: new insights into the role of natural selection in the evolution of HLA-A and HLA-B polymorphisms

(2015) Rodrigo dos Santos Francisco et al.   IMMUNOGENETICS

The impact of next-generation sequencing technologies on HLA research

(2015) Kazuyoshi Hosomichi et al.   JOURNAL OF HUMAN GENETICS

Heterogeneity of $${\varvec{\rm d}}{\varvec{N}}/{\varvec{\rm d}}{\varvec{S}}$$ d N / d S Ratios at the Classical HLA Class I Genes over Divergence Time and Across the Allelic Phylogeny

(2015) Bárbara Domingues Bitarello et al.   JOURNAL OF MOLECULAR EVOLUTION

Long-Term Balancing Selection in LAD1 Maintains a Missense Trans-Species Polymorphism in Humans, Chimpanzees, and Bonobos

(2015) João C. Teixeira et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide patterns of selection in 230 ancient Eurasians

(2015) Iain Mathieson et al.   NATURE

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

Estimating the mutation load in human genomes

(2015) Brenna M. Henn et al.   NATURE REVIEWS GENETICS

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Ancestry, admixture and fitness in Colombian genomes

(2015) Lavanya Rishishwar et al.   Scientific Reports

Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data

(2015) Débora Y. C. Brandt et al.   G3-Genes Genomes Genetics

Loss and Gain of Natural Killer Cell Receptor Function in an African Hunter-Gatherer Population

(2015) Hugo G. Hilton et al.   PLoS Genetics

Performance of HLA allele prediction methods in African Americans for class II genes HLA-DRB1, −DQB1, and –DPB1

(2014) Albert M Levin et al.   BMC GENETICS

Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing

(2014) Vinzenz Lange et al.   BMC GENOMICS

Advantageous diversity maintained by balancing selection in humans

(2014) Felix M Key et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Detecting Structure of Haplotypes and Local Ancestry

(2014) Y. Guan   GENETICS

Celiac Disease as a Model for the Evolution of Multifactorial Disease in Humans

(2014) Aaron Sams et al.   HUMAN BIOLOGY

Maternal KIR in Combination with Paternal HLA-C2 Regulate Human Birth Weight

(2014) S. E. Hiby et al.   JOURNAL OF IMMUNOLOGY

HLA Diversity in the 1000 Genomes Dataset

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

A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data

(2014) Michael DeGiorgio et al.   PLoS Genetics

A Population Genetic Signal of Polygenic Adaptation

(2014) Jeremy J. Berg et al.   PLoS Genetics

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences

(2014) Vincenza Colonna et al.   GENOME BIOLOGY

The Relevance ofHLASequencing in Population Genetics Studies

(2014) Alicia Sanchez-Mazas et al.   Journal of Immunology Research

A catalog of HLA type, HLA expression, and neo-epitope candidates in human cancer cell lines

(2014) Sebastian Boegel et al.   OncoImmunology

Major Histocompatibility Complex Genomics and Human Disease

(2013) John Trowsdale et al.   Annual Review of Genomics and Human Genetics

Selection and Adaptation in the Human Genome

(2013) Wenqing Fu et al.   Annual Review of Genomics and 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

Phase-defined complete sequencing of the HLA genes by next-generation sequencing

(2013) Kazuyoshi Hosomichi et al.   BMC GENOMICS

Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics

(2013) Martin Danzer et al.   BMC GENOMICS

Gene expression drives local adaptation in humans

(2013) H. B. Fraser   GENOME RESEARCH

Estimating and interpreting FST: The impact of rare variants

(2013) G. Bhatia et al.   GENOME RESEARCH

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Inferring population size changes with sequence and SNP data: lessons from human bottlenecks

(2013) L M Gattepaille et al.   HEREDITY

Evidence for Polygenic Adaptation to Pathogens in the Human Genome

(2013) Josephine T. Daub et al.   MOLECULAR BIOLOGY AND EVOLUTION

Negligible impact of rare autoimmune-locus coding-region variants on missing heritability

(2013) Karen A. Hunt et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Genome-wide association analysis identifies new susceptibility loci for Behçet's disease and epistasis between HLA-B*51 and ERAP1

(2013) Yohei Kirino et al.   NATURE GENETICS

HIBAG—HLA genotype imputation with attribute bagging

(2013) X Zheng et al.   PHARMACOGENOMICS JOURNAL

Genome-Wide Landscapes of Human Local Adaptation in Asia

(2013) Wei Qian et al.   PLoS One

Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens

(2013) Xiaoming Jia et al.   PLoS One

An Integrated Tool to Study MHC Region: Accurate SNV Detection and HLA Genes Typing in Human MHC Region Using Targeted High-Throughput Sequencing

(2013) Hongzhi Cao et al.   PLoS One

HLA Typing from 1000 Genomes Whole Genome and Whole Exome Illumina Data

(2013) Endre Major et al.   PLoS One

Pathogen selection drives nonoverlapping associations between HLA loci

(2013) B. S. Penman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

(2013) E. M. Leffler et al.   SCIENCE

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolutionary forces shaping genomic islands of population differentiation in humans

(2012) Tamara Hofer et al.   BMC GENOMICS

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

(2012) Simon M Lank et al.   BMC GENOMICS

PCAdmix: Principal Components-Based Assignment of Ancestry Along Each Chromosome in Individuals with Admixed Ancestry from Two or More Populations

(2012) Abra Brisbin et al.   HUMAN BIOLOGY

16thIHIW: Population Global Distribution of Killer Immunoglobulin-like Receptor (KIR) and Ligands

(2012) J. A. Hollenbach et al.   International Journal of Immunogenetics

A Novel Variant Marking HLA-DP Expression Levels Predicts Recovery from Hepatitis B Virus Infection

(2012) R. Thomas et al.   JOURNAL OF VIROLOGY

The Timing of Pigmentation Lightening in Europeans

(2012) Sandra Beleza et al.   MOLECULAR BIOLOGY AND EVOLUTION

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

(2012) Wenqing Fu et al.   NATURE

Human-specific evolution of killer cell immunoglobulin-like receptor recognition of major histocompatibility complex class I molecules

(2012) P. Parham et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

High-throughput, high-fidelity HLA genotyping with deep sequencing

(2012) C. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HLA DNA typing: past, present, and future

(2012) H. Erlich   TISSUE ANTIGENS

New reservoirs of HLA alleles: pools of rare variants enhance immune defense

(2012) William Klitz et al.   TRENDS IN GENETICS

HLA typing from RNA-Seq sequence reads

(2012) Sebastian Boegel et al.   Genome Medicine

Genome-wide Comparison of African-Ancestry Populations from CARe and Other Cohorts Reveals Signals of Natural Selection

(2011) Gaurav Bhatia et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integration of Genetic and Immunological Insights into a Model of Celiac Disease Pathogenesis

(2011) Valérie Abadie et al.   Annual Review of Immunology

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

(2011) Alexander T. Dilthey et al.   BIOINFORMATICS

Next-generation sequencing for HLA typing of class I loci

(2011) Rachel L Erlich et al.   BMC GENOMICS

Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex

(2011) C. Vandiedonck et al.   GENOME RESEARCH

Differential microRNA regulation of HLA-C expression and its association with HIV control

(2011) Smita Kulkarni et al.   NATURE

New approaches to disease mapping in admixed populations

(2011) Michael F. Seldin et al.   NATURE REVIEWS GENETICS

Evidence for Hitchhiking of Deleterious Mutations within the Human Genome

(2011) Sung Chun et al.   PLoS Genetics

Ancestral Components of Admixed Genomes in a Mexican Cohort

(2011) Nicholas A. Johnson et al.   PLoS Genetics

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

(2011) Matteo Fumagalli et al.   PLoS Genetics

Admixture Mapping Comes of Age

(2010) Cheryl A. Winkler et al.   Annual Review of Genomics and Human Genetics

Natural Selection and the Distribution of Identity-by-Descent in the Human Genome

(2010) Anders Albrechtsen et al.   GENETICS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Extreme Evolutionary Disparities Seen in Positive Selection across Seven Complex Diseases

(2010) Erik Corona et al.   PLoS One

How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings

(2010) L. G. Spurgin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

Constructing genomic maps of positive selection in humans: Where do we go from here?

(2009) J. M. Akey   GENOME RESEARCH

The HLA genomic loci map: expression, interaction, diversity and disease

(2009) Takashi Shiina et al.   JOURNAL OF HUMAN GENETICS

Targets of Balancing Selection in the Human Genome

(2009) A. M. Andres et al.   MOLECULAR BIOLOGY AND EVOLUTION

A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians

(2009) Yoichiro Kamatani et al.   NATURE GENETICS

Genomewide Association Study of Leprosy

(2009) Fu-Ren Zhang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Co-evolution of KIR2DL3 with HLA-C in a human population retaining minimal essential diversity of KIR and HLA class I ligands

(2009) K. Gendzekhadze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-Range LD Can Confound Genome Scans in Admixed Populations

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

A Statistical Method for Predicting Classical HLA Alleles from SNP Data

(2008) Stephen Leslie et al.   AMERICAN JOURNAL OF HUMAN GENETICS

MHC class I-specific inhibitory receptors and their ligands structure diverse human NK-cell repertoires toward a balance of missing self-response

(2008) M. Yawata et al.   BLOOD

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: A meta-analytic review of 497 population studies

(2008) Owen D. Solberg et al.   HUMAN IMMUNOLOGY

Distinct KIR/HLA compound genotypes affect the kinetics of human antiviral natural killer cell responses

(2008) Golo Ahlenstiel et al.   JOURNAL OF CLINICAL INVESTIGATION

A new theory of MHC evolution: beyond selection on the immune genes

(2008) C. van Oosterhout   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

NK receptor interactions with MHC class I molecules in pregnancy

(2008) John Trowsdale et al.   SEMINARS IN IMMUNOLOGY