Steven J. Mack
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View article: HLAtools, Searching Shared HLA Amino Acid Residue Prevalence, and the Global Frequency Browsers: New Computational Resources for Working With HLA Data and Visualizing Global Patterns of HLA Variation
HLAtools, Searching Shared HLA Amino Acid Residue Prevalence, and the Global Frequency Browsers: New Computational Resources for Working With HLA Data and Visualizing Global Patterns of HLA Variation Open
The highly polymorphic HLA genes inform susceptibility and resistance to infectious and autoimmune diseases and cancers and are key for successful solid‐organ and stem‐cell transplantation therapies. Over 41,000 HLA alleles are known and a…
View article: Association between HLA genetics and SARS-CoV-2 infection in a large real-world cohort
Association between HLA genetics and SARS-CoV-2 infection in a large real-world cohort Open
View article: Etiologic Determinants and Characteristics of Diabetes in Haitian Youth (EDDHY Study)
Etiologic Determinants and Characteristics of Diabetes in Haitian Youth (EDDHY Study) Open
Aims: Published information on youth‐onset diabetes in Haiti is scarce, with limited data available on diabetes autoimmunity and genetic susceptibility to the disease. We determined the anthropometric, metabolic, and immunological characte…
View article: P157: Initial findings of the ClinGen Monogenic Systemic and Incomplete Lupus Gene Curation Expert Panel*
P157: Initial findings of the ClinGen Monogenic Systemic and Incomplete Lupus Gene Curation Expert Panel* Open
View article: Natural selection on HLA-DPB1 amino acids operates primarily on DP serologic categories
Natural selection on HLA-DPB1 amino acids operates primarily on DP serologic categories Open
The DPB1 locus is notable among the classical HLA loci in that allele frequencies at this locus are consistent with genetic drift, whereas the frequencies of specific DPβ amino acids are consistent with the action of balancing selection. W…
View article: Population genetic dissection of HLA-DPB1 amino acid polymorphism to infer selection
Population genetic dissection of HLA-DPB1 amino acid polymorphism to infer selection Open
Although allele frequency data for most HLA loci provide strong evidence for balancing selection at the allele level, the DPB1 locus is a notable exception, with allele frequencies compatible with neutral evolution (genetic drift) or direc…
View article: HLAtools: Toolkit for HLA Immunogenomics
HLAtools: Toolkit for HLA Immunogenomics Open
A toolkit for the analysis and management of data for genes in the so-called ``Human Leukocyte Antigen'' (HLA) region.Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (AN-…
View article: Curating Genetic Associations With Rheumatologic Autoimmune Diseases to Improve Patient Outcomes
Curating Genetic Associations With Rheumatologic Autoimmune Diseases to Improve Patient Outcomes Open
Rheumatologists have a remarkable array of therapeutics to treat rheumatic diseases but still largely rely on trial-and-error approaches to optimize management of individual patients. One important way to advance the goals of precision med…
View article: Non-invasive prenatal testing of beta-hemoglobinopathies using next generation sequencing, in-silico sequence size selection, and haplotyping
Non-invasive prenatal testing of beta-hemoglobinopathies using next generation sequencing, in-silico sequence size selection, and haplotyping Open
The combined use of ISS and HBB haplotypes enabled us to correctly predict fetal genotypes in cases where the prediction based on variant read ratios alone was incorrect.
View article: PyPop: a mature open-source software pipeline for population genomics
PyPop: a mature open-source software pipeline for population genomics Open
Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conf…
View article: P826: Evaluating HLA allele-disease associations in ClinGen: Development of a new curation tool
P826: Evaluating HLA allele-disease associations in ClinGen: Development of a new curation tool Open
The Human Leukocyte Antigen (HLA) region, located on the short arm of chromosome 6, is the most complex and polymorphic region in the human genome. This region's high structural and genetic diversity is the result of natural selection for …
View article: Complete <scp>HLA</scp> genotyping of type 1 diabetes patients and controls from Mali reveals both expected and novel disease associations
Complete <span>HLA</span> genotyping of type 1 diabetes patients and controls from Mali reveals both expected and novel disease associations Open
HLA genotyping was performed on 99 type 1 diabetes (T1D) patients and 200 controls from Mali. Next‐generation sequencing of the classical HLA‐A, ‐B, ‐C, ‐DRB1, ‐DRB3, ‐DRB4, ‐DRB5, ‐DQA1, ‐DQB1, ‐DPA1, and ‐DPB1 loci revealed strong T1D as…
View article: The genotype list string code syntax for exchanging <scp>nomenclature‐level</scp> genotyping results in clinical and research data management and analysis systems
The genotype list string code syntax for exchanging <span>nomenclature‐level</span> genotyping results in clinical and research data management and analysis systems Open
The nomenclatures used to describe HLA and killer‐cell immunoglobulin‐like receptor (KIR) alleles distinguish unique nucleotide and peptide sequences, and patterns of expression, but are insufficient for describing genotyping results, as d…
View article: Genotype List String 1.1: Extending the Genotype List String grammar for describing <scp>HLA</scp> and Killer‐cell Immunoglobulin‐like Receptor genotypes
Genotype List String 1.1: Extending the Genotype List String grammar for describing <span>HLA</span> and Killer‐cell Immunoglobulin‐like Receptor genotypes Open
The Genotype List (GL) String grammar for reporting HLA and Killer‐cell Immunoglobulin‐like Receptor (KIR) genotypes in a text string was described in 2013. Since this initial description, GL Strings have been used to describe HLA and KIR …
View article: Analysis of the Origin of Emiratis as Inferred from a Family Study Based on HLA-A, -C, -B, -DRB1, and -DQB1 Genes
Analysis of the Origin of Emiratis as Inferred from a Family Study Based on HLA-A, -C, -B, -DRB1, and -DQB1 Genes Open
In this study, we investigated HLA class I and class II allele and haplotype frequencies in Emiratis and compared them to those of Asian, Mediterranean, and Sub-Saharan African populations. Methods: Two-hundred unrelated Emirati parents of…
View article: Clinical features, biochemistry, and <i>HLA</i> ‐ <i>DRB1</i> status in youth‐onset type 1 diabetes in Mali
Clinical features, biochemistry, and <i>HLA</i> ‐ <i>DRB1</i> status in youth‐onset type 1 diabetes in Mali Open
C-peptide values were higher than expected in those diagnosed as T1D and autoantibody rates lower than in European populations. It is quite possible that some cases have an atypical form of T1D, ketosis-prone T2D, or youth-onset T2D. This …
View article: The immunogenetics of viral antigen response is associated with subtype-specific glioma risk and survival
The immunogenetics of viral antigen response is associated with subtype-specific glioma risk and survival Open
View article: HLA-DRB1 and –DQB1 Alleles, Haplotypes and Genotypes in Emirati Patients with Type 1 Diabetes Underscores the Benefits of Evaluating Understudied Populations
HLA-DRB1 and –DQB1 Alleles, Haplotypes and Genotypes in Emirati Patients with Type 1 Diabetes Underscores the Benefits of Evaluating Understudied Populations Open
Background: HLA class II (DR and DQ) alleles and antigens have historically shown strong genetic predisposition to type 1 diabetes (T1D). This study evaluated the association of DRB1 and DQB1 alleles, genotypes, and haplotypes with T1D in …
View article: Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research
Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research Open
The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico …
View article: Current HLA Investigations on SARS-CoV-2 and Perspectives
Current HLA Investigations on SARS-CoV-2 and Perspectives Open
The rapid, global spread of the SARS-CoV-2 virus during the current pandemic has triggered numerous efforts in clinical and research settings to better understand the host genetics’ interactions and the severity of COVID-19. Due to the est…
View article: The immunogenetics of viral antigen response is associated with sub-type specific glioma risk and survival
The immunogenetics of viral antigen response is associated with sub-type specific glioma risk and survival Open
Glioma is a highly fatal cancer with prognostically significant molecular subtypes and few known risk factors. Multiple studies have implicated infections in glioma susceptibility, but evidence remains inconsistent. Genetic variants in the…
View article: Challenges for the standardized reporting of NGS HLA genotyping: Surveying gaps between clinical and research laboratories
Challenges for the standardized reporting of NGS HLA genotyping: Surveying gaps between clinical and research laboratories Open
View article: Clinical features, biochemistry, and <i>HLA‐DRB1</i> status in youth‐onset type 1 diabetes in Sudan
Clinical features, biochemistry, and <i>HLA‐DRB1</i> status in youth‐onset type 1 diabetes in Sudan Open
Young Sudanese individuals with T1D generally have similar characteristics to reported European-origin T1D populations. However, they have higher rates of DKA and slightly lower autoantibody rates than reported European-origin populations,…
View article: Standard reference sequences for submission of <scp>HLA</scp> genotyping for the 18th International HLA and Immunogenetics Workshop
Standard reference sequences for submission of <span>HLA</span> genotyping for the 18th International HLA and Immunogenetics Workshop Open
The International human leukocyte antigen (HLA) and Immunogenetics Workshops (IHIWs) have fostered international collaborations of researchers and experts in the fields of HLA, histocompatibility and immunology. These IHIW collaborations h…
View article: Author response for "Clinical features, biochemistry, and HLA-DRB1 status in youth-onset type 1 diabetes in Sudan"
Author response for "Clinical features, biochemistry, and HLA-DRB1 status in youth-onset type 1 diabetes in Sudan" Open
View article: SNP‐HLA Reference Consortium (SHLARC): HLA and SNP data sharing for promoting MHC‐centric analyses in genomics
SNP‐HLA Reference Consortium (SHLARC): HLA and SNP data sharing for promoting MHC‐centric analyses in genomics Open
Genome‐wide associations studies have repeatedly identified the major histocompatibility complex genomic region (6p21.3) as key in immune pathologies. Researchers have also aimed to extend the biological interpretation of associations by f…
View article: Clinical features, biochemistry and HLA-DRB1 status in children and adolescents with diabetes in Dhaka, Bangladesh
Clinical features, biochemistry and HLA-DRB1 status in children and adolescents with diabetes in Dhaka, Bangladesh Open
View article: HLA alleles and haplotypes observed in 263 US families
HLA alleles and haplotypes observed in 263 US families Open
View article: Tools for building, analyzing and evaluating HLA haplotypes from families
Tools for building, analyzing and evaluating HLA haplotypes from families Open
View article: Epidemiology of childhood-onset type 1 diabetes in Azerbaijan: Incidence, clinical features, biochemistry, and HLA-DRB1 status
Epidemiology of childhood-onset type 1 diabetes in Azerbaijan: Incidence, clinical features, biochemistry, and HLA-DRB1 status Open