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5. Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest

Author

Pappas, DJ, Lizee, A, Paunic, V, Beutner, KR, Motyer, A, Vukcevic, D, Leslie, S, Biesiada, J, Meller, J, Taylor, KD, Zheng, X, Zhao, LP, Gourraud, P-A, Hollenbach, JA, Mack, SJ, and Maiers, M

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Genetics, Human Genome, Generic health relevance, Alleles, Genetic Variation, Genome, Human, Genome-Wide Association Study, Genotype, HLA Antigens, HLA-A Antigens, HLA-B Antigens, HLA-C Antigens, HLA-DRB1 Chains, Haplotypes, Humans, Polymorphism, Single Nucleotide, White People, Pharmacology & Pharmacy, Pharmacology and pharmaceutical sciences
Abstract

Four single nucleotide polymorphism (SNP)-based human leukocyte antigen (HLA) imputation methods (e-HLA, HIBAG, HLA*IMP:02 and MAGPrediction) were trained using 1000 Genomes SNP and HLA genotypes and assessed for their ability to accurately impute molecular HLA-A, -B, -C and -DRB1 genotypes in the Human Genome Diversity Project cell panel. Imputation concordance was high (>89%) across all methods for both HLA-A and HLA-C, but HLA-B and HLA-DRB1 proved generally difficult to impute. Overall,

Published
2018

11. Genotype List String: a grammar for describing HLA and KIR genotyping results in a text string

Author

Milius, RP, Mack, SJ, Hollenbach, JA, Pollack, J, Heuer, ML, Gragert, L, Spellman, S, Guethlein, LA, Trachtenberg, EA, Cooley, S, Bochtler, W, Mueller, CR, Robinson, J, Marsh, SGE, and Maiers, M

Subjects
Stem Cell Research, Transplantation, Genetics, Algorithms, Alleles, Gene Frequency, Genotype, Genotyping Techniques, HLA Antigens, Hematopoietic Stem Cell Transplantation, Histocompatibility Testing, Humans, Organ Transplantation, Polymorphism, Genetic, Receptors, KIR, Sequence Analysis, DNA, Terminology as Topic, Unrelated Donors, Genotype List String, genotype, human leukocyte antigen, killer-cell immunoglobulin-like receptor
Abstract

Knowledge of an individual's human leukocyte antigen (HLA) genotype is essential for modern medical genetics, and is crucial for hematopoietic stem cell and solid-organ transplantation. However, the high levels of polymorphism known for the HLA genes make it difficult to generate an HLA genotype that unambiguously identifies the alleles that are present at a given HLA locus in an individual. For the last 20 years, the histocompatibility and immunogenetics community has recorded this HLA genotyping ambiguity using allele codes developed by the National Marrow Donor Program (NMDP). While these allele codes may have been effective for recording an HLA genotyping result when initially developed, their use today results in increased ambiguity in an HLA genotype, and they are no longer suitable in the era of rapid allele discovery and ultra-high allele polymorphism. Here, we present a text string format capable of fully representing HLA genotyping results. This Genotype List (GL) String format is an extension of a proposed standard for reporting killer-cell immunoglobulin-like receptor (KIR) genotype data that can be applied to any genetic data that use a standard nomenclature for identifying variants. The GL String format uses a hierarchical set of operators to describe the relationships between alleles, lists of possible alleles, phased alleles, genotypes, lists of possible genotypes, and multilocus unphased genotypes, without losing typing information or increasing typing ambiguity. When used in concert with appropriate tools to create, exchange, and parse these strings, we anticipate that GL Strings will replace NMDP allele codes for reporting HLA genotypes.

Published
2013

12. Common and well‐documented HLA alleles: 2012 update to the CWD catalogue

Author

Mack, SJ, Cano, P, Hollenbach, JA, He, J, Hurley, CK, Middleton, D, Moraes, ME, Pereira, SE, Kempenich, JH, Reed, EF, Setterholm, M, Smith, AG, Tilanus, MG, Torres, M, Varney, MD, Voorter, CEM, Fischer, GF, Fleischhauer, K, Goodridge, D, Klitz, W, Little, A‐M, Maiers, M, Marsh, SGE, Müller, CR, Noreen, H, Rozemuller, EH, Sanchez‐Mazas, A, Senitzer, D, Trachtenberg, E, and Fernandez‐Vina, Marcelo

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Alleles, Databases, Genetic, Gene Frequency, Genetic Loci, Genetics, Population, HLA Antigens, Histocompatibility, Histocompatibility Testing, Humans, Terminology as Topic, allele prevalence, common allele, common and well-documented, human leukocyte antigen, sequence-based typing, well-documented allele, Clinical Sciences, Immunology
Abstract

We have updated the catalogue of common and well-documented (CWD) human leukocyte antigen (HLA) alleles to reflect current understanding of the prevalence of specific allele sequences. The original CWD catalogue designated 721 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, and -DPB1 loci in IMGT (IMmunoGeneTics)/HLA Database release 2.15.0 as being CWD. The updated CWD catalogue designates 1122 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1 and -DPB1 loci as being CWD, and represents 14.3% of the HLA alleles in IMGT/HLA Database release 3.9.0. In particular, we identified 415 of these alleles as being 'common' (having known frequencies) and 707 as being 'well-documented' on the basis of ~140,000 sequence-based typing observations and available HLA haplotype data. Using these allele prevalence data, we have also assigned CWD status to specific G and P designations. We identified 147/151 G groups and 290/415 P groups as being CWD. The CWD catalogue will be updated on a regular basis moving forward, and will incorporate changes to the IMGT/HLA Database as well as empirical data from the histocompatibility and immunogenetics community. This version 2.0.0 of the CWD catalogue is available online at cwd.immunogenomics.org, and will be integrated into the Allele Frequencies Net Database, the IMGT/HLA Database and National Marrow Donor Program's bioinformatics web pages.

Published
2013

13. 16(th) IHIW: immunogenomic data-management methods. report from the immunogenomic data analysis working group (IDAWG).

Author

Hollenbach, JA, Holcomb, C, Hurley, CK, Mabdouly, A, Maiers, M, Noble, JA, Robinson, J, Schmidt, AH, Shi, L, Turner, V, Yao, Y, and Mack, SJ

Subjects
Humans, HLA Antigens, Data Collection, Genetics, Population, Genome, Human, Ethnic Groups, Receptors, KIR, Surveys and Questionnaires, Ethnicity, Genetics, Immunology
Abstract

SummaryThe goal of the immunogenomic data analysis working group (IDAWG) is to facilitate the consistent analysis of HLA and KIR data, and the sharing of those data among the immunogenomic and larger genomic communities. However, the data management approaches currently applied by immunogenomic researchers are not widely discussed or reported in the literature, and the effect of different approaches on data analyses is not known. With ASHI's support, the IDAWG developed a 45 question survey on HLA and KIR data generation, data management and data analysis practices. Survey questions detailed the loci genotyped, typing systems used, nomenclature versions reported, computer operating systems and software used to manage and transmit data, the approaches applied to resolve HLA ambiguity and the methods used for basic population-level analyses. Respondents were invited to demonstrate their HLA ambiguity resolution approaches in simulated data sets. By May 2012, 156 respondents from 35 nations had completed the survey. These survey respondents represent a broad sampling of the Immunogenomic community; 52% were European, 30% North American, 10% Asian, 4% South American and 4% from the Pacific. The project will continue in conjunction with the 17th Workshop, with the aim of developing community data sharing standards, ambiguity resolution documentation formats, single-task data Management tools and novel data analysis methods and applications. While additional project details and plans for the 17th IHIW will be forthcoming, we welcome the input and participation in these projects from the histocompatibility and immunogenetics community.

Published
2013

34. Common and well-documented HLA alleles: 2012 update to the CWD catalogue

Author

Mack, S. J., Cano, P., Hollenbach, J. A., He, J., Hurley, C. K., Middleton, D., Moraes, M. E., Pereira, S. E., Kempenich, J. H., Reed, E. F., Setterholm, M., Smith, A. G., Tilanus, M. G., Torres, M., Varney, M. D., Voorter, C. E. M., Fischer, G. F., Fleischhauer, K., Goodridge, D., Klitz, W., Little, A.-M., Maiers, M., Marsh, S. G. E., Müller, C. R., Noreen, H., Rozemuller, E. H., Sanchez-Mazas, A., Senitzer, D., Trachtenberg, E., and Fernandez-Vina, Marcelo

Published
2013
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37. An update to HLA Nomenclature, 2010

Author

Marsh, S G E, Albert, E D, Bodmer, W F, Bontrop, R E, Dupont, B, Erlich, H A, Fernández-Viña, M, Geraghty, D E, Holdsworth, R, Hurley, C K, Lau, M, Lee, K W, Mach, B, Maiers, M, Mayr, W R, Müller, C R, Parham, P, Petersdorf, E W, Sasazuki, T, Strominger, J L, Svejgaard, A, Terasaki, P I, Tiercy, J M, and Trowsdale, J

Published
2010
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40. Nomenclature for factors of the HLA system, 2010

Author

Marsh, S. G. E., Albert, E. D., Bodmer, W. F., Bontrop, R. E., Dupont, B., Erlich, H. A., Fernández-Viña, M., Geraghty, D. E., Holdsworth, R., Hurley, C. K., Lau, M., Lee, K. W., Mach, B., Maiers, M., Mayr, W. R., Müller, C. R., Parham, P., Petersdorf, E. W., Sasazuki, T., Strominger, J. L., Svejgaard, A., Terasaki, P. I., Tiercy, J. M., and Trowsdale, J.

Published
2010
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