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387 results on '"Fernández-Viña, Marcelo A"'

1. ASTCT Consensus Recommendations on Testing and Treatment of Patients with Donor-specific Anti-HLA Antibodies

Author

Kongtim, Piyanuch, Vittayawacharin, Pongthep, Zou, Jun, Srour, Samer, Shaffer, Brian, Shapiro, Roman M., Varma, Ankur, McGuirk, Joseph, Dholaria, Bhagirathbhai R., McCurdy, Shannon R., DeZern, Amy E., Bejanyan, Nelli, Bashey, Asad, Furst, Sabine, Castagna, Luca, Mariotti, Jacopo, Ruggeri, Annalisa, Bailen, Rebeca, Teshima, Takanori, Xiao-Jun, Huang, Bonfim, Carmen, Aung, Fleur, Cao, Kai, Carpenter, Paul A., Hamadani, Mehdi, Askar, Medhat, Fernandez-Vina, Marcelo, Girnita, Alin, and Ciurea, Stefan O.

Published
2024
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2. An archaic HLA class I receptor allele diversifies natural killer cell-driven immunity in First Nations peoples of Oceania

Author

Loh, Liyen, Saunders, Philippa M., Faoro, Camilla, Font-Porterias, Neus, Nemat-Gorgani, Neda, Harrison, Genelle F., Sadeeq, Suraju, Hensen, Luca, Wong, Shu Cheng, Widjaja, Jacqueline, Clemens, E. Bridie, Zhu, Shiying, Kichula, Katherine M., Tao, Sudan, Zhu, Faming, Montero-Martin, Gonzalo, Fernandez-Vina, Marcelo, Guethlein, Lisbeth A., Vivian, Julian P., Davies, Jane, Mentzer, Alexander J., Oppenheimer, Stephen J., Pomat, William, Ioannidis, Alexander G., Barberena-Jonas, Carmina, Moreno-Estrada, Andrés, Miller, Adrian, Parham, Peter, Rossjohn, Jamie, Tong, Steven Y.C., Kedzierska, Katherine, Brooks, Andrew G., and Norman, Paul J.

Published
2024
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3. Interleukin (IL)-1/IL-6-Inhibitor–Associated Drug Reaction With Eosinophilia and Systemic Symptoms (DReSS) in Systemic Inflammatory Illnesses

Author

Aamir, R., Abulaban, K., Adams, A., Lapsia, C. Aguiar, Akinsete, A., Akoghlanian, S., Al Manaa, M., AlBijadi, A., Allenspach, E., Almutairi, A., Alperin, R., Amarilyo, G., Ambler, W., Amoruso, M., Angeles-Han, S., Ardoin, S., Armendariz, S., Asfaw, L., Aviran Dagan, N., Bacha, C., Balboni, I., Balevic, S., Ballinger, S., Baluta, S., Barillas-Arias, L., Basiaga, M., Baszis, K., Baxter, S., Becker, M., Begezda, A., Behrens, E., Beil, E., Benseler, S., Bermudez-Santiago, L., Bernal, W., Bigley, T., Bingham, C., Binstadt, B., Black, C., Blackmon, B., Blakley, M., Bohnsack, J., Boneparth, A., Bradfield, H., Bridges, J., Brooks, E., Brothers, M., Brunner, H., Buckley, L., Buckley, M., Bukulmez, H., Bullock, D., Canna, S., Cannon, L., Canny, S., Cartwright, V., Cassidy, E., Castro, D., Chalom, E., Chang, J., Chang, M., Chang-Hoftman, A., Chen, A., Chiraseveenuprapund, P., Ciaglia, K., Co, D., Cohen, E., Collinge, J., Conlon, H., Connor, R., Cook, K., Cooper, A., Cooper, J., Corbin, K., Correll, C., Cron, R., Curry, M., Dalrymple, A., Datyner, E., Davis, T., De Ranieri, D., Dean, J., DeCoste, C., Dedeoglu, F., DeGuzman, M., Delnay, N., DeSantis, E., Devine, R., Dhalla, M., Dhanrajani, A., Dissanayake, D., Dizon, B., Drapeau, N., Drew, J., Driest, K., Du, Q., Duncan, E., Dunnock, K., Durkee, D., Dvergsten, J., Eberhard, A., Ede, K., Edelheit, B., Edens, C., El Tal, T., Elder, M., Elzaki, Y., Fadrhonc, S., Failing, C., Fair, D., Favier, L., Feldman, B., Fennell, J., Ferguson, P., Ferguson, I., Figueroa, C., Flanagan, E., Fogel, L., Fox, E., Fox, M., Franklin, L., Fuhlbrigge, R., Fuller, J., Furey, M., Futch-West, T., Gagne, S., Gennaro, V., Gerstbacher, D., Gilbert, M., Gironella, A., Glaser, D., Goh, I., Goldsmith, D., Gorry, S., Goswami, N., Gottlieb, B., Graham, T., Grevich, S., Griffin, T., Grim, A., Grom, A., Guevara, M., Hahn, T., Halyabar, O., Hamda Natur, M., Hammelev, E., Hammond, T., Harel, L., Harris, J., Harry, O., Hausmann, J., Hay, A., Hays, K., Hayward, K., Henderson, L., Henrickson, M., Hersh, A., Hickey, K., Hiraki, L., Hiskey, M., Hobday, P., Hoffart, C., Holland, M., Hollander, M., Hong, S., Horton, D., Horwitz, M., Hsu, J., Huber, A., Huberts, A., Huggins, J., Huie, L., Hui-Yuen, J., Ibarra, M., Imlay, A., Imundo, L., Inman, C., Jackson, A., James, K., Janow, G., Jared, S., Jiang, Y., Johnson, L., Johnson, N., Jones, J., Kafisheh, D., Kahn, P., Kaidar, K., Kasinathan, S., Kaur, R., Kessler, E., Kienzle, B., Kim, S., Kimura, Y., Kingsbury, D., Kitcharoensakkul, M., Klausmeier, T., Klein, K., Klein-Gitelman, M., Knight, A., Kovalick, L., Kramer, S., Kremer, C., Kudas, O., LaFlam, T., Lang, B., Lapidus, S., Lapin, B., Lasky, A., Lawler, C., Lawson, E., Laxer, R., Lee, P., Lee, T., Lee, A., Leisinger, E., Lentini, L., Lerman, M., Levinsky, Y., Levy, D., Li, S., Lieberman, S., Lim, L., Limenis, E., Lin, C., Ling, N., Lionetti, G., Livny, R., Lloyd, M., Lo, M., Long, A., Lopez-Peña, M., Lovell, D., Luca, N., Lvovich, S., Lytch, A., Ma, M., Machado, A., MacMahon, J., Madison, J., Mannion, M., Manos, C., Mansfield, L., Marston, B., Mason, T., Matchett, D., McAllister, L., McBrearty, K., McColl, J., McCurdy, D., McDaniels, K., McDonald, J., Meidan, E., Mellins, E., Mian, Z., Miettunen, P., Miller, M., Milojevic, D., Mitacek, R., Modica, R., Mohan, S., Moore, T., Moore, K., Moorthy, L., Moreno, J., Morgan, E., Moyer, A., Murante, B., Murphy, A., Muscal, E., Mwizerwa, O., Najafi, A., Nanda, K., Nasah, N., Nassi, L., Nativ, S., Natter, M., Nearanz, K., Neely, J., Newhall, L., Nguyen, A., Nigrovic, P., Nocton, J., Nolan, B., Nowicki, K., Oakes, R., Oberle, E., Ogbonnaya-Whittesley, S., Ogbu, E., Oliver, M., Olveda, R., Onel, K., Orandi, A., Padam, J., Paller, A., Pan, N., Pandya, J., Panupattanapong, S., Toledano, A. Pappo, Parsons, A., Patel, J., Patel, P., Patrick, A., Patrizi, S., Paul, S., Perfetto, J., Perron, M., Peskin, M., Ponder, L., Pooni, R., Prahalad, S., Puplava, B., Quinlan-Waters, M., Rabinovich, C., Rafko, J., Rahimi, H., Rampone, K., Ramsey, S., Randell, R., Ray, L., Reed, A., Reid, H., Reiff, D., Richins, S., Riebschleger, M., Rife, E., Riordan, M., Riskalla, M., Robinson, A., Robinson, L., Rodgers, L., Rodriquez, M., Rogers, D., Ronis, T., Rosado, A., Rosenkranz, M., Rosenwasser, N., Rothermel, H., Rothman, D., Rothschild, E., Roth-Wojcicki, E., Rouster-Stevens, K., Rubinstein, T., Rupp, J., Ruth, N., Sabbagh, S., Sadun, R., Santiago, L., Saper, V., Sarkissian, A., Scalzi, L., Schahn, J., Schikler, K., Schlefman, A., Schmeling, H., Schmitt, E., Schneider, R., Schulert, G., Schultz, K., Schutt, C., Seper, C., Sheets, R., Shehab, A., Shenoi, S., Sherman, M., Shirley, J., Shishov, M., Siegel, D., Singer, N., Sivaraman, V., Sloan, E., Smith, C., Smith, J., Smitherman, E., Soep, J., Son, Mary B., Sosna, D., Spencer, C., Spiegel, L., Spitznagle, J., Srinivasalu, H., Stapp, H., Steigerwald, K., Stephens, A., Sterba Rakovchik, Y., Stern, S., Stevens, B., Stevenson, R., Stewart, K., Stewart, W., Stingl, C., Stoll, M., Stringer, E., Sule, S., Sullivan, J., Sundel, R., Sutter, M., Swaffar, C., Swayne, N., Syed, R., Symington, T., Syverson, G., Szymanski, A., Taber, S., Tal, R., Tambralli, A., Taneja, A., Tanner, T., Tarvin, S., Tate, L., Taxter, A., Taylor, J., Tesher, M., Thakurdeen, T., Theisen, A., Thomas, B., Thomas, L., Thomas, N., Ting, T., Todd, C., Toib, D., Torok, K., Tory, H., Toth, M., Tse, S., Tsin, C., Twachtman-Bassett, J., Twilt, M., Valcarcel, T., Valdovinos, R., Vallee, A., Van Mater, H., Vandenbergen, S., Vannoy, L., Varghese, C., Vasquez, N., Vega-Fernandez, P., Velez, J., Verbsky, J., Verstegen, R., von Scheven, E., Vora, S., Wagner-Weiner, L., Wahezi, D., Waite, H., Walker, B., Walters, H., Waterfield, M., Waters, A., Weiser, P., Weiss, P., Weiss, J., Wershba, E., Westheuser, V., White, A., Widrick, K., Williams, C., Wong, S., Woolnough, L., Wright, T., Wu, E., Yalcindag, A., Yasin, S., Yeung, R., Yomogida, K., Zeft, A., Zhang, Y., Zhao, Y., Zhu, A., Saper, Vivian E., Tian, Lu, Verstegen, Ruud H.J., Conrad, Carol K., Cidon, Michal, Hopper, Rachel K., Kuo, Christin S., Osoegawa, Kazutoyo, Baszis, Kevin, Bingham, Catherine A., Ferguson, Ian, Hahn, Timothy, Horne, Annacarin, Isupova, Eugenia A., Jones, Jordan T., Kasapcopur, Özgür, Klein-Gitelman, Marisa S., Kostik, Mikhail M., Ozen, Seza, Phadke, Omkar, Prahalad, Sampath, Randell, Rachel L., Sener, Seher, Stingl, Cory, Abdul-Aziz, Rabheh, Akoghlanian, Shoghik, Al Julandani, Dalila, Alvarez, Marcela B., Bader-Meunier, Brigitte, Balay-Dustrude, Erin E., Balboni, Imelda, Baxter, Sarah K., Berard, Roberta A., Bhattad, Sagar, Bolaria, Roxana, Boneparth, Alexis, Cassidy, Elaine A., Co, Dominic O., Collins, Kathleen P., Dancey, Paul, Dickinson, Aileen M., Edelheit, Barbara S., Espada, Graciela, Flanagan, Elaine R., Imundo, Lisa F., Jindal, Ankur K., Kim, Hyoun-Ah, Klaus, Günter, Lake, Carol, Lapin, W. Blaine, Lawson, Erica F., Marmor, Itay, Mombourquette, Joy, Ogunjimi, Benson, Olveda, Rebecca, Ombrello, Michael J., Onel, Karen, Poholek, Catherine, Ramanan, Athimalaipet V., Ravelli, Angelo, Reinhardt, Adam, Robinson, Amanda D., Rouster-Stevens, Kelly, Saad, Nadine, Schneider, Rayfel, Selmanovic, Velma, Sefic Pasic, Irmina, Shenoi, Susan, Shilo, Natalie R., Soep, Jennifer B., Sura, Angeli, Taber, Sarah F., Tesher, Melissa, Tibaldi, Jessica, Torok, Kathryn S., Tsin, Cathy Mei, Vasquez-Canizares, Natalia, Villacis Nunez, Diana S., Way, Emily E., Whitehead, Benjamin, Zemel, Lawrence S., Sharma, Surbhi, Fernández-Viña, Marcelo A., and Mellins, Elizabeth D.

Published
2024
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5. Challenges for the standardized reporting of NGS HLA genotyping: Surveying gaps between clinical and research laboratories

Author

Osoegawa, Kazutoyo, Montero-Martín, Gonzalo, Mallempati, Kalyan C, Bauer, Miranda, Milius, Robert P, Maiers, Martin, Fernández-Viña, Marcelo A, and Mack, Steven J

Subjects
Biomedical and Clinical Sciences, Immunology, Genetics, Genotyping Techniques, HLA Antigens, High-Throughput Nucleotide Sequencing, Histocompatibility Testing, Humans, Immunogenetics, Laboratories, Sequence Analysis, DNA, Software, Allelic ambiguity, Genotypic ambiguity, GL String, MIRING, HML
Abstract

Next generation sequencing (NGS) is being applied for HLA typing in research and clinical settings. NGS HLA typing has made it feasible to sequence exons, introns and untranslated regions simultaneously, with significantly reduced labor and reagent cost per sample, rapid turnaround time, and improved HLA genotype accuracy. NGS technologies bring challenges for cost-effective computation, data processing and exchange of NGS-based HLA data. To address these challenges, guidelines and specifications such as Genotype List (GL) String, Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING), and Histoimmunogenetics Markup Language (HML) were proposed to streamline and standardize reporting of HLA genotypes. As part of the 17th International HLA and Immunogenetics Workshop (IHIW), we implemented standards and systems for HLA genotype reporting that included GL String, MIRING and HML, and found that misunderstanding or misinterpretations of these standards led to inconsistencies in the reporting of NGS HLA genotyping results. This may be due in part to a historical lack of centralized data reporting standards in the histocompatibility and immunogenetics community. We have worked with software and database developers, clinicians and scientists to address these issues in a collaborative fashion as part of the Data Standard Hackathons (DaSH) for NGS. Here we report several categories of challenges to the consistent exchange of NGS HLA genotyping data we have observed. We hope to address these challenges in future DaSH for NGS efforts.

Published
2021

6. High-resolution HLA allele and haplotype frequencies in several unrelated populations determined by next generation sequencing: 17th International HLA and Immunogenetics Workshop joint report

Author

Creary, Lisa E, Sacchi, Nicoletta, Mazzocco, Michela, Morris, Gerald P, Montero-Martin, Gonzalo, Chong, Winnie, Brown, Colin J, Dinou, Amalia, Stavropoulos-Giokas, Catherine, Gorodezky, Clara, Narayan, Saranya, Periathiruvadi, Srinivasan, Thomas, Rasmi, De Santis, Dianne, Pepperall, Jennifer, ElGhazali, Gehad E, Al Yafei, Zain, Askar, Medhat, Tyagi, Shweta, Kanga, Uma, Marino, Susana R, Planelles, Dolores, Chang, Chia-Jung, and Fernández-Viña, Marcelo A

Subjects
Genetics, 2.1 Biological and endogenous factors, Aetiology, Alleles, Disease Susceptibility, Gene Frequency, Genetic Association Studies, Genetics, Population, HLA Antigens, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Immunogenetics, Transplantation Immunology, Human leukocyte antigen, Next-generation sequencing, International HLA and Immunogenetics, Workshop, Allele frequency, Haplotype frequency, International HLA and Immunogenetics Workshop, Immunology
Abstract

The primary goal of the unrelated population HLA diversity (UPHD) component of the 17th International HLA and Immunogenetics Workshop was to characterize HLA alleles at maximum allelic-resolution in worldwide populations and re-evaluate patterns of HLA diversity across populations. The UPHD project included HLA genotype and sequence data, generated by various next-generation sequencing methods, from 4,240 individuals collated from 12 different countries. Population data included well-defined large datasets from the USA and smaller samples from Europe, Australia, and Western Asia. Allele and haplotype frequencies varied across populations from distant geographical regions. HLA genetic diversity estimated at 2- and 4-field allelic resolution revealed that diversity at the majority of loci, particularly for European-descent populations, was lower at the 2-field resolution. Several common alleles with identical protein sequences differing only by intronic substitutions were found in distinct haplotypes, revealing a more detailed characterization of linkage between variants within the HLA region. The examination of coding and non-coding nucleotide variation revealed many examples in which almost complete biunivocal relations between common alleles at different loci were observed resulting in higher linkage disequilibrium. Our reference data of HLA profiles characterized at maximum resolution from many populations is useful for anthropological studies, unrelated donor searches, transplantation, and disease association studies.

Published
2021

7. Next-Generation Sequencing Identifies Extended HLA Class I and II Haplotypes Associated With Early-Onset and Late-Onset Myasthenia Gravis in Italian, Norwegian, and Swedish Populations

Author

Creary, Lisa E, Gangavarapu, Sridevi, Caillier, Stacy J, Cavalcante, Paola, Frangiamore, Rita, Lie, Benedicte A, Bengtsson, Mats, Harbo, Hanne Flinstad, Brauner, Susanna, Hollenbach, Jill A, Oksenberg, Jorge R, Bernasconi, Pia, Maniaol, Angelina Hatlø, Hammarström, Lennart, Mantegazza, Renato, and Fernández-Viña, Marcelo A

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Rare Diseases, Autoimmune Disease, Myasthenia Gravis, Neurosciences, Clinical Research, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Adult, Age of Onset, Alleles, Female, Genetic Predisposition to Disease, HLA-B Antigens, HLA-DR Antigens, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Italy, Male, Middle Aged, Norway, Sweden, myasthenia gravis, human leukocyte antigen, next-generation sequencing, European, susceptibility, protection, Immunology, Medical Microbiology, Biochemistry and cell biology
Abstract

Genetic susceptibility to myasthenia gravis (MG) associates with specific HLA alleles and haplotypes at the class I and II regions in various populations. Previous studies have only examined alleles at a limited number of HLA loci that defined only broad serotypes or alleles defined at the protein sequence level. Consequently, genetic variants in noncoding and untranslated HLA gene segments have not been fully explored but could also be important determinants for MG. To gain further insight into the role of HLA in MG, we applied next-generation sequencing to analyze sequence variation at eleven HLA genes in early-onset (EO) and late-onset (LO) non-thymomatous MG patients positive for the acetylcholine receptor (AChR) antibodies and ethnically matched controls from Italy, Norway, and Sweden. For all three populations, alleles and haplotype blocks present on the ancestral haplotype AH8.1 were associated with risk in AChR-EOMG patients. HLA-B*08:01:01:01 was the dominant risk allele in Italians (OR = 3.28, P = 1.83E-05), Norwegians (OR = 3.52, P = 4.41E-16), and in Swedes HLA-B*08:01 was the primary risk allele (OR = 4.24, P

Published
2021

8. High-Resolution Characterization of KIR Genes in a Large North American Cohort Reveals Novel Details of Structural and Sequence Diversity

Author

Amorim, Leonardo M, Augusto, Danillo G, Nemat-Gorgani, Neda, Montero-Martin, Gonzalo, Marin, Wesley M, Shams, Hengameh, Dandekar, Ravi, Caillier, Stacy, Parham, Peter, Fernández-Viña, Marcelo A, Oksenberg, Jorge R, Norman, Paul J, and Hollenbach, Jill A

Subjects
Biotechnology, Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Alleles, Cohort Studies, Genomic Structural Variation, Genotype, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, North America, Polymorphism, Genetic, Polymorphism, Single Nucleotide, Receptors, Immunologic, Receptors, KIR, White People, NK receptors, alleles, high resolution, NGS, sequencing, population, population, Immunology, Medical Microbiology
Abstract

The KIR (killer-cell immunoglobulin-like receptor) region is characterized by structural variation and high sequence similarity among genes, imposing technical difficulties for analysis. We undertook the most comprehensive study to date of KIR genetic diversity in a large population sample, applying next-generation sequencing in 2,130 United States European-descendant individuals. Data were analyzed using our custom bioinformatics pipeline specifically designed to address technical obstacles in determining KIR genotypes. Precise gene copy number determination allowed us to identify a set of uncommon gene-content KIR haplotypes accounting for 5.2% of structural variation. In this cohort, KIR2DL4 is the framework gene that most varies in copy number (6.5% of all individuals). We identified phased high-resolution alleles in large multi-locus insertions and also likely founder haplotypes from which they were deleted. Additionally, we observed 250 alleles at 5-digit resolution, of which 90 have frequencies ≥1%. We found sequence patterns that were consistent with the presence of novel alleles in 398 (18.7%) individuals and contextualized multiple orphan dbSNPs within the KIR complex. We also identified a novel KIR2DL1 variant, Pro151Arg, and demonstrated by molecular dynamics that this substitution is predicted to affect interaction with HLA-C. No previous studies have fully explored the full range of structural and sequence variation of KIR as we present here. We demonstrate that pairing high-throughput sequencing with state-of-art computational tools in a large cohort permits exploration of all aspects of KIR variation including determination of population-level haplotype diversity, improving understanding of the KIR system, and providing an important reference for future studies.

Published
2021

10. Killer Cell Immunoglobulin-like Receptor Variants Are Associated with Protection from Symptoms Associated with More Severe Course in Parkinson Disease

Author

Anderson, Kirsten M, Augusto, Danillo G, Dandekar, Ravi, Shams, Hengameh, Zhao, Chao, Yusufali, Tasneem, Montero-Martín, Gonzalo, Marin, Wesley M, Nemat-Gorgani, Neda, Creary, Lisa E, Caillier, Stacy, Mofrad, Mohammad RK, Parham, Peter, Fernández-Viña, Marcelo, Oksenberg, Jorge R, Norman, Paul J, and Hollenbach, Jill A

Subjects
Brain Disorders, Genetics, Neurodegenerative, Neurosciences, Clinical Research, Parkinson's Disease, Aging, Aetiology, 2.1 Biological and endogenous factors, Neurological, Inflammatory and immune system, Alleles, Female, Genotype, HLA-B Antigens, Humans, Killer Cells, Natural, Ligands, Male, Middle Aged, Parkinson Disease, Polymorphism, Genetic, Receptors, KIR3DL1, Severity of Illness Index, Immunology
Abstract

Immune dysfunction plays a role in the development of Parkinson disease (PD). NK cells regulate immune functions and are modulated by killer cell immunoglobulin-like receptors (KIR). KIR are expressed on the surface of NK cells and interact with HLA class I ligands on the surface of all nucleated cells. We investigated KIR-allelic polymorphism to interrogate the role of NK cells in PD. We sequenced KIR genes from 1314 PD patients and 1978 controls using next-generation methods and identified KIR genotypes using custom bioinformatics. We examined associations of KIR with PD susceptibility and disease features, including age at disease onset and clinical symptoms. We identified two KIR3DL1 alleles encoding highly expressed inhibitory receptors associated with protection from PD clinical features in the presence of their cognate ligand: KIR3DL1*015/HLA-Bw4 from rigidity (p c = 0.02, odds ratio [OR] = 0.39, 95% confidence interval [CI] 0.23-0.69) and KIR3DL1*002/HLA-Bw4i from gait difficulties (p c = 0.05, OR = 0.62, 95% CI 0.44-0.88), as well as composite symptoms associated with more severe disease. We also developed a KIR3DL1/HLA interaction strength metric and found that weak KIR3DL1/HLA interactions were associated with rigidity (pc = 0.05, OR = 9.73, 95% CI 2.13-172.5). Highly expressed KIR3DL1 variants protect against more debilitating symptoms of PD, strongly implying a role of NK cells in PD progression and manifestation.

Published
2020

11. Next-generation sequencing reveals new information about HLA allele and haplotype diversity in a large European American population

Author

Creary, Lisa E, Gangavarapu, Sridevi, Mallempati, Kalyan C, Montero-Martín, Gonzalo, Caillier, Stacy J, Santaniello, Adam, Hollenbach, Jill A, Oksenberg, Jorge R, and Fernández-Viña, Marcelo A

Subjects
Genetics, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Aged, Aged, 80 and over, Alleles, Cohort Studies, Europe, Female, Gene Frequency, Genetic Loci, Genetics, Population, HLA Antigens, Haplotypes, High-Throughput Nucleotide Sequencing, Histocompatibility Testing, Humans, Linkage Disequilibrium, Male, Middle Aged, United States, White People, Young Adult, Human leukocyte antigen, Next-generation sequencing, European Americans, Allele frequency, Haplotype frequency, Linkage disequilibrium, Haplotype blocks, Population genetics, Immunology
Abstract

The human leukocyte antigen (HLA) genes are extremely polymorphic and are useful molecular markers to make inferences about human population history. However, the accuracy of the estimation of genetic diversity at HLA loci very much depends on the technology used to characterize HLA alleles; high-resolution genotyping of long-range HLA gene products improves the assessment of HLA population diversity as well as other population parameters compared to lower resolution typing methods. In this study we examined allelic and haplotype HLA diversity in a large healthy European American population sourced from the UCSF-DNA bank. A high-resolution next-generation sequencing method was applied to define non-ambiguous 3- and 4-field alleles at the HLA-A, HLA-C, HLA-B, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1 loci in samples provided by 2248 unrelated individuals. A number of population parameters were examined including balancing selection and various measurements of linkage disequilibrium were calculated. There were no detectable deviations from Hardy-Weinberg proportions at HLA-A, HLA-DRB1, HLA-DQA1 and HLA-DQB1. For the remaining loci moderate and significant deviations were detected at HLA-C, HLA-B, HLA-DRB3/4/5, HLA-DPA1 and HLA-DPB1 loci mostly from population substructures. Unique 4-field associations were observed among alleles at 2 loci and haplotypes extending large intervals that were not apparent in results obtained using testing methodologies with limited sequence coverage and phasing. The high diversity at HLA-DPA1 results from detection of intron variants of otherwise well conserved protein sequences. It may be speculated that divergence in exon sequences may be negatively selected. Our data provides a valuable reference source for future population studies that may allow for precise fine mapping of coding and non-coding sequences determining disease susceptibility and allo-immunogenicity.

Published
2019

12. HLA alleles and haplotypes observed in 263 US families

Author

Osoegawa, Kazutoyo, Mallempati, Kalyan C, Gangavarapu, Sridevi, Oki, Arisa, Gendzekhadze, Ketevan, Marino, Susana R, Brown, Nicholas K, Bettinotti, Maria P, Weimer, Eric T, Montero-Martín, Gonzalo, Creary, Lisa E, Vayntrub, Tamara A, Chang, Chia-Jung, Askar, Medhat, Mack, Steven J, and Fernández-Viña, Marcelo A

Subjects
Transplantation, Genetics, Clinical Research, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Alleles, Base Sequence, Child, Ethnicity, Exons, Gene Frequency, HLA Antigens, Haplotypes, High-Throughput Nucleotide Sequencing, Histocompatibility Testing, Humans, Introns, Linkage Disequilibrium, Nuclear Family, Pedigree, Software, United States, Untranslated Regions, Family, HLA haplotype, Linkage disequilibrium, Immunology
Abstract

The 17th International HLA and Immunogenetics Workshop (IHIW) conducted a project entitled "The Study of Haplotypes in Families by NGS HLA". We investigated the HLA haplotypes of 1017 subjects in 263 nuclear families sourced from five US clinical immunogenetics laboratories, primarily as part of the evaluation of related donor candidates for hematopoietic stem cell and solid organ transplantation. The parents in these families belonged to five broad groups - African (72 parents), Asian (115), European (210), Hispanic (118) and "Other" (11). High-resolution HLA genotypes were generated for each subject using next-generation sequencing (NGS) HLA typing systems. We identified the HLA haplotypes in each family using HaplObserve, software that builds haplotypes in families by reviewing HLA allele segregation from parents to children. We calculated haplotype frequencies within each broad group, by treating the parents in each family as unrelated individuals. We also calculated standard measures of global linkage disequilibrium (LD) and conditional asymmetric LD for each ethnic group, and used untruncated and two-field allele names to investigate LD patterns. Finally we demonstrated the utility of consensus DNA sequences in identifying novel variants, confirming them using HLA allele segregation at the DNA sequence level.

Published
2019

13. Tools for building, analyzing and evaluating HLA haplotypes from families

Author

Osoegawa, Kazutoyo, Mack, Steven J, Prestegaard, Matthew, and Fernández-Viña, Marcelo A

Subjects
Clinical Research, Clinical Trials and Supportive Activities, Genetics, Human Genome, Alleles, Child, Gene Frequency, Genetic Loci, HLA Antigens, Haplotypes, Heterozygote, Humans, Linkage Disequilibrium, Nuclear Family, Pedigree, Software, 17th International HLA and Immunogenetics Workshop, HLA, Haplotype, Linkage disequilibrium, Next generation sequencing, Immunology
Abstract

The highly polymorphic classical human leukocyte antigen (HLA) genes display strong linkage disequilibrium (LD) that results in conserved multi-locus haplotypes. For unrelated individuals in defined populations, HLA haplotype frequencies can be estimated using the expectation-maximization (EM) method. Haplotypes can also be constructed using HLA allele segregation from nuclear families. It is straightforward to identify many HLA genotyping inconsistencies by visually reviewing HLA allele segregation in family members. It is also possible to identify potential crossover events when two or more children are available in a nuclear family. This process of visual inspection can be unwieldy, and we developed the "HaplObserve" program to standardize the process and automatically build haplotypes using family-based HLA allele segregation. HaplObserve facilitates systematically building haplotypes, and reporting potential crossover events. HLA Haplotype Validator (HLAHapV) is a program originally developed to impute chromosomal phase from genotype data using reference haplotype data. We updated and adapted HLAHapV to systematically compare observed and estimated haplotypes. We also used HLAHapV to identify haplotypes when uninformative HLA genotypes are present in families. Finally, we developed "pould", an R package that calculates haplotype frequencies, and estimates standard measures of global (locus-level) LD from both observed and estimated haplotypes.

Published
2019

15. Three Fields Allelic Haplotype Frequencies of HLA‐DPA1 and ‐DPB1 Typed by Next Generation Sequencing of 563 Families in Chinese Han Population.

Author

Wang, Jian‐Ling, He, Jun‐Bo, Li, Zhi‐Min, Zhu, Ya‐Nan, Cao, DaJiang, Fu, Hong‐Lei, Zhang, Xian, Fernández‐Viña, Marcelo A., Rozemuller, Erik, and Liu, XiangJun

Subjects
HEMATOPOIETIC stem cell transplantation, NUCLEOTIDE sequencing, CHINESE people, HAPLOTYPES, NUCLEAR families
Abstract

The present study investigated the HLA‐DPA1 and ‐DPB1 allele and haplotype frequencies in the Chinese Han population. A total of 563 families, which have been typed for the purpose of haematopoietic stem cell transplantation, were included, and three‐field allelic resolution typing of HLA‐DPA1 and ‐DPB1 of all individuals were defined by the next‐generation sequencing method. HLA‐DPA1~DPB1 haplotypes were determined by allele segregation within a nuclear family. A total of 9 HLA‐DPA1 and 39 HLA‐DPB1 alleles, and 62 HLA‐DPA1~DPB1 haplotypes were identified. The three most frequent alleles at HLA‐DPA1 locus are HLA‐DPA1*02:02:02 (46.581%), HLA‐DPA1*01:03:01 (36.456%) and HLA‐DPA1*02:01:01 (12.167%); and the three most frequent HLA‐DPB1 alleles are HLA‐DPB1*05:01:01 (34.014%), HLA‐DPB1*02:01:02 (18.428%) and HLA‐DPB1*04:01:01 (10.124%). The three most frequent haplotypes are HLA‐DPA1*02:02:02~DPB1*05:01:01 (32.327%), HLA‐DPA1*01:03:01 ~ DPB1*02:01:02 (14.654%) and HLA‐DPA1*01:03:01~DPB1*04:01:01 (9.458%). The HLA‐DPA1*02:01~DPB1*02:02 and HLA‐DPA1*04:01~DPB1*05:01 haplotypes appear to be unique in Han Chinese. Strong global linkage disequilibrium (LD) between HLA‐DPA1 and ‐DPB1 was confirmed (D′ = 0.848, Wn = 0.684). Moreover, the haplotype frequencies based on the family study were compared with the frequencies estimated by the expectation–maximisation algorithm, and the equivalent results were obtained except for haplotypes with very low frequencies. Our data provide a solid base for HLA‐DP dimer association studies and useful information for transplantation and disease association studies. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Report from the Killer-cell Immunoglobulin-like Receptors (KIR) component of the 17th International HLA and Immunogenetics Workshop

Author

Misra, Maneesh K, Augusto, Danillo G, Martin, Gonzalo Montero, Nemat-Gorgani, Neda, Sauter, Jürgen, Hofmann, Jan A, Traherne, James A, González-Quezada, Betsy, Gorodezky, Clara, Bultitude, Will P, Marin, Wesley, Vierra-Green, Cynthia, Anderson, Kirsten M, Balas, Antonio, Caro-Oleas, Jose L, Cisneros, Elisa, Colucci, Francesco, Dandekar, Ravi, Elfishawi, Sally M, Fernández-Viña, Marcelo A, Fouda, Merhan, González-Fernández, Rafael, Große, Arend, Herrero-Mata, Maria J, Hollenbach, Sam Q, Marsh, Steven GE, Mentzer, Alex, Middleton, Derek, Moffett, Ashley, Moreno-Hidalgo, Miguel A, Mossallam, Ghada I, Nakimuli, Annettee, Oksenberg, Jorge R, Oppenheimer, Stephen J, Parham, Peter, Petzl-Erler, Maria-Luiza, Planelles, Dolores, Sánchez-García, Florentino, Sánchez-Gordo, Francisco, Schmidt, Alexander H, Trowsdale, John, Vargas, Luciana B, Vicario, Jose L, Vilches, Carlos, Norman, Paul J, and Hollenbach, Jill A

Subjects
Clinical Research, Genetics, Gene Frequency, Genetics, Population, Genotype, HLA Antigens, Haplotypes, Humans, Immunogenetics, Multigene Family, Protein Isoforms, Receptors, KIR, Sequence Analysis, DNA, KIR3DL1/S1, KIR3DL2, KIR3DL3, Immunology
Abstract

The goals of the KIR component of the 17th International HLA and Immunogenetics Workshop (IHIW) were to encourage and educate researchers to begin analyzing KIR at allelic resolution, and to survey the nature and extent of KIR allelic diversity across human populations. To represent worldwide diversity, we analyzed 1269 individuals from ten populations, focusing on the most polymorphic KIR genes, which express receptors having three immunoglobulin (Ig)-like domains (KIR3DL1/S1, KIR3DL2 and KIR3DL3). We identified 13 novel alleles of KIR3DL1/S1, 13 of KIR3DL2 and 18 of KIR3DL3. Previously identified alleles, corresponding to 33 alleles of KIR3DL1/S1, 38 of KIR3DL2, and 43 of KIR3DL3, represented over 90% of the observed allele frequencies for these genes. In total we observed 37 KIR3DL1/S1 allotypes, 40 for KIR3DL2 and 44 for KIR3DL3. As KIR allotype diversity can affect NK cell function, this demonstrates potential for high functional diversity worldwide. Allelic variation further diversifies KIR haplotypes. We determined KIR3DL3 ∼ KIR3DL1/S1 ∼ KIR3DL2 haplotypes from five of the studied populations, and observed multiple population-specific haplotypes in each. This included 234 distinct haplotypes in European Americans, 191 in Ugandans, 35 in Papuans, 95 in Egyptians and 86 in Spanish populations. For another 35 populations, encompassing 642,105 individuals we focused on KIR3DL2 and identified another 375 novel alleles, with approximately half of them observed in more than one individual. The KIR allelic level data gathered from this project represents the most comprehensive summary of global KIR allelic diversity to date, and continued analysis will improve understanding of KIR allelic polymorphism in global populations. Further, the wealth of new data gathered in the course of this workshop component highlights the value of collaborative, community-based efforts in immunogenetics research, exemplified by the IHIW.

Published
2018

18. Curating Genetic Associations With Rheumatologic Autoimmune Diseases to Improve Patient Outcomes.

Author

Bridges, S. Louis, Shapira, Rachel, Aksentijevich, Ivona, Mack, Steven J., Merriman, Tony R., Klein, Clarissa J., Bowen, B. Monica, Klein, Teri E., Ainsworth, Hannah C., Langefeld, Carl D., de Jesus, Adriana A., Deuitch, Natalie T., Ombrello, Michael J., Fernandez‐Ruiz, Ruth, Fernández‐Viña, Marcelo, Keseler, Ingrid M., Wright, Matt W., Lakhanpal, Amit, Laufer, Vincent A., and Varga, John

Subjects
RHEUMATISM diagnosis, GENETICS of autoimmune diseases, PROTEINS, TREATMENT effectiveness, CONSORTIA, GENETIC mutation, ACCURACY, RHEUMATISM, GENETICS, GENETIC testing, HLA-B27 antigen, PHENOTYPES, ALLELES, COMMITTEES, GROUP process, SYMPTOMS
Abstract

The article offers update on the curation of genetic associations with rheumatologic autoimmune diseases to improve patient outcomes. Topics discussed include monogenic autoimmune and/or autoinflammatory conditions, development of a framework for curation of HLA disease associations, development of a methodology for curation of complex, multigenic diseases, and curation of disease-associated somatic variants.

Published
2024
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19. A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinson’s disease

Author

Hollenbach, Jill A., Norman, Paul J., Creary, Lisa E., Damotte, Vincent, Montero-Martin, Gonzalo, Caillier, Stacy, Anderson, Kirsten M., Misra, Maneesh K., Nemat-Gorgani, Neda, Osoegawa, Kazutoyo, Santaniello, Adam, Renschen, Adam, Marin, Wesley M., Dandekar, Ravi, Parham, Peter, Tanner, Caroline M., Hauser, Stephen L., Fernandez-Viña, Marcelo, and Oksenberg, Jorge R.

Published
2019

20. Specific Class I HLA Supertypes but Not HLA Zygosity or Expression Are Associated with Outcomes following HLA-Matched Allogeneic Hematopoietic Cell Transplant: HLA Supertypes Impact Allogeneic HCT Outcomes

Author

Camacho-Bydume, Christine, Wang, Tao, Sees, Jennifer A., Fernandez-Viña, Marcelo, Abid, Muhammad Bilal, Askar, Medhat, Beitinjaneh, Amer, Brown, Valerie, Castillo, Paul, Chhabra, Saurabh, Gadalla, Shahinaz M., Hsu, Jing-Mei, Kamoun, Malek, Lazaryan, Aleksandr, Nishihori, Taiga, Page, Kristin, Schetelig, Johannes, Fleischhauer, Katharina, Marsh, Steven G.E., Paczesny, Sophie, Spellman, Stephen R., Lee, Stephanie J., and Hsu, Katharine C.

Published
2020
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21. Complement-Binding Donor-Specific Anti-HLA Antibodies and Risk of Primary Graft Failure in Hematopoietic Stem Cell Transplantation.

Author

Ciurea, Stefan, Thall, Peter, Milton, Denái, Barnes, Titus, Carmazzi, Yudith, López, Asdrúbal, Yap, Dianne, Popat, Uday, Rondon, Gabriela, Lichtiger, Benjamin, Aung, Fleur, Afshar-Kharghan, Vahid, Ma, Qing, Fernández-Viña, Marcelo, Champlin, Richard, Cao, Kai, and Kongtim, Piyanuch

Subjects
Buffy coat, C1q, Complement-binding DSA, Desensitization, Donor-specific anti-HLA antibodies, Graft rejection, Hematopoietic stem cell transplantation, Adolescent, Adult, Aged, Female, Graft Rejection, Graft Survival, HLA Antigens, Hematopoietic Stem Cell Transplantation, Histocompatibility Testing, Humans, Isoantibodies, Male, Middle Aged, Retrospective Studies, Transplantation Conditioning, Young Adult
Abstract

Detection of donor-specific anti-HLA antibodies (DSA) has been associated with graft rejection in all forms of transplantation. The mechanism by which DSA increase the risk of graft failure remains unclear. We hypothesized that complement-binding DSA are associated with engraftment failure in hematopoietic stem cell transplantation (HSCT) and analyzed 122 haploidentical transplant recipients tested prospectively for DSA. Retrospective analysis to detect C1q binding DSA (C1q+DSA) was performed on 22 allosensitized recipients. Twenty-two of 122 patients (18%) had DSA, 19 of which were women (86%). Seven patients with DSA (32%) rejected the graft. Median DSA level at transplant for patients who failed to engraft was 10,055 mean fluorescence intensity (MFI) versus 2065 MFI for those who engrafted (P = .007). Nine patients with DSA were C1q positive in the initial samples with median DSA levels of 15,279 MFI (range, 1554 to 28,615), compared with 7 C1q-negative patients with median DSA levels of 2471 MFI (range, 665 to 12,254) (P = .016). Of 9 patients who were C1q positive in the initial samples, 5 patients remained C1q positive at time of transplant (all with high DSA levels [median, 15,279; range, 6487 to 22,944]) and experienced engraftment failure, whereas 4 patients became C1q negative pretransplant and all engrafted the donor cells (P = .008). In conclusion, patients with high DSA levels (>5000 MFI) and complement-binding DSA antibodies (C1q positive) appear to be at much higher risk of primary graft failure. The presence of C1q+DSA should be assessed in allosensitized patients before HSCT. Reduction of C1q+DSA levels might prevent engraftment failure in HSCT.

Published
2015

23. HLA Haplotypes In 250 Families: The Baylor Laboratory Results And A Perspective On A Core NGS Testing Model For The 17th International HLA And Immunogenetics Workshop

Author

Askar, Medhat, Madbouly, Abeer, Zhrebker, Leah, Willis, Amanda, Kennedy, Shawna, Padros, Karin, Rodriguez, Maria Beatriz, Bach, Christian, Spriewald, Bernd, Ameen, Reem, Shemmari, Salem Al, Tarassi, Katerina, Tsirogianni, Alexandra, Hamdy, Nayera, Mossallam, Ghada, Hönger, Gideon, Spinnler, Regina, Fischer, Gottfried, Fae, Ingrid, Charlton, Ronald, Dunk, Arthur, Vayntrub, Tamara A., Halagan, Michael, Osoegawa, Kazutoyo, and Fernández-Viña, Marcelo

Published
2019
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25. Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-lymphoblastoid cell lines: Report from the 17th International HLA and Immunogenetics Workshop

Author

Creary, Lisa E., Guerra, Sandra G., Chong, Winnie, Brown, Colin J., Turner, Thomas R., Robinson, James, Bultitude, Will P., Mayor, Neema P., Marsh, Steven G.E., Saito, Katsuyuki, Lam, Kevin, Duke, Jamie L., Mosbruger, Timothy L., Ferriola, Deborah, Monos, Dimitrios, Willis, Amanda, Askar, Medhat, Fischer, Gottfried, Saw, Chee Loong, Ragoussis, Jiannis, Petrek, Martin, Serra-Pagés, Carles, Juan, Manel, Stavropoulos-Giokas, Catherine, Dinou, Amalia, Ameen, Reem, Al Shemmari, Salem, Spierings, Eric, Gendzekhadze, Ketevan, Morris, Gerald P., Zhang, Qiuheng, Kashi, Zahra, Hsu, Susan, Gangavarapu, Sridevi, Mallempati, Kalyan C., Yamamoto, Fumiko, Osoegawa, Kazutoyo, Vayntrub, Tamara, Chang, Chia-Jung, Hansen, John A., and Fernández-Viňa, Marcelo A.

Published
2019
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26. High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing

Author

Montero-Martín, Gonzalo, Mallempati, Kalyan C., Gangavarapu, Sridevi, Sánchez-Gordo, Francisco, Herrero-Mata, Maria J., Balas, Antonio, Vicario, Jose L., Sánchez-García, Florentino, González-Escribano, Maria F., Muro, Manuel, Moya-Quiles, Maria R., González-Fernández, Rafael, Ocejo-Vinyals, Javier G., Marín, Luis, Creary, Lisa E., Osoegawa, Kazutoyo, Vayntrub, Tamara, Caro-Oleas, Jose L., Vilches, Carlos, Planelles, Dolores, and Fernández-Viña, Marcelo A.

Published
2019
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28. Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop

Author

Osoegawa, Kazutoyo, Vayntrub, Tamara A., Wenda, Sabine, De Santis, Dianne, Barsakis, Konstantinos, Ivanova, Milena, Hsu, Susan, Barone, Jonathan, Holdsworth, Rhonda, Diviney, Mary, Askar, Medhat, Willis, Amanda, Railton, Dawn, Laflin, Sophie, Gendzekhadze, Ketevan, Oki, Arisa, Sacchi, Nicoletta, Mazzocco, Michela, Andreani, Marco, Ameen, Reem, Stavropoulos-Giokas, Catherine, Dinou, Amalia, Torres, Margareth, dos Santos Francisco, Rodrigo, Serra-Pages, Carles, Goodridge, Damian, Balladares, Sandra, Bettinotti, Maria P., Iglehart, Brian, Kashi, Zahra, Martin, Russell, Saw, Chee Loong, Ragoussis, Jiannis, Downing, Jonathan, Navarrete, Cristina, Chong, Winnie, Saito, Katsuyuki, Petrek, Martin, Tokic, Stana, Padros, Karin, Beatriz Rodriguez, Ma, Zakharova, Viktoria, Shragina, Olga, Marino, Susana R., Brown, Nicholas K., Shiina, Takashi, Suzuki, Shingo, Spierings, Eric, Zhang, Qiuheng, Yin, Yuxin, Morris, Gerald P., Hernandez, Ana, Ruiz, Phillip, Khor, Seik-Soon, Tokunaga, Katsushi, Geretz, Aviva, Thomas, Rasmi, Yamamoto, Fumiko, Mallempati, Kalyan C., Gangavarapu, Sridevi, Kanga, Uma, Tyagi, Shweta, Marsh, Steven G.E., Bultitude, Will P., Liu, Xiangjun, Cao, Dajiang, Penning, Maarten, Hurley, Carolyn K., Cesbron, Anne, Mueller, Claudia, Mytilineos, Joannis, Weimer, Eric T., Bengtsson, Mats, Fischer, Gottfried, Hansen, John A., Chang, Chia-Jung, Mack, Steven J., Creary, Lisa E., and Fernandez-Viña, Marcelo A.

Published
2019
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29. The Impact of Patterns in Linkage Disequilibrium and Sequencing Quality on the Imprint of Balancing Selection

Author

Hayeck, Tristan J, primary, Li, Yang, additional, Mosbruger, Timothy L, additional, Bradfield, Jonathan P, additional, Gleason, Adam G, additional, Damianos, George, additional, Shaw, Grace Tzun-Wen, additional, Duke, Jamie L, additional, Conlin, Laura K, additional, Turner, Tychele N, additional, Fernández-Viña, Marcelo A, additional, Sarmady, Mahdi, additional, and Monos, Dimitri S, additional

Published
2024
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33. Effect of nonpermissive HLA-DPB1 mismatches after unrelated allogeneic transplantation with in vivo T-cell depletion

Author

Oran, Betül, Saliba, Rima M., Carmazzi, Yudith, de Lima, Marcos, Rondon, Gabriela, Ahmed, Sairah, Alousi, Amin, Andersson, Borje S., Anderlini, Paolo, Alvarez, Michelle, Bashir, Qasier, Ciurea, Stefan, Fernandez-Vina, Marcelo, Hosing, Chitra, Kebriaei, Partow, Korbling, Martin, Cano, Pedro, Khouri, Issa, Marin, David, Nieto, Yago, Olson, Amanda, Popat, Uday, Rezvani, Katy, Qazilbash, Muzaffar, Shpall, Elizabeth J., Champlin, Richard E., and Cao, Kai

Published
2018
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36. MHC Class I Chain-Related Gene A (MICA) Donor-Recipient Mismatches and MICA-129 Polymorphism in Unrelated Donor Hematopoietic Cell Transplantations Has No Impact on Outcomes in Acute Lymphoblastic Leukemia, Acute Myeloid Leukemia, or Myelodysplastic Syndrome: A Center for International Blood and Marrow Transplant Research Study

Author

Askar, Medhat, Sobecks, Ronald, Wang, Tao, Haagenson, Mike, Majhail, Navneet, Madbouly, Abeer, Thomas, Dawn, Zhang, Aiwen, Fleischhauer, Katharina, Hsu, Katharine, Verneris, Michael, Lee, Stephanie J., Spellman, Stephen R., and Fernández-Viña, Marcelo

Published
2017
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37. Exceptional diversity of KIR and HLA class I in Egypt

Author

Montero‐Martin, Gonzalo, primary, Kichula, Katherine M., additional, Misra, Maneesh K., additional, de Brito Vargas, Luciana, additional, Marin, Wesley M., additional, Hollenbach, Jill A., additional, Fernández‐Viña, Marcelo A., additional, Elfishawi, Sally, additional, and Norman, Paul J., additional

Published
2023
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41. The effect of donor characteristics on survival after unrelated donor transplantation for hematologic malignancy

Author

Kollman, Craig, Spellman, Stephen R., Zhang, Mei-Jie, Hassebroek, Anna, Anasetti, Claudio, Antin, Joseph H., Champlin, Richard E., Confer, Dennis L., DiPersio, John F., Fernandez-Viña, Marcelo, Hartzman, Robert J., Horowitz, Mary M., Hurley, Carolyn K., Karanes, Chatchada, Maiers, Martin, Mueller, Carlheinz R., Perales, Miguel-Angel, Setterholm, Michelle, Woolfrey, Ann E., Yu, Neng, and Eapen, Mary

Published
2016
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42. Diversity of HLA Class I and Class II blocks and conserved extended haplotypes in Lacandon Mayans

Author

Barquera, Rodrigo, Zuniga, Joaquin, Flores-Rivera, José, Corona, Teresa, Penman, Bridget S., Hernández-Zaragoza, Diana Iraíz, Soler, Manuel, Jonapá-Gómez, Letisia, Mallempati, Kalyan C., Yescas, Petra, Ochoa-Morales, Adriana, Barsakis, Konstantinos, Aguilar-Vázquez, José Artemio, García-Lechuga, Maricela, Mindrinos, Michael, Yunis, María, Jiménez-Alvarez, Luis, Mena-Hernández, Lourdes, Ortega, Esteban, Cruz-Lagunas, Alfredo, Tovar-Méndez, Víctor Hugo, Granados, Julio, Fernández-Viña, Marcelo, and Yunis, Edmond

Published
2020
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43. Exceptional diversity of KIR and HLA class I in Egypt.

Author

Montero‐Martin, Gonzalo, Kichula, Katherine M., Misra, Maneesh K., de Brito Vargas, Luciana, Marin, Wesley M., Hollenbach, Jill A., Fernández‐Viña, Marcelo A., Elfishawi, Sally, and Norman, Paul J.

Subjects
KILLER cell receptors, KILLER cells, IMMUNOGLOBULIN receptors, NATURAL selection, HAPLOTYPES, HISTOCOMPATIBILITY class I antigens, REPRODUCTIVE health
Abstract

Genetically determined variation of killer cell immunoglobulin like receptors (KIR) and their HLA class I ligands affects multiple aspects of human health. Their extreme diversity is generated through complex interplay of natural selection for pathogen resistance and reproductive health, combined with demographic structure and dispersal. Despite significant importance to multiple health conditions of differential effect across populations, the nature and extent of immunogenetic diversity is under‐studied for many geographic regions. Here, we describe the first high‐resolution analysis of KIR and HLA class I combinatorial diversity in Northern Africa. Analysis of 125 healthy unrelated individuals from Cairo in Egypt yielded 186 KIR alleles arranged in 146 distinct centromeric and 79 distinct telomeric haplotypes. The most frequent haplotypes observed were KIR‐A, encoding two inhibitory receptors specific for HLA‐C, two that are specific for HLA‐A and ‐B, and no activating receptors. Together with 141 alleles of HLA class I, 75 of which encode a KIR ligand, we identified a mean of six distinct interacting pairs of inhibitory KIR and HLA allotypes per individual. We additionally characterize 16 KIR alleles newly identified in the study population. Our findings place Egyptians as one of the most highly diverse populations worldwide, with important implications for transplant matching and studies of immune‐mediated diseases. [ABSTRACT FROM AUTHOR]

Published
2024
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45. Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing

Author

Mack, Steven J., Milius, Robert P., Gifford, Benjamin D., Sauter, Jürgen, Hofmann, Jan, Osoegawa, Kazutoyo, Robinson, James, Groeneweg, Mathijs, Turenchalk, Gregory S., Adai, Alex, Holcomb, Cherie, Rozemuller, Erik H., Penning, Maarten T., Heuer, Michael L., Wang, Chunlin, Salit, Marc L., Schmidt, Alexander H., Parham, Peter R., Müller, Carlheinz, Hague, Tim, Fischer, Gottfried, Fernandez-Viňa, Marcelo, Hollenbach, Jill A., Norman, Paul J., and Maiers, Martin

Published
2015
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46. HLA Mismatch Is Associated with Worse Outcomes after Unrelated Donor Reduced-Intensity Conditioning Hematopoietic Cell Transplantation: An Analysis from the Center for International Blood and Marrow Transplant Research

Author

Verneris, Michael R., Lee, Stephanie J., Ahn, Kwang Woo, Wang, Hai-Lin, Battiwalla, Minoo, Inamoto, Yoshihiro, Fernandez-Vina, Marcelo A., Gajewski, James, Pidala, Joseph, Munker, Reinhold, Aljurf, Mahmoud, Saber, Wael, Spellman, Stephen, and Koreth, John

Published
2015
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47. Impact of KIR and HLA Genotypes on Outcomes after Reduced-Intensity Conditioning Hematopoietic Cell Transplantation

Author

Sobecks, Ronald M., Wang, Tao, Askar, Medhat, Gallagher, Meighan M., Haagenson, Michael, Spellman, Stephen, Fernandez-Vina, Marcelo, Malmberg, Karl-Johan, Müller, Carlheinz, Battiwalla, Minoo, Gajewski, James, Verneris, Michael R., Ringdén, Olle, Marino, Susana, Davies, Stella, Dehn, Jason, Bornhäuser, Martin, Inamoto, Yoshihiro, Woolfrey, Ann, Shaw, Peter, Pollack, Marilyn, Weisdorf, Daniel, Milller, Jeffrey, Hurley, Carolyn, Lee, Stephanie J., and Hsu, Katharine

Published
2015
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49. HLA-DPB1 and HLA Class I Confer Risk of and Protection from Narcolepsy

Author

Ollila, Hanna M., Ravel, Jean-Marie, Han, Fang, Faraco, Juliette, Lin, Ling, Zheng, Xiuwen, Plazzi, Giuseppe, Dauvilliers, Yves, Pizza, Fabio, Hong, Seung-Chul, Jennum, Poul, Knudsen, Stine, Kornum, Birgitte R., Dong, Xiao Song, Yan, Han, Hong, Heeseung, Coquillard, Cristin, Mahlios, Joshua, Jolanki, Otto, Einen, Mali, Arnulf, Isabelle, Högl, Birgit, Frauscher, Birgit, Crowe, Catherine, Partinen, Markku, Huang, Yu Shu, Bourgin, Patrice, Vaarala, Outi, Désautels, Alex, Montplaisir, Jacques, Mack, Steven J., Mindrinos, Michael, Fernandez-Vina, Marcelo, and Mignot, Emmanuel

Published
2015
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