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Using Whole Genome Sequencing to Characterize Clinically Significant Blood Groups Among Healthy Older Australians. Blood Adv 2022; 6:4593-4604. [PMID: 35420653 PMCID: PMC9636324 DOI: 10.1182/bloodadvances.2022007505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 03/29/2022] [Indexed: 12/02/2022] Open
Abstract
There have been no comprehensive studies of a full range of blood group polymorphisms within the Australian population. This problem is compounded by the absence of any databases carrying genomic information on chronically transfused patients and low frequency blood group antigens in Australia. Here, we use RBCeq, a web server–based blood group genotyping software, to identify unique blood group variants among Australians and compare the variation detected vs global data. Whole-genome sequencing data were analyzed for 2796 healthy older Australians from the Medical Genome Reference Bank and compared with data from 1000 Genomes phase 3 (1KGP3) databases comprising 661 African, 347 American, 503 European, 504 East Asian, and 489 South Asian participants. There were 661 rare variants detected in this Australian sample population, including 9 variants that had clinical associations. Notably, we identified 80 variants that were computationally predicted to be novel and deleterious. No clinically significant rare or novel variants were found associated with the genetically complex ABO blood group system. For the Rh blood group system, 2 novel and 15 rare variants were found. Our detailed blood group profiling results provide a starting point for the creation of an Australian blood group variant database.
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Jadhao S, Hoy W, Lee S, Patel HR, McMorran BJ, Flower RL, Nagaraj SH. The genomic landscape of blood groups in Indigenous Australians in remote communities. Transfusion 2022; 62:1110-1120. [PMID: 35403234 PMCID: PMC9544628 DOI: 10.1111/trf.16873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 02/02/2022] [Accepted: 02/11/2022] [Indexed: 11/28/2022]
Abstract
Background Methods and materials Results Conclusion
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Affiliation(s)
- Sudhir Jadhao
- Centre for Genomics and Personalised Health Queensland University of Technology Brisbane Queensland Australia
- Translational Research Institute Brisbane Queensland Australia
| | - Wendy Hoy
- Faculty of Medicine University of Queensland Brisbane Queensland Australia
| | - Simon Lee
- Centre for Genomics and Personalised Health Queensland University of Technology Brisbane Queensland Australia
- Translational Research Institute Brisbane Queensland Australia
| | - Hardip R. Patel
- National Centre for Indigenous Genomics Australian National University Canberra Australian Capital Territory Australia
| | - Brendan J. McMorran
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, College of Health and Medicine The Australian National University Canberra Australian Capital Territory Australia
| | - Robert L. Flower
- Research and Development Australian Red Cross Lifeblood Red Cell Reference Laboratory Brisbane Queensland Australia
| | - Shivashankar H. Nagaraj
- Centre for Genomics and Personalised Health Queensland University of Technology Brisbane Queensland Australia
- Translational Research Institute Brisbane Queensland Australia
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Sadeghi-Bojd Y, Amirizadeh N, Oodi A. RHD Genotyping of Rh-Negative and Weak D Phenotype among Blood Donors in Southeast Iran. Int J Hematol Oncol Stem Cell Res 2021; 15:213-220. [PMID: 35291662 PMCID: PMC8888359 DOI: 10.18502/ijhoscr.v15i4.7476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 10/31/2020] [Indexed: 11/29/2022] Open
Abstract
Background: The D antigen is a subset of Rh blood group antigens involved in the hemolytic disease of the newborn [HDFN] and hemolytic transfusion reaction [HTR]. The hybrid Rhesus box that was created after RH gene deletion, was known as a mechanism of the Rh-negative phenotype. Hybrid marker identification is used to confirm the deletion of the RHD gene and to determine zygosity. This study aims to detect this marker in Rh-negative and weak D phenotype blood donors of the southeast of Iran. Materials and Methods: The molecular analysis of the hybrid Rhesus box was performed on the 200 Rh-negative blood donors in Sistan and Baluchestan province, southeast Iran. The presence of alleles responsible for the D variants was assessed by DNA sequencing in 26 weak D phenotype donors. Results: Of the 200 Rh-negative blood samples, 198 samples were homozygous (99%), and two samples were heterozygous (1%). Heterozygous samples had RHD*01N.73 allele and the RHD*01N.18 allele. Of the 26 samples with weak D phenotype, 16 partial DLO (61%), 4 partial DBT1 (15.3%), 2 partial DV type 2 (7.7%), 1 weak D type 1, 1 weak D type 4.2.3, 1weak D type 105 and 1 RHD (S103P) (4%) were determined. Conclusion: Since RHD gene deletion is the main mechanism of the Rh-negativity in Sistan and Baluchestan provinces, a hybrid Rhesus box marker can be used in resolving RhD typing discrepancies by RHD genotyping methods.
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Affiliation(s)
- Younes Sadeghi-Bojd
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Naser Amirizadeh
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Arezoo Oodi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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Al-Riyami AZ, Al-Marhoobi A, Al-Hosni S, Al Mahrooqi S, Schmidt M, O'Brien S, Al-Khabori M. Prevalence of Red Blood Cell Major Blood Group Antigens and Phenotypes among Omani Blood Donors. Oman Med J 2019; 34:496-503. [PMID: 31745413 PMCID: PMC6851071 DOI: 10.5001/omj.2019.92] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Objectives Most literature on the frequencies of red blood cell (RBC) phenotypes are published in Europeans and Africans countries, with the frequencies in the Omani population unknown. We sought to determine the prevalence of RBC blood group phenotypes among Omani blood donors. Methods Blood group ABO, RhD type, and phenotyping were performed for 21 blood group antigens on enrolled blood donors. The following antigens were assessed serologically: Rh (C, c, E, e), Kell (K, k, Kpa, Kpb), Kidd (Jka, Jkb), Duffy (Fya, Fyb), Lewis (Lea, Leb), Lutheran (Lua, Lub), MNS (M, N, S, s), and P1. Results A total of 337 Omani blood donors were tested. The most common blood group was O+ (44.9%). Among the tested blood donors studied, 89.3% were RhD positive with R1r being the most common Rh phenotype. The k antigen was found at a frequency of 99.4%, while 4.5% of the blood donors studied were K+. The most common phenotype in the Duffy blood group system was Fy(a-b-), while the most common phenotypes in the Kidd and MNS blood group systems were Jk(a+b+) and M+N-S+s+ at 47.0% and 22.6%, respectively. The Le(a+) and Le(b+) antigens were found in 21.7% and 67.3% of the blood donors, respectively. One Jk(a-b-), one Le(a+b+), and two Lu(a-b-) individuals were identified. Conclusion This is the first study to examine the frequencies of RBC phenotypes among the Omani blood donors. The study's results show Duffy blood group frequencies that resemble what has been reported in the African population, and higher frequencies of the rare null phenotypes compared to European populations.
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Affiliation(s)
- Arwa Z Al-Riyami
- Department of Hematology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Ali Al-Marhoobi
- Department of Hematology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Saif Al-Hosni
- Department of Hematology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Sabah Al Mahrooqi
- Department of Hematology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Michael Schmidt
- Department of the German Red Cross Blood Donor Service, Baden-Württemberg Hesse, Germany
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Abstract
PURPOSE OF REVIEW To summarize recent advances in red blood cell (RBC) blood group genotyping, with an emphasis on advances in the use of NGS next generation sequencing (NGS) to detect clinically relevant blood group gene variation. RECENT FINDINGS Genetic information is useful in predicting RBC blood group antigen expression in several clinical contexts, particularly, for patients at high-risk for allosensitization, such as multiple transfused patients. Blood group antigen expression is directed by DNA variants affecting multiply genes. With over 300 known antigens, NGS offers the attractive prospect of comprehensive blood group genotyping. Recent studies from several groups show that NGS reliably detects blood group gene single nucleotide variants (SNVs) with good correlation with other genetic methods and serology. Additionally, new custom NGS methods accurately detect complex DNA variants, including hybrid RH alleles. Thus, recent work shows that NGS detects known and novel blood group gene variants in patients, solves challenging clinical cases, and detects relevant blood group variation in donors. SUMMARY New work shows that NGS is particularly robust in identifying SNVs in blood group genes, whereas custom genomic tools can be used to identify known and novel complex structural variants, including in the RH system.
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Montemayor-Garcia C, Karagianni P, Stiles DA, Reese EM, Smellie DA, Loy DA, Levy KY, Nwokocha M, Bueno MU, Miller JL, Klein HG. Genomic coordinates and continental distribution of 120 blood group variants reported by the 1000 Genomes Project. Transfusion 2018; 58:2693-2704. [PMID: 30312480 DOI: 10.1111/trf.14953] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/25/2018] [Accepted: 07/13/2018] [Indexed: 01/25/2023]
Abstract
BACKGROUND The 1000 Genomes Project provides a database of genomic variants from whole genome sequencing of 2504 individuals across five continental superpopulations. This database can enrich our background knowledge of worldwide blood group variant geographic distribution and identify novel variants of potential clinical significance. STUDY DESIGN AND METHODS The 1000 Genomes database was analyzed to 1) expand knowledge about continental distributions of known blood group variants, 2) identify novel variants with antigenic potential and their geographic association, and 3) establish a baseline scaffold of chromosomal coordinates to translate next-generation sequencing output files into a predicted red blood cell (RBC) phenotype. RESULTS Forty-two genes were investigated. A total of 604 known variants were mapped to the GRCh37 assembly; 120 of these were reported by 1000 Genomes in at least one superpopulation. All queried variants, including the ACKR1 promoter silencing mutation, are located within exon pull-down boundaries. The analysis yielded 41 novel population distributions for 34 known variants, as well as 12 novel blood group variants that warrant further validation and study. Four prediction algorithms collectively flagged 79 of 109 (72%) known antigenic or enzymatically detrimental blood group variants, while 4 of 12 variants that do not result in an altered RBC phenotype were flagged as deleterious. CONCLUSION Next-generation sequencing has known potential for high-throughput and extended RBC phenotype prediction; a database of GRCh37 and GRCh38 chromosomal coordinates for 120 worldwide blood group variants is provided as a basis for this clinical application.
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Affiliation(s)
- Celina Montemayor-Garcia
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland
| | | | - David A Stiles
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Erika M Reese
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Danielle A Smellie
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Debrean A Loy
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Kimberly Y Levy
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Magdalene Nwokocha
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Marina U Bueno
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Jeffery L Miller
- Genetics of Development and Disease Branch, NIDDK, National Institutes of Health, Bethesda, Maryland
| | - Harvey G Klein
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland
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Saleh RM, Zefarina Z, Che Mat NF, Chambers GK, Edinur HA. Transfusion Medicine and Molecular Genetic Methods. Int J Prev Med 2018; 9:45. [PMID: 29899883 PMCID: PMC5981227 DOI: 10.4103/ijpvm.ijpvm_232_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/05/2017] [Indexed: 02/07/2023] Open
Abstract
Transfusion procedures are always complicated by potential genetic mismatching between donor and recipient. Compatibility is determined by several major antigens, such as the ABO and Rhesus blood groups. Matching for other blood groups (Kell, Kidd, Duffy, and MNS), human platelet antigens, and human leukocyte antigens (HLAs) also contributes toward the successful transfusion outcomes, especially in multitransfused or highly immunized patients. All these antigens of tissue identity are highly polymorphic and thus present great challenges for finding suitable donors for transfusion patients. The ABO blood group and HLA markers are also the determinants of transplant compatibility, and mismatched antigens will cause graft rejection or graft-versus-host disease. Thus, a single and comprehensive registry covering all of the significant transfusion and transplantation antigens is expected to become an important tool in providing an efficient service capable of delivering safe blood and quickly locating matching organs/stem cells. This review article is intended as an accessible guide for physicians who care for transfusion-dependent patients. In particular, it serves to introduce the new molecular screening methods together with the biology of these systems, which underlies the tests.
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Affiliation(s)
| | - Zulkafli Zefarina
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Nor Fazila Che Mat
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | - Hisham Atan Edinur
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
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Arend P. Position of human blood group O(H) and phenotype-determining enzymes in growth and infectious disease. Ann N Y Acad Sci 2018; 1425:5-18. [PMID: 29754430 PMCID: PMC7676429 DOI: 10.1111/nyas.13694] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/22/2018] [Accepted: 03/06/2018] [Indexed: 12/12/2022]
Abstract
The human ABO(H) blood group phenotypes arise from the evolutionarily oldest genetic system found in primate populations. While the blood group antigen A is considered the ancestral primordial structure, under the selective pressure of life‐threatening diseases blood group O(H) came to dominate as the most frequently occurring blood group worldwide. Non‐O(H) phenotypes demonstrate impaired formation of adaptive and innate immunoglobulin specificities due to clonal selection and phenotype formation in plasma proteins. Compared with individuals with blood group O(H), blood group A individuals not only have a significantly higher risk of developing certain types of cancer but also exhibit high susceptibility to malaria tropica or infection by Plasmodium falciparum. The phenotype‐determining blood group A glycotransferase(s), which affect the levels of anti‐A/Tn cross‐reactive immunoglobulins in phenotypic glycosidic accommodation, might also mediate adhesion and entry of the parasite to host cells via trans‐species O‐GalNAc glycosylation of abundantly expressed serine residues that arise throughout the parasite's life cycle, while excluding the possibility of antibody formation against the resulting hybrid Tn antigen. In contrast, human blood group O(H), lacking this enzyme, is indicated to confer a survival advantage regarding the overall risk of developing cancer, and individuals with this blood group rarely develop life‐threatening infections involving evolutionarily selective malaria strains.
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Affiliation(s)
- Peter Arend
- Department of Medicine, Philipps University Marburg, Marburg/Lahn, Germany. Gastroenterology Research Laboratory, College of Medicine, University of Iowa, Iowa City, Iowa. Research Laboratories, Chemie Grünenthal GmbH, Aachen, Germany
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Dezan MR, Ribeiro IH, Oliveira VB, Vieira JB, Gomes FC, Franco LAM, Varuzza L, Ribeiro R, Chinoca KZ, Levi JE, Krieger JE, Pereira AC, Gualandro SFM, Rocha VG, Mendrone-Junior A, Sabino EC, Dinardo CL. RHD and RHCE genotyping by next-generation sequencing is an effective strategy to identify molecular variants within sickle cell disease patients. Blood Cells Mol Dis 2017; 65:8-15. [PMID: 28388467 DOI: 10.1016/j.bcmd.2017.03.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/21/2017] [Accepted: 03/21/2017] [Indexed: 01/03/2023]
Abstract
BACKGROUND The complexity of Rh genetic variation among sickle cell disease (SCD) patients is high. Conventional molecular assays cannot identify all genetic variants already described for the RH locus as well as foresee novel alleles. Sequencing RHD and RHCE is indicated to broaden the search for Rh genetic variants. AIMS To standardize the Next Generation Sequencing (NGS) strategy to assertively identify Rh genetic variants among SCD patients with serologic suspicion of Rh variants and evaluate if it can improve the transfusion support. METHODS Thirty-five SCD patients with unexplained Rh antibodies were enrolled. A NGS-based strategy was developed to genotype RHD and RHCE using gene-specific primers. Genotype and serological data were compared. RESULTS Data obtained from the NGS-based assay were gene-specific. Ten and 25 variant RHD and RHCE alleles were identified, respectively. Among all cases of unexplained Rh antibodies, 62% had been inaccurately classified by serological analysis and, of these, 73.1% were considered as relevant, as were associated with increased risk of hemolytic reactions and shortage of units suitable for transfusion. CONCLUSION The NGS assay designed to genotype RH coding regions was effective and accurate in identifying variants. The proposed strategy clarified the Rh phenotype of most patients, improving transfusion support.
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Affiliation(s)
- Marcia R Dezan
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
| | | | | | | | | | - Lucas A M Franco
- Institute of Tropical Medicine, Department of Infectious Disease, University of São Paulo, São Paulo, Brazil
| | - Leonardo Varuzza
- Institute of Tropical Medicine, Department of Infectious Disease, University of São Paulo, São Paulo, Brazil
| | - Roberto Ribeiro
- Institute of Tropical Medicine, Department of Infectious Disease, University of São Paulo, São Paulo, Brazil
| | - Karen Ziza Chinoca
- Discipline of Hematology, University of São Paulo School of Medicine, São Paulo, Brazil
| | | | - José Eduardo Krieger
- Discipline of Hematology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Alexandre Costa Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo school of Medicine
| | - Sandra F M Gualandro
- Discipline of Hematology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Vanderson G Rocha
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil; Discipline of Hematology, University of São Paulo School of Medicine, São Paulo, Brazil
| | | | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, Department of Infectious Disease, University of São Paulo, São Paulo, Brazil
| | - Carla Luana Dinardo
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil; Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo school of Medicine.
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