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Fichou Y, Berlivet I, Richard G, Tournamille C, Castilho L, Férec C. Defining Blood Group Gene Reference Alleles by Long-Read Sequencing: Proof of Concept in the ACKR1 Gene Encoding the Duffy Antigens. Transfus Med Hemother 2019; 47:23-32. [PMID: 32110191 DOI: 10.1159/000504584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/01/2019] [Indexed: 01/31/2023] Open
Abstract
Background In the novel era of blood group genomics, (re-)defining reference gene/allele sequences of blood group genes has become an important goal to achieve, both for diagnostic and research purposes. As novel potent sequencing technologies are available, we thought to investigate the variability encountered in the three most common alleles of ACKR1, the gene encoding the clinically relevant Duffy antigens, at the haplotype level by a long-read sequencing approach. Materials and Methods After long-range PCR amplification spanning the whole ACKR1 gene locus (∼2.5 kilobases), amplicons generated from 81 samples with known genotypes were sequenced in a single read by using the Pacific Biosciences (PacBio) single molecule, real-time (SMRT) sequencing technology. Results High-quality sequencing reads were obtained for the 162 alleles (accuracy >0.999). Twenty-two nucleotide variations reported in databases were identified, defining 19 haplotypes: four, eight, and seven haplotypes in 46 ACKR1*01, 63 ACKR1*02, and 53 ACKR1*02N.01 alleles, respectively. Discussion Overall, we have defined a subset of reference alleles by third-generation (long-read) sequencing. This technology, which provides a "longitudinal" overview of the loci of interest (several thousand base pairs) and is complementary to the second-generation (short-read) next-generation sequencing technology, is of critical interest for resolving novel, rare, and null alleles.
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Affiliation(s)
- Yann Fichou
- EFS, Inserm, Univ Brest, UMR 1078, GGB, Brest, France.,Laboratoire d'Excellence GR-Ex, Paris, France
| | | | | | - Christophe Tournamille
- Laboratoire d'Excellence GR-Ex, Paris, France.,IMRB-Inserm U955 Equipe 2 Transfusion et Maladies du Globule Rouge, EFS Ile-de-France, Créteil, France
| | | | - Claude Férec
- EFS, Inserm, Univ Brest, UMR 1078, GGB, Brest, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHU Morvan, Brest, France
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Menegati SFP, Santos TD, Macedo MD, Castilho L. Discrepancies between red cell phenotyping and genotyping in daily immunohematology laboratory practice. Transfus Apher Sci 2019; 59:102585. [PMID: 31303508 DOI: 10.1016/j.transci.2019.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/11/2019] [Accepted: 06/24/2019] [Indexed: 11/18/2022]
Abstract
False-positive and false-negative reactions exist for serological and molecular antigen typing methods. If the predicted phenotype is inconsistent with the patient`s known antibodies or serological phenotype, the discrepancy must be investigated. False-negative and false-positive results are clinically problematic in blood donors and patients. In this study, we investigated discrepant results between serology and molecular testing in patients and blood donors that occurred in daily molecular laboratory practice over a two year-period. SCD patients represented a large percentage of our cases of discrepancies but we also observed a high prevalence of discrepancies between phenotypes and genotypes in blood donors. The main reasons that led to discrepancies were recent transfusions and limitations of phenotyping. Discrepancies classified as false positive phenotype/true negative genotype and false negative phenotype/true positive genotype occurred mainly in patients with recent transfusions and individuals with RH variants while those classified as true negative phenotype/false positive genotype involved null phenotypes due to silent genes. Despite the limitations of molecular methods currently employed, we found more false-negative and false-positive phenotypes than genotypes demonstrating that genotyping is more efficient to define the blood types, especially in transfusion dependent patients.
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Thongbut J, Raud L, Férec C, Promwong C, Nuchnoi P, Fichou Y. Comprehensive Molecular Analysis of Serologically D-Negative and Weak/Partial D Phenotype in Thai Blood Donors. Transfus Med Hemother 2019; 47:54-60. [PMID: 32110194 DOI: 10.1159/000499087] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/21/2019] [Indexed: 12/13/2022] Open
Abstract
Background Molecular genetics of the Rh system has been extensively studied in Caucasians, Black Africans, East Asians, and Indians more recently. In this work, we sought to investigate the molecular basis of variant D expression in the Thai population, which remains unknown. Materials and Methods Blood samples from 450 Thai donors showing the variant D phenotype were collected. The RHD gene was analyzed by quantitative multiplex polymerase chain reaction of short fluorescent fragments and/or Sanger sequencing. Results The most frequent alleles in 200 D-negative and 121 DEL samples were the whole RHD gene deletion and the Asian DEL alleles, respectively. In 129 weak/partial D samples, 36 variant alleles were identified, including eight novel alleles. RHD*06.03, which is common in variant D samples from South China, is the most prevalent variant allele, followed by the recently reported Indian RHD*01W.150 allele. Discussion For the first time, a comprehensive overview of the nature and distribution of variant RHD alleles in Thailand is reported. It is a milestone to pave the way towards improvement of the current screening strategy to identify DEL donors accurately. The next step will be the design and implementation of a simple molecular test for screening the most frequent alleles, specifically in this population.
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Affiliation(s)
- Jairak Thongbut
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.,National Blood Centre, Thai Red Cross Society, Bangkok, Thailand
| | - Loann Raud
- Univ Brest, INSERM, EFS, UMR 1078, GGB, Brest, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHU Morvan, Brest, France
| | - Claude Férec
- Univ Brest, INSERM, EFS, UMR 1078, GGB, Brest, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHU Morvan, Brest, France.,Laboratory of Excellence GR-Ex, Brest, France
| | | | - Pornlada Nuchnoi
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.,Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Yann Fichou
- Univ Brest, INSERM, EFS, UMR 1078, GGB, Brest, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHU Morvan, Brest, France
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Fichou Y, Mariez M, Le Maréchal C, Férec C. The experience of extended blood group genotyping by next-generation sequencing (NGS): investigation of patients with sickle-cell disease. Vox Sang 2016; 111:418-424. [PMID: 27442304 DOI: 10.1111/vox.12432] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND Patients suffering from haemoglobinopathies may be treated by red blood cell (RBC) transfusion on a regular basis and then exposed to multiple antigens with a recurrent, potential risk of alloimmunization routinely prevented by extended RBC antigen cross-matching. While time-consuming and labour-intensive serological analyses are the gold standard for RBC typing, genotyping by current high-throughput molecular tools, including next-generation sequencing (NGS), appears to offer a potent alternative. STUDY DESIGN AND METHODS The potential of extended blood group genotyping (EBGG) by NGS of 17 genes involved in 14 blood group systems was evaluated in a cohort of 48 patients with sickle-cell disease. Sample preparation and sequencing were simplified and automated for future routine implementation. RESULTS Sequencing data were obtained for all DNA samples with two different sequencing machines. Prediction of phenotypes could be made in 12 blood group systems and partially in two other blood group systems (Rh and MNS). Importantly, predicted phenotypes in the MNS (S/s), Duffy, Kidd and Kell systems matched well with serological data (98·9%), when available. Unreferenced alleles in the ACHE and ART4 genes, respectively, involved in the Yt and Dombrock blood groups, were identified, then contributing to extend the current knowledge of blood group molecular genetics. CONCLUSIONS Overall, we consider that our strategy for NGS-based EBGG, assisted by a simple method for genotyping exons 1 and 2 of the pairs of homologous genes (i.e. RHD/RHCE and GYPA/GYPB), as well as the future support of potent bioinformatics tools, may be implemented for routine diagnosis in specific populations.
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Affiliation(s)
- Y Fichou
- Etablissement Français du Sang (EFS) - Région Bretagne, Brest, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1078, Brest, France
| | - M Mariez
- Etablissement Français du Sang (EFS) - Région Bretagne, Brest, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1078, Brest, France
| | - C Le Maréchal
- Etablissement Français du Sang (EFS) - Région Bretagne, Brest, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1078, Brest, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire (CHRU), Hôpital Morvan, Brest, France.,Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
| | - C Férec
- Etablissement Français du Sang (EFS) - Région Bretagne, Brest, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1078, Brest, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire (CHRU), Hôpital Morvan, Brest, France.,Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
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Svensson AM, Delaney M. Considerations of red blood cell molecular testing in transfusion medicine. Expert Rev Mol Diagn 2015; 15:1455-64. [PMID: 26367503 DOI: 10.1586/14737159.2015.1086646] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The field of transfusion medicine is on the threshold of a paradigm shift, as the technology for genotyping of red blood cell antigens, including US FDA-approved arrays, is now moving into standard practice. Access to cost-efficient, high-resolution genotyping has the potential to increase the quality of care by decreasing the risk for alloimmunization and incompatible transfusions in individuals on long-term blood transfusion protocols, including patient groups with hemoglobinopathies and other chronic diseases. Current and future applications of molecular methods in transfusion medicine and blood banking are discussed, with emphasis on indications for genotyping in various clinical scenarios. Furthermore, limitations of the current gold standard methodology and serology, as well as of contemporary molecular methodology, are examined.
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Affiliation(s)
- Annika M Svensson
- a 1 Department of Pathology, School of Medicine, University of Colorado , Denver, USA.,b 2 Department of Pathology and Laboratory Medicine, Children's Hospital Colorado , Colorado, USA
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