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Amphonritthisak P, Nathalang O, Leetrakool N, Mitundee S, Intharanut K. Application of a simplified PCR-SSP method to detect A4GALT*01 and A4GALT*02 typing among Thai blood donors. Transfus Clin Biol 2023; 30:436-442. [PMID: 37673392 DOI: 10.1016/j.tracli.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
OBJECTIVES An intronic A4GALT single nucleotide variant, rs5751348:G>T, P2 or A4GALT*02 allele has a lower level of the enzyme-encoding A4GALT transcripts than the P1 individuals. Here, we first develop and validate a simple inhouse PCR-SSP method to detect A4GALT*01 and A4GALT*02 alleles, and second, apply this method to compare the allele frequencies between Thai and other populations. MATERIAL AND METHODS The conventional test tube technique was used to detect the P1 antigen in 222 blood samples from Thai blood donors at Thammasat University Hospital. A PCR-SSP method was optimized and validated for reproducibility and specificity to identify these alleles and was subsequently tested on 1,840 DNA samples of unknown phenotypes obtained from central, northern and southern Thais. In addition, allele frequencies of central Thais were compared with those of other populations. RESULTS In the tested cohort (n = 222), P1 and P2 phenotypes were typed in 26.13 and 73.87% of donors, respectively. The developed PCR-SSP was successfully optimized, and the outcomes were consistent with those of serological phenotyping and DNA sequencing results, demonstrating its validity for predicting P1/P2 phenotype. For central, northern and southern Thais, the A4GALT*01 frequency was 0.1579 (430/2,724), 0.1183 (71/600), and 0.2575 (206/800), whereas the A4GALT*02 frequency was 0.8421 (2,294/2,724), 0.8817 (529/600), and 0.7425 (594/800), respectively. Their observed frequencies among central Thais significantly differed from those in other populations (p < 0.05). CONCLUSION Our study has successfully developed a simple, precise, and reliable method to genotype A4GALT*01 and A4GALT*02 using inhouse developed PCR-SSP for predicting P1/P2 status.
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Affiliation(s)
- Pattaranit Amphonritthisak
- Graduate Program in Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Oytip Nathalang
- Graduate Program in Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Nipapan Leetrakool
- Blood Bank Section, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Supattra Mitundee
- Regional Blood Centre 12(th) Songkhla, Thai Red Cross Society, Songkhla, Thailand
| | - Kamphon Intharanut
- Graduate Program in Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand.
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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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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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Sasaki K, Suzuki Y, Isa K, Osabe T, Watanabe-Okochi N, Azuma F, Uchikawa M, Ogasawara K, Satake M. GENOTYPING OF RED CELL BLOOD GROUPS BY THE LIQUID BEAD ARRAY SYSTEM (LUMINEX). ACTA ACUST UNITED AC 2017. [DOI: 10.3925/jjtc.63.112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
| | - Yumi Suzuki
- Japanese Red Cross Kanto-Koshinetsu Block Blood Center
| | - Kazumi Isa
- Japanese Red Cross Central Blood Institute
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Affiliation(s)
- T. Peyrard
- Département Centre National de Référence pour les Groupes Sanguins; Institut National de la Transfusion Sanguine (INTS); Paris France
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McBean RS, Hyland CA, Flower RL. Approaches to determination of a full profile of blood group genotypes: single nucleotide variant mapping and massively parallel sequencing. Comput Struct Biotechnol J 2014; 11:147-51. [PMID: 25408849 PMCID: PMC4232566 DOI: 10.1016/j.csbj.2014.09.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/17/2022] Open
Abstract
The number of blood group systems, currently 35, has increased in the recent years as genetic variations defining red cell antigens continue to be discovered. At present, 44 genes and 1568 alleles have been defined as encoding antigens within the 35 blood group systems. This paper provides a brief overview of two genetic technologies: single nucleotide variant (SNV) mapping by DNA microarray and massively parallel sequencing, with respect to blood group genotyping. The most frequent genetic change associated with blood group antigens are SNVs. To predict blood group antigen phenotypes, SNV mapping which involves highly multiplexed genotyping, can be performed on commercial microarray platforms. Microarrays detect only known SNVs, therefore, to type rare or novel alleles not represented in the array, further Sanger sequencing of the region is often required to resolve genotype. An example discussed in this article is the identification of rare and novel RHD alleles in the Australian population. Massively parallel sequencing, also known as next generation sequencing, has a high-throughput capacity and maps all points of variation from a reference sequence, allowing for identification of novel SNVs. Examples of the application of this technology to resolve the genetic basis of orphan blood group antigens are presented here. Overall, the determination of a full profile of blood group SNVs, in addition to serological phenotyping, provides a basis for provision of compatible blood thus offering improved transfusion safety.
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Affiliation(s)
- Rhiannon S McBean
- Research and Development, Australian Red Cross Blood Service, Brisbane, Australia
| | - Catherine A Hyland
- Research and Development, Australian Red Cross Blood Service, Brisbane, Australia
| | - Robert L Flower
- Research and Development, Australian Red Cross Blood Service, Brisbane, Australia
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Scott SA, Nagl L, Tilley L, Liew YW, Condon J, Flower R, Hyland CA. The RHD(1227G>A) DEL-associated allele is the most prevalent DEL allele in Australian D- blood donors with C+ and/or E+ phenotypes. Transfusion 2014; 54:2931-40. [PMID: 24894016 DOI: 10.1111/trf.12701] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 02/20/2014] [Accepted: 03/02/2014] [Indexed: 12/16/2022]
Abstract
BACKGROUND Red blood cells (RBCs) with D antigen levels only detected by anti-D adsorption-elution and an antiglobulin test express a DEL phenotype. For two DEL types, including RHD(1227G>A), immunization of D- recipients has been reported. This study's aim was to measure the prevalence of DEL-associated RHD alleles in a cohort of Australian D- donors to develop a model to estimate alloimmunization risk. STUDY DESIGN AND METHODS D-, C+ and/or E+ blood donors were screened for RHD exons using quantitative polymerase chain reaction. Donors with RHD signals were DEL phenotyped with MCAD6 anti-D. RHD alleles were characterized via single-nucleotide polymorphism array or sequencing. Extended DEL phenotyping was performed with an anti-D panel. RESULTS Among 2027 donors, 39 carried RHD alleles that have been previously reported to associate with either the DEL or the weak D phenotype. An additional five donors carried previously unreported RHD alleles and exhibited the DEL phenotype: RHD(IVS2-2delA), RHD(IVS1+5G>C), RHD(ex9:del/CE), and RHD(ex8:del/CE) represented twice. In total, DEL/weak D-associated RHD alleles were detected in 44 of 2027 donors or 2.17% (95% confidence interval, 1.54%-2.81%). The RHD(1227G>A) DEL allele was the most frequent (n = 16). The risk of transfusing D- females not more than 40 years of age with an RHD(1227G>A) DEL RBC unit (when managed as D-) is estimated to be one in 149,109 transfusions (range, 100,680-294,490). CONCLUSION DEL/weak D-associated RHD alleles were found in 2.17% of Australian D-, C+ and/or E+ blood donors. This differs from previous European reports in that the clinically significant RHD(1227G>A) DEL allele is the most prevalent.
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Affiliation(s)
- Stacy A Scott
- Research and Development, Australian Red Cross Blood Service, Brisbane, Australia
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