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McGowan EC, Storry JR, Olsson ML. An intronic polymorphism associated with 2,3-bisphosphoglycerate levels in human red cells is linked to expression of RhCE blood groups. Proc Natl Acad Sci U S A 2024; 121:e2412585121. [PMID: 39172775 DOI: 10.1073/pnas.2412585121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024] Open
Affiliation(s)
- Eunike C McGowan
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Biomedical Center C14, Lund University, Lund SE-221 84, Sweden
| | - Jill R Storry
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Biomedical Center C14, Lund University, Lund SE-221 84, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund SE-221 85, Sweden
| | - Martin L Olsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Biomedical Center C14, Lund University, Lund SE-221 84, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund SE-221 85, Sweden
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McGowan EC, Wu PC, Hellberg Å, Lopez GH, Hyland CA, Olsson ML. A Bioinformatically Initiated Approach to Evaluate GATA1 Regulatory Regions in Samples with Weak D, Del, or D- Phenotypes Despite Normal RHD Exons. Transfus Med Hemother 2024; 51:252-264. [PMID: 39021419 PMCID: PMC11250534 DOI: 10.1159/000538469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/19/2024] [Indexed: 07/20/2024] Open
Abstract
Introduction With over 360 blood group antigens in systems recognized, there are antigens, such as RhD, which demonstrate a quantitative reduction in antigen expression due to nucleotide variants in the non-coding region of the gene that result in aberrant splicing or a regulatory mechanism. This study aimed to evaluate bioinformatically predicted GATA1-binding regulatory motifs in the RHD gene for samples presenting with weak or apparently negative RhD antigen expression but showing normal RHD exons. Methods Publicly available open chromatin region data were overlayed with GATA1 motif candidates in RHD. Genomic DNA from weak D, Del or D- samples with normal RHD exons (n = 13) was used to confirm RHD zygosity by quantitative PCR. Then, RHD promoter, intron 1, and intron 2 regions were amplified for Sanger sequencing to detect potential disruptions in the GATA1 motif candidates. Electrophoretic mobility shift assay (EMSA) was performed to assess GATA1-binding. Luciferase assays were used to assess transcriptional activity. Results Bioinformatic analysis identified five of six GATA1 motif candidates in the promoter, intron 1 and intron 2 for investigation in the samples. Luciferase assays showed an enhancement in transcription for GATA1 motifs in intron 1 and for intron 2 only when the R 2 haplotype variant (rs675072G>A) was present. GATA1 motifs were intact in 12 of 13 samples. For one sample with a Del phenotype, a novel RHD c.1-110A>C variant disrupted the GATA1 motif in the promoter which was supported by a lack of a GATA1 supershift in the EMSA and 73% transcriptional activity in the luciferase assay. Two samples were D+/D- chimeras. Conclusion The bioinformatic predictions enabled the identification of a novel DEL allele, RHD c.1-110A>C, which disrupted the GATA1 motif in the proximal promoter. Although the majority of the samples investigated here remain unexplained, we provide GATA1 targets which may benefit future RHD regulatory investigations.
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Affiliation(s)
- Eunike C. McGowan
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ping Chun Wu
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Åsa Hellberg
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Genghis H. Lopez
- Research and Development, Australian Red Cross Lifeblood, Brisbane, QLD, Australia
- School of Health, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Catherine A. Hyland
- Research and Development, Australian Red Cross Lifeblood, Brisbane, QLD, Australia
- Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Martin L. Olsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund, Sweden
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Li M, Wang L, Li A, Wang B, Yang X, Zhang Y, Chen C, Sun F, Zhu Z, Ye L. Integrated analyses reveal unexpected complex inversion and recombination in RH genes. Blood Adv 2024; 8:3154-3165. [PMID: 38551808 PMCID: PMC11222952 DOI: 10.1182/bloodadvances.2023012147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/28/2024] [Indexed: 06/15/2024] Open
Abstract
ABSTRACT Phenotype D-- is associated with severe hemolytic transfusion reactions and hemolytic disease of the fetus and newborn. It is typically caused by defective RHCE genes. In this study, we identified a D-- phenotype proband and verified Rh phenotypes of other 6 family members. However, inconsistent results between the phenotypic analysis and Sanger sequencing revealed intact RHCE exons with no mutations in the D-- proband, but the protein was not expressed. Subsequent whole-genome sequencing by Oxford Nanopore Technologies of the proband revealed an inversion with ambiguous breakpoints in intron 2 and intron 7 and copy number variation loss in the RHCE gene region. Given that the RHCE gene is highly homologous to the RHD gene, we conducted a comprehensive analysis using Pacific Biosciences long-read target sequencing, Bionano optical genome mapping, and targeted next-generation sequencing. Our findings revealed that the proband had 2 novel recombinant RHCE haplotypes, RHCE∗Ce(1-2)-D(3-10) and RHCE∗Ce(1-2)-D(3-10)-Ce(10-8)-Ce(3-10), with clear-cut breakpoints identified. Furthermore, the RH haplotypes of the family members were identified and verified. In summary, we made, to our knowledge, a novel discovery of hereditary large inversion and recombination events occurring between the RHD and RHCE genes, leading to a lack of RhCE expression. This highlights the advantages of using integrated genetic analyses and also provides new insights into RH genotyping.
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Affiliation(s)
- Minghao Li
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
| | - Liping Wang
- Blood Transfusion Department, Weifang People’s Hospital, Shandong, China
| | - Aijing Li
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
| | - Bo Wang
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Xiaohong Yang
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Yue Zhang
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Chaoqiong Chen
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Futing Sun
- Blood Transfusion Department, Weifang People’s Hospital, Shandong, China
| | - Ziyan Zhu
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
| | - Luyi Ye
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
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Srivastava K, Bueno MU, Flegel WA. Breakpoint regions of an RHD-CE(4-9)-D allele and a rare JK allele in a Pacific Islander individual. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2024; 22:189-197. [PMID: 37677094 PMCID: PMC11073622 DOI: 10.2450/bloodtransfus.534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/07/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND Among 710 RHD alleles, 3 alleles have been shown to express CcEe antigens and, among 67 hybrid alleles of the RHD gene, 2 alleles have evolved to include RHCE exons 4-9. No breakpoint region had been described for such RHD-CE(4-9)-D hybrid alleles. In the Kidd blood group system, the JK*02N.01 null allele is found with high prevalence in the Polynesian population. We investigated a self-identified Pacific Islander with discrepant serologic and molecular results for his C and Jkb antigens. Another 8 samples with genotype-phenotype discrepancies in the Kidd blood group system were assessed. MATERIALS AND METHODS A combination of published molecular methods and commercial kits were applied to analyze the RHD, RHCE, and SLC14A1 gene sequences, as were hemagglutination tests to determine the serologic phenotypes. RESULTS Nucleotide sequencing of the RHD gene in the index case, including relevant intron stretches, and cDNA identified an RHD-CE(4-9)-D hybrid allele. Nucleotide sequencing of his RHCE gene confirmed the presence of 2 RHCE*ce alleles despite expressing the C antigen. Sequencing of his SLC14A1 gene documented the JK*02N.01 null allele. In the other 8 samples, 5 previously known SLC14A1 nucleotide substitutions were identified. The JK*02N.17 allele was determined to be Jkb-positive. DISCUSSION We determined the 2 breakpoint regions of his RHD-CE(4-9)-D hybrid allele, which was likely distinct from the 2 previously published hybrid alleles due to the differences in the linked RHCE allele. His RHD variant was shown to express the C antigen. An SLC14A1 substitution was underlying his unexpected Jkb-negative phenotype. In a quality improvement project, we resolved 8 samples with similarly discrepant results between Jk serology and red cell genotyping.
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Affiliation(s)
- Kshitij Srivastava
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Marina U Bueno
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Willy A Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, United States of America
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Elgun T, Musteri Oltulu Y, Yurttas Gok A, Agyuz U, Kilic U. DETERMINATION OF RH TYPE AND GENDER USING CIRCULATING CELL-FREE FETAL DNA IN EARLY PREGNANCY OF RH NEGATIVE WOMEN IN TURKEY. Transfus Clin Biol 2023:S1246-7820(23)00063-0. [PMID: 37116742 DOI: 10.1016/j.tracli.2023.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/14/2023] [Accepted: 04/21/2023] [Indexed: 04/30/2023]
Abstract
INTRODUCTION Choosing the right clinical approach for early and reliable diagnosis/screening is becoming more important day by day. The aim of the study was to determine the early RhD type with cff-DNA obtained from maternal plasma, especially in the light of recent developments. In this way, it is aimed to apply Rh Ig only to mothers who are determined to have RhD (+) fetuses and to prevent unnecessary further tests that may possess a risk for RhD (-) fetuses. METHODS Prediction of fetal gender and RH genotype was performed by using RT-qPCR method. With simultaneous amplification of sequences of SRY, DYS14 and RH genes (exon 7 and exon 10). Fetal gender and RhD were determined in 30 RHD (-) pregnant women with cfDNA. RESULTS As a result of genotyping, the gender of 67% (20/30) fetuses was determined as male; the gender of 33% (10/30) fetuses was determined as female in a sample group of 30 pregnancies. It was determined that the DYS14 100% (20/20) gene was more sensitive than the SRY 97% (18/20) gene in gender determination after examining prenatal and postnatal results. As a result of the analysis, the presence of 17% (5/30) RhD (-) fetuses and 83% (25/30) RhD (+) fetuses were determined which is 100% compatible with postnatal results. DISCUSSION Detecting fetal RhD gene in maternal plasma made an important contribution to its use in non-invasive prenatal screening. This study shows that unnecessary intervention and cost can be avoided with successful genotyping analysis performed with RT-qPCR.
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Affiliation(s)
- Tugba Elgun
- Department of Medical Biology/Biruni University/Faculty of Medicine/ Istanbul, Turkey.
| | | | - Asiye Yurttas Gok
- Department of Biochemistry/ Istanbul Health and Technology University/Faculty of Pharmacy/Istanbul, Turkey.
| | | | - Ulkan Kilic
- Department of Medical Biology/University of Health Science/Hamidiye School of Medicine/Istanbul, Turkey.
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Gueuning M, Thun GA, Wittig M, Galati AL, Meyer S, Trost N, Gourri E, Fuss J, Sigurdardottir S, Merki Y, Neuenschwander K, Busch Y, Trojok P, Schäfer M, Gottschalk J, Franke A, Gassner C, Peter W, Frey BM, Mattle-Greminger MP. Haplotype sequence collection of ABO blood group alleles by long-read sequencing reveals putative A1-diagnostic variants. Blood Adv 2023; 7:878-892. [PMID: 36129841 PMCID: PMC10025113 DOI: 10.1182/bloodadvances.2022007133] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/21/2022] [Accepted: 09/03/2022] [Indexed: 11/20/2022] Open
Abstract
In the era of blood group genomics, reference collections of complete and fully resolved blood group gene alleles have gained high importance. For most blood groups, however, such collections are currently lacking, as resolving full-length gene sequences as haplotypes (ie, separated maternal/paternal origin) remains exceedingly difficult with both Sanger and short-read next-generation sequencing. Using the latest third-generation long-read sequencing, we generated a collection of fully resolved sequences for all 6 main ABO allele groups: ABO∗A1/A2/B/O.01.01/O.01.02/O.02. We selected 77 samples from an ABO genotype data set (n = 25 200) of serologically typed Swiss blood donors. The entire ABO gene was amplified in 2 overlapping long-range polymerase chain reactions (covering ∼23.6 kb) and sequenced by long-read Oxford Nanopore sequencing. For quality validation, 2 samples per ABO group were resequenced using Illumina and Pacific Biosciences technology. All 154 full-length ABO sequences were resolved as haplotypes. We observed novel, distinct sequence patterns for each ABO group. Most genetic diversity was found between, not within, ABO groups. Phylogenetic tree and haplotype network analyses highlighted distinct clades of each ABO group. Strikingly, our data uncovered 4 genetic variants putatively specific for ABO∗A1, for which direct diagnostic targets are currently lacking. We validated A1-diagnostic potential using whole-genome data (n = 4872) of a multiethnic cohort. Overall, our sequencing strategy proved powerful for producing high-quality ABO haplotypes and holds promise for generating similar collections for other blood groups. The publicly available collection of 154 haplotypes will serve as a valuable resource for molecular analyses of ABO, as well as studies about the function and evolutionary history of ABO.
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Affiliation(s)
- Morgan Gueuning
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Gian Andri Thun
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | | | - Stefan Meyer
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Nadine Trost
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Elise Gourri
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Janina Fuss
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Sonja Sigurdardottir
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Yvonne Merki
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Kathrin Neuenschwander
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | | | | | | | - Jochen Gottschalk
- Department of Pathogen Screening, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Christoph Gassner
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
- Institute for Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Wolfgang Peter
- Stefan Morsch Foundation, Birkenfeld, Germany
- Institute for Transfusion Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Beat M. Frey
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
- Department of Pathogen Screening, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
| | - Maja P. Mattle-Greminger
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Schlieren, Switzerland
- Correspondence: Maja P. Mattle-Greminger, Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, Rütistrasse 19, 8952 Schlieren, Switzerland;
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Escamilla-Guerrero G, García-Rosales JC. [Genotyping and its applications, a look to the future]. REVISTA MEDICA DEL INSTITUTO MEXICANO DEL SEGURO SOCIAL 2023; 61:S37-S45. [PMID: 36378105 PMCID: PMC10396029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
The detection of the most significant erythrocyte antigens present in each one of the individuals is fundamental when carrying out a transfusion or a transplant. Detection to date is performed by conventional serological methods through the antigen-antibody reaction. But several drawbacks may arise depending on the pathology under study, limiting the availability of blood components. Molecular methods such as genotyping is a tool that complements sensitivity and specificity and has come to revolutionize immunohematology in the blood bank, allowing not only the detection of erythrocyte antigens but also platelet antigens. These methodologies are applicable in patients and in large-scale donors, starting from the allelic variants present in each of the genes that code for the antigens of clinical interest, using microarray systems or systems based on particles labeled with specific probes or their variants that allow an analysis from the immunohematological point of view.
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Affiliation(s)
- Guillermo Escamilla-Guerrero
- Limogen, Laboratorio de Innovación Molecular y Genética, Laboratorio de Biología Molecular e Inmunohematología. Tlalnepantla, Estado de México, MéxicoLimogenMéxico
| | - Juan Carlos García-Rosales
- Limogen, Laboratorio de Innovación Molecular y Genética, Laboratorio de Biología Molecular e Inmunohematología. Tlalnepantla, Estado de México, MéxicoLimogenMéxico
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Tounsi WA, Lenis VP, Tammi SM, Sainio S, Haimila K, Avent ND, Madgett TE. Rh Blood Group D Antigen Genotyping Using a Portable Nanopore-based Sequencing Device: Proof of Principle. Clin Chem 2022; 68:1196-1201. [PMID: 35652461 DOI: 10.1093/clinchem/hvac075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/13/2022] [Indexed: 11/12/2022]
Abstract
BACKGROUND Nanopore sequencing is direct sequencing of a single-stranded DNA molecule using biological pores. A portable nanopore-based sequencing device from Oxford Nanopore Technologies (MinION) depends on driving a DNA molecule through nanopores embedded in a membrane using a voltage. Changes in current are then measured by a sensor, thousands of times per second and translated to nucleobases. METHODS Genomic DNA (gDNA) samples (n = 13) were tested for Rh blood group D antigen (RHD) gene zygosity using droplet digital PCR. The RHD gene was amplified in 6 overlapping amplicons using long-range PCR. Amplicons were purified, and the sequencing library was prepared following the 1D Native barcoding gDNA protocol. Sequencing was carried out with 1D flow cells R9 version. Data analysis included basecalling, aligning to the RHD reference sequence, and calling variants. Variants detected were compared to the results acquired previously by the Ion Personal Genome Machine (Ion PGM). RESULTS Up to 500× sequence coverage across the RHD gene allowed accurate variant calling. Exonic changes in the RHD gene allowed RHD allele determination for all samples sequenced except 1 RHD homozygous sample, where 2 heterozygous RHD variant alleles are suspected. There were 3 known variant RHD alleles (RHD*01W.02, RHD*11, and RHD*15) and 6 novel RHD variant alleles, as previously seen in Ion PGM sequencing data for these samples. CONCLUSIONS MinION was effective in blood group genotyping, provided enough sequencing data to achieve high coverage of the RHD gene, and enabled confident calling of variants and RHD allele determination.
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Affiliation(s)
- Wajnat A Tounsi
- Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
| | - Vasileios P Lenis
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
- School of Health and Life Sciences, Teesside University, Middlesbrough, Tees Valley, UK
| | - Silja M Tammi
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Susanna Sainio
- Blood Group Unit, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Katri Haimila
- Blood Group Unit, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Neil D Avent
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
| | - Tracey E Madgett
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
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He Y, Hong X, Zhang J, He J, Zhu F, Huang H. Analysis of the Genomic Sequence of ABO Allele Using Next-Generation Sequencing Method. Front Immunol 2022; 13:814263. [PMID: 35874750 PMCID: PMC9298404 DOI: 10.3389/fimmu.2022.814263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundAlthough many molecular diagnostic methods have been used for ABO genotyping, there are few reports on the full-length genomic sequence analysis of the ABO gene. Recently, next-generation sequencing (NGS) has been shown to provide fast and high-throughput results and is widely used in the clinical laboratory. Here, we established an NGS method for analyzing the sequence of the start codon to the stop codon in the ABO gene.Study Design and MethodsTwo pairs of primers covering the partial 5’-untranslated region (UTR) to 3’-UTR of the ABO gene were designed. The sequences covering from the start codon to the stop codon of the ABO gene were amplified using these primers, and an NGS method based on the overlap amplicon was developed. A total of 110 individuals, including 88 blood donors with normal phenotypes and 22 ABO subtypes, were recruited and analyzed. All these specimens were first detected by serological tests and then determined by polymerase chain reaction sequence-based typing (PCR-SBT) and NGS. The sequences, including all the intron regions for the specimens, were analyzed by bioinformatics software.ResultsAmong the 88 blood donors with a normal phenotype, 48 homozygous individuals, 39 heterozygous individuals, and one individual with a novel O allele were found according to the results of the PCR-SBT method. Some single-nucleotide variants (SNV) in intronic regions were found to be specific for different ABO alleles from 48 homozygous individuals using the NGS method. Sequences in the coding region of all specimens using the NGS method were the same as those of the PCR-SBT method. Three intronic SNVs were found to be associated with the ABO subtypes, including one novel intronic SNV (c.28+5956T>A). Moreover, six specimens were found to exhibit DNA recombination.ConclusionAn NGS method was established to analyze the sequence from the start codon to the stop codon of the ABO gene. Two novel ABO alleles were identified, and DNA recombination was found to exist in the ABO alleles.
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Affiliation(s)
- Yanmin He
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Transfusion medicine, Blood Center of Zhejiang Province, Hangzhou, China
- Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Xiaozhen Hong
- Institute of Transfusion medicine, Blood Center of Zhejiang Province, Hangzhou, China
- Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Jingjing Zhang
- Institute of Transfusion medicine, Blood Center of Zhejiang Province, Hangzhou, China
- Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Ji He
- Institute of Transfusion medicine, Blood Center of Zhejiang Province, Hangzhou, China
- Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Faming Zhu
- Institute of Transfusion medicine, Blood Center of Zhejiang Province, Hangzhou, China
- Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
- *Correspondence: He Huang, ; Faming Zhu,
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, China
- *Correspondence: He Huang, ; Faming Zhu,
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Kim TY, Yu H, Phan MTT, Jang JH, Cho D. Application of Blood Group Genotyping by Next-Generation Sequencing in Various Immunohaematology Cases. Transfus Med Hemother 2022; 49:88-96. [PMID: 35611383 PMCID: PMC9082207 DOI: 10.1159/000517565] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/31/2021] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) technology has been recently introduced into blood group genotyping; however, there are few studies using NGS-based blood group genotyping in real-world clinical settings. In this study, we applied NGS-based blood group genotyping into various immunohaematology cases encountered in routine clinical practice. METHODS This study included 4 immunohaematology cases: ABO subgroup, ABO chimerism, antibody to a high-frequency antigen (HFA), and anti-CD47 interference. We designed a hybridization capture-based NGS panel targeting 39 blood group-related genes and applied it to the 4 cases. RESULTS NGS analysis revealed a novel intronic variant (NM_020469.3:c.29-10T>G) in a patient with an Ael phenotype and detected a small fraction of ABO*A1.02 (approximately 3-6%) coexisting with the major genotype ABO*B.01/O.01.02 in dizygotic twins. In addition, NGS analysis found a homozygous stop-gain variant (NM_004827.3:c.376C>T, p.Gln126*; ABCG2*01N.01) in a patient with an antibody to an HFA; consequently, this patient's phenotype was predicted as Jr(a-). Lastly, blood group phenotypes predicted by NGS were concordant with those determined by serology in 2 patients treated with anti-CD47 drugs. CONCLUSION NGS-based blood group genotyping can be used for identifying ABO subgroup alleles, low levels of blood group chimerism, and antibodies to HFAs. Furthermore, it can be applied to extended blood group antigen matching for patients treated with anti-CD47 drugs.
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Affiliation(s)
- Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - HongBi Yu
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Minh-Trang Thi Phan
- Stem Cell and Regenerative Medicine Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Duck Cho
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
- Stem Cell and Regenerative Medicine Institute, Samsung Medical Center, Seoul, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, Republic of Korea
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11
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Zhang Z, An HH, Vege S, Hu T, Zhang S, Mosbruger T, Jayaraman P, Monos D, Westhoff CM, Chou ST. Accurate long-read sequencing allows assembly of the duplicated RHD and RHCE genes harboring variants relevant to blood transfusion. Am J Hum Genet 2022; 109:180-191. [PMID: 34968422 DOI: 10.1016/j.ajhg.2021.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/07/2021] [Indexed: 12/18/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have transformed medical genetics. However, short-read lengths pose a limitation on identification of structural variants, sequencing repetitive regions, phasing of distant nucleotide changes, and distinguishing highly homologous genomic regions. Long-read sequencing technologies may offer improvements in the characterization of genes that are currently difficult to assess. We used a combination of targeted DNA capture, long-read sequencing, and a customized bioinformatics pipeline to fully assemble the RH region, which harbors variation relevant to red cell donor-recipient mismatch, particularly among patients with sickle cell disease. RHD and RHCE are a pair of duplicated genes located within an ∼175 kb region on human chromosome 1 that have high sequence similarity and frequent structural variations. To achieve the assembly, we utilized palindrome repeats in PacBio SMRT reads to obtain consensus sequences of 2.1 to 2.9 kb average length with over 99% accuracy. We used these long consensus sequences to identify 771 assembly markers and to phase the RHD-RHCE region with high confidence. The dataset enabled direct linkage between coding and intronic variants, phasing of distant SNPs to determine RHD-RHCE haplotypes, and identification of known and novel structural variations along with the breakpoints. A limiting factor in phasing is the frequency of heterozygous assembly markers and therefore was most successful in samples from African Black individuals with increased heterogeneity at the RH locus. Overall, this approach allows RH genotyping and de novo assembly in an unbiased and comprehensive manner that is necessary to expand application of NGS technology to high-resolution RH typing.
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Affiliation(s)
- Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hyun Hyung An
- Division of Hematology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sunitha Vege
- Immunohematology and Genomics, New York Blood Center, New York, NY 11101, USA
| | - Taishan Hu
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shiping Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Timothy Mosbruger
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pushkala Jayaraman
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dimitri Monos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman Schools of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Connie M Westhoff
- Immunohematology and Genomics, New York Blood Center, New York, NY 11101, USA
| | - Stella T Chou
- Division of Hematology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Transfusion Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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12
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Ying Y, Zhang J, Hong X, Xu X, He J, Zhu F. The Significance of RHD Genotyping and Characteristic Analysis in Chinese RhD Variant Individuals. Front Immunol 2021; 12:755661. [PMID: 34867989 PMCID: PMC8633534 DOI: 10.3389/fimmu.2021.755661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
Background RhD is the most important and complex blood group system because of its highly polymorphic and immunogenic nature. RhD variants can induce immune response by allogeneic transfusion, organ transplantation, and fetal immunity. The transfusion strategies are different for RhD variants formed by various alleles. Therefore, extensive investigation of the molecular mechanism underlying RhD variants is critical for preventing immune-related blood transfusion reactions and fetal immunity. Methods RhD variants were collected from donors and patients in Zhejiang Province, China. The phenotypes were classified using the serologic method. The full coding regions of RHD gene were analyzed using the PCR-SBT method. The multiplex ligation-dependent probe amplification (MLPA) assay was used to analyze the genotype and gene copy number. SWISS-MODLE and PyMOL software were used to analyze 3D structures of RhD caused by the variant alleles. The effect of non-synonymous substitutions was predicted using Polymorphism Phenotyping algorithm (PolyPhen-2), Sorting Intolerant From Tolerant (SIFT), and Protein Variation Effect Analyzer (PROVEAN) software. Results In the collected RhD variants, 28 distinct RHD variant alleles were identified, including three novel variant alleles. RH-MLPA assay is advantageous for determining the copy number of RHD gene. 3D homology modeling predicted that protein conformation was disrupted and may explain RhD epitope differential expression. A total of 14 non-synonymous mutations were determined to be detrimental to the protein structure. Discussion We revealed the diversity of RHD alleles present in eastern Chinese RhD variants. The bioinformatics of these variant alleles extended our knowledge of RhD variants, which was crucial for evaluating their impact to guide transfusion support and avoid immune-related blood transfusion reactions.
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Affiliation(s)
- Yanling Ying
- Blood Center of Zhejiang Province, Institute of Transfusion Medicine, Hangzhou, China.,Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Jingjing Zhang
- Blood Center of Zhejiang Province, Institute of Transfusion Medicine, Hangzhou, China.,Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Xiaozhen Hong
- Blood Center of Zhejiang Province, Institute of Transfusion Medicine, Hangzhou, China.,Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Xianguo Xu
- Blood Center of Zhejiang Province, Institute of Transfusion Medicine, Hangzhou, China.,Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Ji He
- Blood Center of Zhejiang Province, Institute of Transfusion Medicine, Hangzhou, China.,Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Faming Zhu
- Blood Center of Zhejiang Province, Institute of Transfusion Medicine, Hangzhou, China.,Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
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13
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Kim TY, Yu H, Cho D. The intronic variant RHD:c.149-29G>C designated as RHD*01EL.32 does not cause a DEL phenotype. Transfusion 2021; 61:986-987. [PMID: 33719044 DOI: 10.1111/trf.16233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/22/2020] [Accepted: 11/22/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - HongBi Yu
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea
| | - Duck Cho
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea
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14
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Srivastava K, Fratzscher AS, Lan B, Flegel WA. Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database. BMC Bioinformatics 2021; 22:273. [PMID: 34039276 PMCID: PMC8150616 DOI: 10.1186/s12859-021-04169-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
Background Clinically effective and safe genotyping relies on correct reference sequences, often represented by haplotypes. The 1000 Genomes Project recorded individual genotypes across 26 different populations and, using computerized genotype phasing, reported haplotype data. In contrast, we identified long reference sequences by analyzing the homozygous genomic regions in this online database, a concept that has rarely been reported since next generation sequencing data became available. Study design and methods Phased genotype data for a 80.6 kb region of chromosome 1 was downloaded for all 2,504 unrelated individuals of the 1000 Genome Project Phase 3 cohort. The data was centered on the ACKR1 gene and bordered by the CADM3 and FCER1A genes. Individuals with heterozygosity at a single site or with complete homozygosity allowed unambiguous assignment of an ACKR1 haplotype. A computer algorithm was developed for extracting these haplotypes from the 1000 Genome Project in an automated fashion. A manual analysis validated the data extracted by the algorithm. Results We confirmed 902 ACKR1 haplotypes of varying lengths, the longest at 80,584 nucleotides and shortest at 1,901 nucleotides. The combined length of haplotype sequences comprised 19,895,388 nucleotides with a median of 16,014 nucleotides. Based on our approach, all haplotypes can be considered experimentally confirmed and not affected by the known errors of computerized genotype phasing. Conclusions Tracts of homozygosity can provide definitive reference sequences for any gene. They are particularly useful when observed in unrelated individuals of large scale sequence databases. As a proof of principle, we explored the 1000 Genomes Project database for ACKR1 gene data and mined long haplotypes. These haplotypes are useful for high throughput analysis with next generation sequencing. Our approach is scalable, using automated bioinformatics tools, and can be applied to any gene. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04169-6.
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Affiliation(s)
- Kshitij Srivastava
- Laboratory Services Section, Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anne-Sophie Fratzscher
- Laboratory Services Section, Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bo Lan
- Laboratory Services Section, Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Willy Albert Flegel
- Laboratory Services Section, Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA.
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15
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Next-generation sequencing of 35 RHD variants in 16 253 serologically D- pregnant women in the Finnish population. Blood Adv 2021; 4:4994-5001. [PMID: 33057632 DOI: 10.1182/bloodadvances.2020001569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Fetal RHD screening for targeted routine antenatal anti-D prophylaxis has been implemented in many countries, including Finland, since the 2010s. Comprehensive knowledge of the RHD polymorphism in the population is essential for the performance and safety of the anti-D prophylaxis program. During the first 3 years of the national screening program in Finland, over 16 000 samples from RhD- women were screened for fetal RHD; among them, 79 samples (0.5%) containing a maternal variant allele were detected. Of the detected maternal variants, 35 cases remained inconclusive using the traditional genotyping methods and required further analysis by next-generation sequencing (NGS) of the whole RHD gene to uncover the variant allele. In addition to the 13 RHD variants that have been previously reported in different populations, 8 novel variants were also detected, indicating that there is more variation of RHD in the RhD- Finnish population than has been previously known. Three of the novel alleles were identified in multiple samples; thus, they are likely specific to the original Finnish population. National screening has thus provided new information about the diversity of RHD variants in the Finnish population. The results show that NGS is a powerful method for genotyping the highly polymorphic RHD gene compared with traditional methods that rely on the detection of specific nucleotides by polymerase chain reaction amplification.
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16
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Halls JBL, Vege S, Simmons DP, Aeschlimann J, Bujiriri B, Mah HH, Lebo MS, Vijay Kumar PK, Westhoff CM, Lane WJ. Overcoming the challenges of interpreting complex and uncommon RH alleles from whole genomes. Vox Sang 2020; 115:790-801. [PMID: 32567058 DOI: 10.1111/vox.12963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/09/2020] [Accepted: 05/27/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND AND OBJECTIVES Rh is one of the most diverse and complex blood group systems. Recently, next generation sequencing (NGS) has proven to be a viable option for RH genotyping. We have developed automated software (bloodTyper) for determining alleles encoding RBC antigens from NGS-based whole genome sequencing (WGS). The bloodTyper algorithm has not yet been optimized and evaluated for complex and uncommon RH alleles. MATERIALS AND METHODS Twenty-two samples with previous polymerase chain reaction (PCR) and Sanger sequencing-based RH genotyping underwent WGS. bloodTyper was used to detect RH alleles including those defined by structural variation (SV) using a combination of three independent strategies: sequence read depth of coverage, split reads and paired reads. RESULTS bloodTyper was programmed to identify D negative and positive phenotypes as well as the presence of alleles encoding weak D, partial D and variant RHCE. Sequence read depth of coverage calculation accurately determined RHD zygosity and detected the presence of RHD/RHCE hybrids. RHCE*C was determined by sequence read depth of coverage and by split read methods. RHD hybrid alleles and RHCE*C were confirmed by using a paired read approach. Small SVs present in RHCE*CeRN and RHCE*ceHAR were detected by a combined read depth of coverage and paired read approach. CONCLUSIONS The combination of several different interpretive approaches allowed for automated software based-RH genotyping of WGS data including RHD zygosity and complex compound RHD and RHCE heterozygotes. The scalable nature of this automated analysis will enable RH genotyping in large genomic sequencing projects.
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Affiliation(s)
- Justin B L Halls
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Daimon P Simmons
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Baderha Bujiriri
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Helen H Mah
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew S Lebo
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Laboratory for Molecular Medicine, Boston, MA, USA.,Partners Personalized Medicine, Boston, MA, USA
| | | | | | - William J Lane
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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17
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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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18
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Fürst D, Tsamadou C, Neuchel C, Schrezenmeier H, Mytilineos J, Weinstock C. Next-Generation Sequencing Technologies in Blood Group Typing. Transfus Med Hemother 2019; 47:4-13. [PMID: 32110189 DOI: 10.1159/000504765] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
Sequencing of the human genome has led to the definition of the genes for most of the relevant blood group systems, and the polymorphisms responsible for most of the clinically relevant blood group antigens are characterized. Molecular blood group typing is used in situations where erythrocytes are not available or where serological testing was inconclusive or not possible due to the lack of antisera. Also, molecular testing may be more cost-effective in certain situations. Molecular typing approaches are mostly based on either PCR with specific primers, DNA hybridization, or DNA sequencing. Particularly the transition of sequencing techniques from Sanger-based sequencing to next-generation sequencing (NGS) technologies has led to exciting new possibilities in blood group genotyping. We describe briefly the currently available NGS platforms and their specifications, depict the genetic background of blood group polymorphisms, and discuss applications for NGS approaches in immunohematology. As an example, we delineate a protocol for large-scale donor blood group screening established and in use at our institution. Furthermore, we discuss technical challenges and limitations as well as the prospect for future developments, including long-read sequencing technologies.
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Affiliation(s)
- Daniel Fürst
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Chrysanthi Tsamadou
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Christine Neuchel
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Joannis Mytilineos
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Christof Weinstock
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
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19
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Storry JR, Jöud M, Olsson ML. Automatic for the people: a rapidly evolving movement for the future of genotyping. Transfusion 2019; 59:3545-3547. [PMID: 31667851 DOI: 10.1111/trf.15561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/03/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Jill R Storry
- Clinical Immunology and Transfusion Medicine, Office of Medical Services, Region Skåne, Sweden.,Department of Laboratory Medicine, Division of Hematology and Transfusion Medicine, Lund University, Lund, Sweden
| | - Magnus Jöud
- Clinical Immunology and Transfusion Medicine, Office of Medical Services, Region Skåne, Sweden
| | - Martin L Olsson
- Clinical Immunology and Transfusion Medicine, Office of Medical Services, Region Skåne, Sweden.,Department of Laboratory Medicine, Division of Hematology and Transfusion Medicine, Lund University, Lund, Sweden
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20
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Montemayor C, Brunker PAR, Keller MA. Banking with precision: transfusion medicine as a potential universal application in clinical genomics. Curr Opin Hematol 2019; 26:480-487. [PMID: 31490317 PMCID: PMC7302862 DOI: 10.1097/moh.0000000000000536] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW To summarize the most recent scientific progress in transfusion medicine genomics and discuss its role within the broad genomic precision medicine model, with a focus on the unique computational and bioinformatic aspects of this emergent field. RECENT FINDINGS Recent publications continue to validate the feasibility of using next-generation sequencing (NGS) for blood group prediction with three distinct approaches: exome sequencing, whole genome sequencing, and PCR-based targeted NGS methods. The reported correlation of NGS with serologic and alternative genotyping methods ranges from 92 to 99%. NGS has demonstrated improved detection of weak antigens, structural changes, copy number variations, novel genomic variants, and microchimerism. Addition of a transfusion medicine interpretation to any clinically sequenced genome is proposed as a strategy to enhance the cost-effectiveness of precision genomic medicine. Interpretation of NGS in the blood group antigen context requires not only advanced immunohematology knowledge, but also specialized software and hardware resources, and a bioinformatics-trained workforce. SUMMARY Blood transfusions are a common inpatient procedure, making blood group genomics a promising facet of precision medicine research. Further efforts are needed to embrace transfusion bioinformatic challenges and evaluate its clinical utility.
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Affiliation(s)
- Celina Montemayor
- Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD
| | - Patricia A. R. Brunker
- Division of Transfusion Medicine, Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD
- American Red Cross, Greater Chesapeake and Potomac Region, Baltimore, MD
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21
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Lane WJ, Vege S, Mah HH, Lomas-Francis C, Aguad M, Smeland-Wagman R, Koch C, Killian JM, Gardner CL, De Castro M, Lebo MS, Kaufman RM, Green RC, Westhoff CM. Automated typing of red blood cell and platelet antigens from whole exome sequences. Transfusion 2019; 59:3253-3263. [PMID: 31392742 DOI: 10.1111/trf.15473] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Genotyping has expanded the number red blood cell (RBC) and platelet (PLT) antigens that can readily be typed, but often represents an additional testing cost. The analysis of existing genomic data offers a cost-effective approach. We recently developed automated software (bloodTyper) for determination of RBC and PLT antigens from whole genome sequencing. Here we extend the algorithm to whole exome sequencing (WES). STUDY DESIGN AND METHODS Whole exome sequencing was performed on samples from 75 individuals. WES-based bloodTyper RBC and PLT typing was compared to conventional polymerase chain reaction (PCR) RHD zygosity testing and serologic and single-nucleotide polymorphism (SNP) typing for 38 RBC antigens in 12 systems (17 serologic and 35 SNPs) and 22 PLT antigens (22 SNPs). Samples from the first 20 individuals were used to modify bloodTyper to interpret WES followed by blinded typing of 55 samples. RESULTS Over the first 20 samples, discordances were noted for C, M, and N antigens, which were due to WES-specific biases. After modification, bloodTyper was 100% accurate on blinded evaluation of the last 55 samples and outperformed both serologic (99.67% accurate) and SNP typing (99.97% accurate) reflected by two Fyb and one N serologic typing errors and one undetected SNP encoding a Jknull phenotype. RHD zygosity testing by bloodTyper was 100% concordant with a combination of hybrid Rhesus box PCR and PCR-restriction fragment length polymorphism for all samples. CONCLUSION The automated bloodTyper software was modified for WES biases to allow for accurate RBC and PLT antigen typing. Such analysis could become a routing part of future WES efforts.
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Affiliation(s)
- William J Lane
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | | | - Helen H Mah
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Maria Aguad
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | | | | | | | | | | | - Matthew S Lebo
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Partners Personalized Medicine, Boston, Massachusetts.,Laboratory for Molecular Medicine, Boston, Massachusetts
| | - Richard M Kaufman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Robert C Green
- Harvard Medical School, Boston, Massachusetts.,Partners Personalized Medicine, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Boston, Massachusetts.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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22
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Hyland CA, Roulis EV, Schoeman EM. Developments beyond blood group serology in the genomics era. Br J Haematol 2019; 184:897-911. [PMID: 30706459 DOI: 10.1111/bjh.15747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Blood group serology and single nucleotide polymorphism-based genotyping platforms are accurate but do not provide a comprehensive cover for all 36 blood group systems and do not cover the antigen diversity observed among population groups. This review examines the extent to which genomics is shaping blood group serology. Resources for genomics include the Human Reference Genome Sequence assembly; curated blood group tables listing variants; public databases providing information on genetic variants from world-wide studies; and massively parallel sequencing technologies. Blood group genomic studies span the spectrum, from bioinformatic data mining of huge data sets containing whole genome and whole exome information to laboratory investigations utilising targeted sequencing approaches. Blood group predictions based on genome sequencing and genomic studies are proving accurate, and have shown utility in both research and reference settings. Overall, studies confirm the potential for blood group genomics to reshape donor and patient transfusion management strategies to provide more compatible blood transfusions.
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Affiliation(s)
- Catherine A Hyland
- Clinical Services and Research, Australian Red Cross Blood Service, Kelvin Grove, Queensland, Australia
| | - Eileen V Roulis
- Clinical Services and Research, Australian Red Cross Blood Service, Kelvin Grove, Queensland, Australia
| | - Elizna M Schoeman
- Clinical Services and Research, Australian Red Cross Blood Service, Kelvin Grove, Queensland, Australia
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