ORCID Profile
0000-0003-0461-6841
Current Organisation
Proteomics International
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Publisher: Wiley
Date: 24-03-2017
DOI: 10.1111/TRF.14054
Abstract: Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS. Donor s les (n = 28) that were extensively phenotyped and genotyped using single nucleotide polymorphism typing, were analyzed using the TruSight One Sequencing Panel and MiSeq platform. Genes for 28 protein-based blood group systems, GATA1, and KLF1 were analyzed. Copy number variation analysis was used to characterize complex structural variants in the GYPC and RH systems. The average sequencing depth per target region was 66.2 ± 39.8. Each s le harbored on average 43 ± 9 variants, of which 10 ± 3 were used for genotyping. For the 28 s les, massively parallel sequencing variant sequences correctly matched expected sequences based on single nucleotide polymorphism genotyping data. Copy number variation analysis defined the Rh C/c alleles and complex RHD hybrids. Hybrid RHD*D-CE-D variants were correctly identified, but copy number variation analysis did not confidently distinguish between D and CE exon deletion versus rearrangement. The targeted exome sequencing strategy employed extended the range of blood group genotypes detected compared with single nucleotide polymorphism typing. This single-test format included detection of complex MNS hybrid cases and, with copy number variation analysis, defined RH hybrid genes along with the RHCE*C allele hitherto difficult to resolve by variant detection. The approach is economical compared with whole-genome sequencing and is suitable for a red blood cell reference laboratory setting.
Publisher: Elsevier BV
Date: 05-2009
Publisher: Wiley
Date: 16-07-2017
DOI: 10.1111/TRF.14250
Publisher: Wiley
Date: 08-11-2018
DOI: 10.1111/TRF.14393
Abstract: We previously demonstrated that targeted exome sequencing accurately defined blood group genotypes for reference panel s les characterized by serology and single-nucleotide polymorphism (SNP) genotyping. Here we investigate the application of this approach to resolve problematic serology and SNP-typing cases. The TruSight One sequencing panel and MiSeq platform was used for sequencing. CLC Genomics Workbench software was used for data analysis of the blood group genes implicated in the serology and SNP-typing problem. Sequence variants were compared to public databases listing blood group alleles. The effect of predicted amino acid changes on protein function for novel alleles was assessed using SIFT and PolyPhen-2. Among 29 unresolved s les, sequencing defined SNPs in blood group genes consistent with serologic observation: 22 s les exhibited SNPs associated with varied but known blood group alleles and one s le exhibited a chimeric RH genotype. Three s les showed novel variants in the CROM, LAN, and RH systems, respectively, predicting respective amino acid changes with possible deleterious impact. Two s les harbored rare variants in the RH and FY systems, respectively, not previously associated with a blood group allele or phenotype. A final s le comprised a rare variant within the KLF1 transcription factor gene that may modulate DNA-binding activity. Targeted exome sequencing resolved complex serology problems and defined both novel blood group alleles (CD55:c.203G>A, ABCB6:c.1118_1124delCGGATCG, ABCB6:c.1656-1G>A, and RHD:c.452G>A) and rare variants on blood group alleles associated with altered phenotypes. This study illustrates the utility of exome sequencing, in conjunction with serology, as an alternative approach to resolve complex cases.
Publisher: Elsevier BV
Date: 12-2017
DOI: 10.1016/J.PATHOL.2017.08.010
Abstract: Non-invasive fetal RHD genotyping in Australia to reduce anti-D usage will need to accommodate both prolonged s le transport times and a erse population demographic harbouring a range of RHD blood group gene variants. We compared RHD genotyping accuracy using two blood s le collection tube types for RhD negative women stratified into deleted RHD gene haplotype and RHD gene variant cohorts. Maternal blood s les were collected into EDTA and cell-free (cf)DNA stabilising (BCT) tubes from two sites, one interstate. Automated DNA extraction and polymerase chain reaction (PCR) were used to lify RHD exons 5 and 10 and CCR5. Automated analysis flagged maternal RHD variants, which were classified by genotyping. Time between s le collection and processing ranged from 2.9 to 187.5 hours. cfDNA levels increased with time for EDTA (range 0.03-138 ng/μL) but not BCT s les (0.01-3.24 ng/μL). For the 'deleted' cohort (n=647) all fetal RHD genotyping outcomes were concordant, excepting for one unexplained false negative EDTA s le. Matched against cord RhD serology, negative predictive values using BCT and EDTA tubes were 100% and 99.6%, respectively. Positive predictive values were 99.7% for both types. Overall 37.2% of subjects carried an RhD negative baby. The 'variant' cohort (n=15) included one novel RHD and eight hybrid or African pseudogene variants. Review for fetal RHD specific signals, based on one exon, showed three EDTA s les discordant to BCT, attributed to high maternal cfDNA levels arising from prolonged transport times. For the deleted haplotype cohort, fetal RHD genotyping accuracy was comparable for s les collected in EDTA and BCT tubes despite higher cfDNA levels in the EDTA tubes. Capacity to predict fetal RHD genotype for maternal carriers of hybrid or pseudogene RHD variants requires stringent control of cfDNA levels. We conclude that fetal RHD genotyping is feasible in the Australian environment to avoid unnecessary anti-D immunoglobulin prophylaxis.
Publisher: Springer Science and Business Media LLC
Date: 16-03-2017
Publisher: Elsevier BV
Date: 02-2016
Publisher: Elsevier BV
Date: 04-2019
DOI: 10.1016/J.TMRV.2019.01.004
Abstract: Erythroid-specific Krüppel-like factor 1, or KLF1, is an integral transcriptional activator for erythropoiesis. Genetic variants within KLF1 can result in a range of erythropoietic clinical phenotypes from benign to significant. The In(Lu) phenotype refers to changes in the quantitative expression of blood group-associated red cell surface molecules due to KLF1 variants which are otherwise clinically benign. These clinically benign KLF1 variants are associated with a reduced expression of 1 or more red cell membrane proteins/carbohydrates that carry blood group antigens for the LU (Lutheran), IN (Indian), P1PK, LW (Landsteiner-Wiener), KN (Knops), OK, RAPH, and I blood group systems. This is of significance during routine serologic blood typing when expression falls below the test sensitivity and therefore impacts on the ability to accurately detect the presence of affected blood group antigens. This is of clinical importance because the transfusion requirements for in iduals with the In(Lu) phenotype differ from those of in iduals that have a true Lu
Publisher: Wiley
Date: 06-12-2019
DOI: 10.1111/TRF.15047
Abstract: The distribution of RBC antigens, which define blood group types, differs among populations. In contrast to many world populations, blood group profiles for Indigenous Australians have not been well studied. As it is now possible to predict comprehensive blood group antigen profiles from genomic data sets, we aimed to apply this for Indigenous Australians and to provide a comparison to other major world populations. Whole exome sequence data for 72 Western Desert Indigenous Australians was provided by the Telethon Kids Institute. Variants (against hg19) were annotated using computer software (ANNOVAR, Qiagen Bioinformatics) and filtered to include only variants in genes for 36 blood group systems, and the transcription factors KLF1 and GATA1. The RHCE*C allele and RHD zygosity were identified by copy number variant analysis of sequence alignments. The impact of missense variants was investigated in silico using a meta-predictor of disease-causing variants (Meta-SNP). For 21 blood group systems the predicted blood group antigen frequencies were comparable to those for other major world populations. For 13 systems, interesting points of contrast were identified. Furthermore, we identified 12 novel variants, one novel D allele, and four rare variants with potential clinical significance. This is the first systematic assessment of genomic data to elucidate blood group antigen profiles for Indigenous Australians who are linguistically and culturally erse. Our study paves the way to understanding the geographic distribution of blood group variants in different Indigenous groups and the associated RBC phenotypes. This in turn is expected to guide transfusion practice for Indigenous in iduals.
Publisher: Wiley
Date: 05-03-2018
DOI: 10.1111/TRF.14562
Publisher: Wiley
Date: 17-09-2018
DOI: 10.1111/TRF.14926
Abstract: KLF1 is an essential transcriptional activator that drives erythropoiesis. KLF1 variants can result in the Inhibitor of Lutheran, or In(Lu), phenotype where red blood cells (RBCs) have reduced BCAM (LU) and CD44 (IN). Other RBC surface molecules also have changed expression however, there is controversy in the literature regarding which are truly impacted. We aimed to investigate KLF1 variants in the Australian population. In(Lu) s les were sourced through screening and through the RBC reference laboratory. Blood donor s les (8036) were screened to identify weakened/absent Lu Four of 8036 donors were identified to be In(Lu), and two previously identified In(Lu) s les were provided from the RBC reference laboratory. Five different KLF1 variants were identified two were novel: c.954G>C .Trp318Cys and c.421C>T .Arg141*. BCAM and CD44 were reduced in all s les, consistent with previous reports. As a group, In(Lu) RBCs had reduced CD35 (KN), ICAM4 (LW), and CD147 (OK), and demonstrated increased binding of lectins ECA and SNAI. One In(Lu) s le had elevated HbF and another elevated HbA2. Different KLF1 variants may potentially produce variable phenotypes. A framework for investigating KLF1 variants and their phenotypic impact has been provided. In the future, given available international databases, further testing algorithms (as advocated here) will allow for correlation of phenotype with genotype and therefore accurately document this variability between KLF1 variants.
Publisher: Wiley
Date: 02-2019
DOI: 10.1111/BJH.15747
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 ersity 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.
Publisher: Wiley
Date: 06-12-2018
DOI: 10.1111/TRF.14439
Abstract: The RhD blood group antigen is extremely polymorphic and the DEL phenotype represents one such class of polymorphisms. The DEL phenotype prevalent in East Asian populations arises from a synonymous substitution defined as RHD*1227A. However, initially, based on genomic and cDNA studies, the genetic basis for a DEL phenotype in Taiwan was attributed to a deletion of RHD Exon 9 that was never verified at the genomic level by any other independent group. Here we investigate the genetic basis for a Caucasian donor with a DEL partial D phenotype and compare the genomic findings to those initial molecular studies. The 3'-region of the RHD gene was lified by long-range polymerase chain reaction (PCR) for massively parallel sequencing. Primers were designed to encompass a deletion, flanking Exon 9, by standard PCR for Sanger sequencing. Targeted sequencing of exons and flanking introns was also performed. Genomic DNA exhibited a 1012-bp deletion spanning from Intron 8, across Exon 9 into Intron 9. The deletion breakpoints occurred between two 25-bp repeat motifs flanking Exon 9 such that one repeat sequence remained. Deletion mutations bordered by repeat sequences are a hallmark of slipped-strand mispairing (SSM) event. We propose this genetic mechanism generated the germline deletion in the Caucasian donor. Extensive studies show that the RHD*1227A is the most prevalent DEL allele in East Asian populations and may have confounded the initial molecular studies. Review of the literature revealed that the SSM model explains some of the extreme polymorphisms observed in the clinically significant RhD blood group antigen.
Publisher: Wiley
Date: 08-07-2016
DOI: 10.1111/TRF.13713
Abstract: Blood donors whose red blood cells (RBCs) exhibit a partial RhD phenotype, lacking some D epitopes, present as D+ in routine screening. Such phenotypes can exhibit low-frequency antigens (LFAs) of clinical significance. The aim of this study was to describe the serologic and genetic profile for a blood donor with an apparent D+ phenotype carrying a variant RHD gene where D Exons 5 and 6 are replaced by RHCE Exon (5-6). Anti-D monoclonal antibodies were used to characterize the presentation of RhD epitopes on the RBCs. RHD exon scanning and DNA sequencing of short- and long-range polymerase chain reaction licons were used to determine the RHD structure and sequence. Extended phenotyping for LFAs RH23 (D(W) ) and Rh32 was performed. The donor serology profile was consistent with partial RhD epitope presentation. The donor was hemizygous for an RHD variant allele described as RHD*D-CE(5-6)-D hybrid. The RHCE gene insert is at least 3.868 kb with 5' and 3' breakpoints between IVS4 + 132-c.667 and IVS6 + 1960-IVS6 + 2099, respectively. The sequence for this hybrid was assigned GenBank Accession Number KT099190.2. The RBCs were RH23 (D(W) )+ and Rh32-. A novel RHD*D-CE(5-6)-D hybrid allele encodes a partial RhD epitope and carries the LFA RH23 (D(W) ). This and the epitope profile resemble the partial DVa phenotype. Given that RBCs from this in idual lack some RhD epitopes, there is an alloimmunization risk if the donor is exposed to D+ RBCs. Conversely, transfusions of RH23 (D(W) )+ cells to RH23 (D(W) )- recipients also pose an alloimmunization risk.
Publisher: Wiley
Date: 17-09-2018
DOI: 10.1111/TRF.14944
Abstract: RhD DEL variants may show complete or partial expression of RhD epitopes. There have been only rare reports of anti-D causing hemolytic disease of the fetus and newborn (HDFN) in this context. We report a case of severe HDFN associated with a recently described DEL variant. A multiparous woman presented with an allo-anti-D and showed incongruent phenotyping and genotyping results on initial study. Further investigations identified the RHD mutation, defined as RHD*148+1T and named RHD*01EL.31, which had been previously associated with a DEL phenotype. Extended RhD phenotyping by adsorption-elution showed that there was reactivity with four of nine monoclonal anti-D antibodies, suggesting a partial DEL phenotype. The first child showed no clinical evidence of HDFN, although the cord direct antiglobulin test was positive. The second child developed fetal anemia treated with intrauterine transfusion, and neonatal hyperbilirubinemia requiring exchange transfusion. The RHD allele, RHD*148+1T, results in a partial Del phenotype, and the anti-D formed in pregnant women with this phenotype is capable of causing severe HDFN.
Publisher: Springer Science and Business Media LLC
Date: 18-01-2012
Publisher: Wiley
Date: 20-07-2020
DOI: 10.1111/TRF.15945
Publisher: Wiley
Date: 16-02-2020
DOI: 10.1111/BJH.16500
Publisher: Elsevier BV
Date: 02-2022
No related grants have been discovered for Elizna Schoeman.