Rapid genotyping of blood group antigens by multiplex polymerase chain reaction and DNA microarray hybridization

Large-scale blood group genotyping: clinical implications

The molecular background of blood group antigen expression of the major clinically significant blood group antigens has been largely accomplished. Despite this large body of work, blood group phenotype prediction by genotyping has a marginal supporting role in the routine blood bank. It has however had a major impact in the prenatal determination of fetal blood group status in the management of haemolytic disease of the fetus and newborn. In the past few years several high throughput systems have been in development that have the potential capacity to perform genotyping on a mass scale. Such systems have been designed for use on donor- and patient-derived DNA and provide much more comprehensive information regarding an individuals blood group than is possible by using serological methods alone. DNA-based typing methodology is easier to standardize than serology and has the potential to replace it as a front line diagnostic in blood banks. This review overviews the current situation in this area and attempts to predict how blood group genotyping will evolve in the future.

New technologies to replace current blood typing reagents

PURPOSE OF REVIEW

This review summarizes recent developments in blood grouping and compatibility testing in transfusion medicine.

RECENT FINDINGS

Identification of the molecular characteristics of the major human blood groups has provided an opportunity to develop methods for blood group phenotyping using DNA-based technology. Various studies have demonstrated the feasibility of such an approach and have demonstrated the potential to change current procedures for identifying compatible blood, both in routine settings and in highly immunized patients, for whom compatible blood is difficult to obtain. In the obstetric setting, isolation of cell-free DNA from maternal plasma for fetal blood grouping provides a minimally invasive method for determining the risk for haemolytic disease in the newborn. Recombinant technology for synthesizing blood group proteins, although in its infancy, has the potential to change longstanding antibody identification procedures.

SUMMARY

The molecular revolution occurring throughout medicine is broadly manifest in all areas of transfusion medicine and should contribute to transfusion safety.

Multicolor real-time polymerase chain reaction genotyping of six human platelet antigens using displacing probes

BACKGROUND

Several genotyping methods for six clinically relevant human platelet antigens (HPAs) have been reported. A four-color real-time polymerase chain reaction (PCR) method using displacing probes for genotyping of the six HPAs is described.

STUDY DESIGN AND METHODS

Primers and four differently fluorophor-labeled displacing probes were designed and synthesized to detect single-nucleotide polymorphisms responsible for each of the HPA-1, -2, -3, -4, -5, and -15 genotypes. Two HPA systems were analyzed in a single PCR procedure. After validation with samples of known genotypes, a total of 150 blood samples from healthy donors were genotyped. The results were compared with PCR with sequence-specific primers (SSP), PCR-restriction fragment length polymorphism (RFLP), and/or direct DNA sequencing. The frequencies of each HPA allele were calculated.

RESULTS

Unequivocal real-time PCR genotyping results were obtained with minimal manual manipulation and carryover contamination. All 150 blood samples were correctly genotyped as confirmed by PCR-SSP, PCR-RFLP, and/or direct DNA sequencing. The allelic frequencies of HPA-1 through -5 and -15 among the Chinese population in Xiamen were comparable with those previously reported with Chinese living in other territories. For each specimen, genotyping of all six HPA biallelic systems was achieved in three tubes of PCR within 90 minutes and with material cost of no more than $1.

CONCLUSION

Genotyping of HPA with real-time PCR using displacing probes is more rapid and reliable compared with PCR-SSP and PCR-RFLP methods and is more affordable than existing real-time PCR-based HPA genotyping assays. Thus, our approach is more suitable for routine HPA analysis and ideal for both urgent clinical testing and high-throughput screening.

Report of the Second International Workshop on molecular blood group genotyping

The second International Society of Blood Transfusion and International Council for Standardization in Haematology workshop on molecular blood group genotyping was held in 2006. Forty-one laboratories participated. Six samples were distributed: two representing DNA from transfusion-dependent patients for testing for all clinically important polymorphisms; two representing DNA from amniotic fluid for RhD, Rhc, and K testing; and two plasma samples from RhD-negative pregnant women for fetal RhD testing (only tested by 20 laboratories). Overall, a high level of accuracy was achieved by most of the laboratories, although the error rate caused by RHDPsi was not acceptable and needs to be addressed. With greater care and attention to detail, very high standards could be set for molecular blood group genotyping.

[Future technological evolutions in blood donation qualification]

In the past decades, blood donation screening contributed significantly to blood safety improvement, thanks to the increasing performances of serological and nucleic acid testing (NAT) assays, as well as the evolution of automated systems technology. The rapid pace of NAT development can be clearly seen to extend into the future. NAT for additional viruses as well as the use of new automated systems for individual donation or smaller mini-pool testing, with multiplex assays, is currently debated. However, few added benefit is expected for blood safety from such developments, while cost-effectiveness appears to be poor. The next step in laboratory automation will probably be the implementation of robotic pre- and post-analytical procedures. In this article we review the potential future evolutions of screening technologies in blood qualification platforms, particularly those derived from nanobiotechnologies. DNA microarrays, Lab-On-Chips, biosensors and nanoparticles (quantum dots) will probably play a major role in the coming decade.

Large scale blood group genotyping

Determination of predicted blood group phenotype by determination of genotype has been performed since the 1990s. This evolved due to the rapid accrual of information surrounding the molecular basis of blood group antigen expression, which started in 1990 with ABO and RH systems and has now resulted in the molecular description of 28 of the 29 blood groups. Blood group genotyping is currently performed mostly for fetal blood group incompatibility and for assessment of multi-transfused patients. Both of these clinical scenarios are either dangerous or technically difficult, respectively to define serologically. With the simultaneous development of mass scale genotyping platforms it has now permitted the application of them to blood group genotype determination. In this paper, I describe some recently published work that has demonstrated that mass scale genotyping approaches are feasible. These approaches may lead to more effective management of blood stocks and patient cross-matching by reducing the dependence on serology during the time critical pre-transfusion phase. It is most probable that large scale studies, perhaps involving many European Union and North American based blood suppliers, may drive the introduction of this technology and convince red cell serologists that this approach may allow their work to be more focussed.

Small world - advance of microarrays: current status and future trends

Microarrays have the potential to become the next generation blood-testing platform. This commentary covers various aspects of such development presented in part at the Scotblood 2006 Meeting. Current mandatory testing includes antibody and antigen determination in both blood grouping and microbiology testing. While antibody determination is limited to phenotypic assays, antigen detection can be accomplished by genotyping or phenotyping. Applicability of various types of assays to microarrays, precision and sensitivity levels and correlation between genotyping and phenotyping results are briefly discussed and some of the main questions that need to be answered highlighted in future trends.

FY*X real-time polymerase chain reaction with melting curve analysis associated with a complete one-step real-time FY genotyping

BACKGROUND AND OBJECTIVES

The Duffy (FY) blood group system is controlled by four major alleles: FY*A and FY*B, the Caucasian common alleles, encoding Fy(a) and Fy(b) antigens; FY*X allele responsible for a poorly expressed Fy(b) antigen, and FY*Fy a silent predominant allele among Black population. Despite the recent development of a real-time fluorescent polymerase chain reaction (PCR) method for FY genotyping FY*X genotyping has not been described by this method. This study focused on the real-time FY*X genotyping development associated with a complete, one-step real-time FY genotyping, based on fluorescence resonance energy transfer (FRET) technology.

MATERIALS AND METHODS

Seventy-two blood samples from Fy(a+b-) Caucasian blood donors were studied by real-time PCR only. Forty-seven Caucasian and Black individual blood samples, referred to our laboratory, were studied by PCR-RFLP and real-time PCR. For each individual, the result of the genotype was compared to the known phenotype.

RESULTS

The FY*X allele frequency calculated in an Fy(a+b-) Caucasian blood donors population was 0.014. With the Caucasian and Black patient samples we found a complete correlation between PCR-RFLP and the real-time PCR method whatever the alleles combination tested. When the known phenotype was not correlated to FY*X genotype, the presence of the Fy(b) antigen was always confirmed by adsorption-elution.

CONCLUSION

The real-time technology method is rapid and accurate for FY genotyping. From now, we are able to detect the FY*X allele in all the alleles combinations studied. Regarding its significant frequency, the detection of the FY*X allele is useful for the correct typing of blood donors and recipients considering the therapeutic use of blood units and the preparation of test red blood cells for antibody screening.

Determination of 24 minor red blood cell antigens for more than 2000 blood donors by high-throughput DNA analysis

BACKGROUND

A "BeadChip" array permits reliable simultaneous DNA typing of single-nucleotide polymorphisms for minor blood groups. A high-throughput DNA analysis was studied as a routine method of phenotype prediction and software was developed to interpret and analyze the large volume of data points.

STUDY DESIGN AND METHODS

DNA was extracted from whole blood of donors of known phenotypes and self-identified ethnicity. Analysis of single-nucleotide polymorphisms (SNPs) associated with 24 antigens of 10 blood group systems was performed with BeadChips (BioArray Solutions), and the results were compared to historical serologic typings. Phenotypes were predicted for individual samples, and phenotype prevalence was determined for ethnicities. The BeadChip was expanded to incorporate SNPs that silence the S antigen, validated, and tested with 369 DNA samples. A time-motion analysis was conducted.

RESULTS

Results of BeadChip analyses were concordant with prediction of antigen negativity for 4,510 antigens. Eight discordant results were due to silencing of GYPB(S) and 16 were likely errors in recording serological results or data entry. The analyses produced 19,457 antigen-negative typings not serologically defined, identified 21 rare donors (Co(a-b+) [n = 1], Jo(a-) [n = 6], S-s-[n = 12], and K+k-[n = 2]), and determined allele frequencies and antigen prevalence for four ethnicities. The expanded panel detected 30 SS, 235 ss, 100 Ss, and 4 U- samples. The format processes 192 DNA samples (two plates) per 8-hour shift per technician, including automated data analysis and report generation.

CONCLUSION

DNA analysis with BeadChip format, combined with computerized data entry and analysis, permits the prediction of minor blood group antigens.

Blood transfusions in athletes. Old dogmas, new tricks

Blood doping consists of any illicit means used to increase and optimize oxygen delivery to the muscles and includes blood transfusions, administration of erythropoiesis-stimulating substances, blood substitutes, natural or artificial altitude facilities, and innovative gene therapies. The use of blood transfusion, an extremely straightforward, practical and effective means of increasing an athlete's red blood-cell supply in advance of competition, became rather popular in the 1970s, but it has suddenly declined following the widespread use of recombinant human erythropoietin among elite endurance athletes. Most recently, following implementation of reliable tests to screen for erythropoiesis-stimulating substances, blood transfusions have made a strong resurgence, as attested by several positive doping tests. Doping by blood transfusion can be classified as homologous, where the blood is infused into someone other than the donor, and autologous, where the blood donor and transfusion recipient are the same. The former case produces more clinically relevant side effects, but is easily detectable using current antidoping protocols based on erythrocyte phenotyping by flow cytometry and, eventually, erythrocyte genotyping by DNA testing. Since the donor and recipient blood are identical in autologous blood doping, this is less risky, though much more challenging to detect. Indirect strategies, relying on significant deviations from individual hematological profiles following autologous blood donation and reinfusion, are currently being investigated. For the time being, the storage of athletes' blood samples to allow testing and sanctioning of guilty athletes once a definitive test has been introduced may represent a reliable deterrent policy.

Establishment of an HPA-1- to -16-typed platelet donor registry in China

In order to determine gene frequencies of human platelet antigen (HPA) and establish a panel of accredited HPA-1a, -2a, -4a, -5a and -6a-negative donors as well as an HPA-typed platelet donor registry, a total of 1000 Chinese donors of Han nationality (500 from north China and 500 from south China) were typed for HPA-1 through -16 using a DNA-based polymerase chain reaction with sequence-specific primers genotyping method. The gene frequencies of HPA-1b, -2b, -3b, -4b, -5b, -6bw, -10bw and -15b were 0.0060, 0.0485, 0.4055, 0.0045, 0.0140, 0.0135, 0.0005 and 0.4680, respectively. The HPA-7bw, -8bw, -9bw, -11bw, -12bw, -13bw, -14bw and -16bw alleles were not found. The HPA-2b and -5b homozygous donors were detected at low frequencies. The HPA mismatch probabilities potentially leading to alloimmunization in random platelet transfusion vary with a region from 0.1% to 37% depending on the distribution patterns of common and less common alleles in each system. This study provides a useful HPA-typed plateletpheresis donor registry in China and could improve platelet antibody detection and HPA-matched platelet transfusion in alloimmune thrombocytopenic patients.

Molecular testing for transfusion medicine

PURPOSE OF REVIEW

Molecular testing methods were introduced to the blood bank and transfusion medicine community more than a decade ago after cloning of the genes made genetic testing for blood groups, that is genotyping, possible. This review summarizes the progress made in the last decade in applying genotyping to prenatal practice and clinical transfusion medicine.

RECENT FINDINGS

Assays that target allelic polymorphisms prevalent in all populations are reproducible and highly correlated with red blood cell phenotype. For some blood groups, assays that detect silencing mutations are also required for accurate typing, and for ABO and Rh, multiple regions of the genes must be sampled. Genotyping is a powerful adjunct to serologic testing and is superior for typing transfused patients, for D-zygosity determination, for noninvasive fetal typing, and for antigen-matching in sickle cell patients.

SUMMARY

Implementation of molecular testing for transfusion medicine has been a conservative process and limited primarily to reference laboratory environments. With the development of high-throughput platforms, genotyping is poised to move into the mainstream, revolutionizing the provision of antigen-negative donor units. This will enable electronic selection of units antigen matched to recipients at multiple blood group loci, potentially eliminating alloimmunization and significantly improving transfusion outcomes.

KEL6 and KEL7 genotyping with sequence-specific primers

BACKGROUND

Although antibodies to Js(a) and Js(b) are clinically significant, reagent-quality anti-Js(a) and anti-Js(b) are not readily available. A sequence-specific primer-polymerase chain reaction (SSP-PCR) genotyping assay was tested that makes use of two single-nucleotide polymorphisms (SNPs) at positions 1910 and 2019 of KEL. These SNPs distinguish the gene encoding Js(a), KEL6; and Js(b), KEL7.

STUDY DESIGN AND METHODS

Four primer sets that selectively amplified KEL6 and KEL7 from genomic DNA were developed. Two sets detected the SNP at bp 1910 and two sets detected the bp 2019 SNP. KEL6 and KEL7 genotyping and Js(a) and Js(b) phenotyping results were compared among 64 subjects.

RESULTS

The SSP-PCRs were specific for KEL6 and KEL7 when testing DNA for three donors of known Js phenotype: Js(a+b-), Js(a-b+), and Js(a+b+). Genotyping results for the 1910 SNP were identical to the phenotyping results in all 64 subjects, but for the 2019 SNP, the genotyping and phenotyping results were identical for only 49 subjects. In 12 subjects with the Js(a-b+) phenotype, the 2019 SNP was heterozygous KEL6, KEL7; in 2 with Js(a-b+) and in 1 with Js(a+b+), the 2019 SNP was homozygous KEL6.

CONCLUSION

KEL 2019-bp SNP does not always correlate with the Js phenotype owing to the presence of an atypical KEL gene with a KEL7 polymorphism at 1910 and a KEL6 polymorphism at 2019. The KEL polymorphism at 2019 is silent and this allele yields a Js(a-b+) phenotype. Only analysis of the 1910-bp SNP can be used to genotype KEL6 and KEL7.

Diagnostic applications of microarrays

Microarrays were designed to monitor the expression of many genes in parallel, providing substantially more information than Northern blots or reverse transcription polymerase chain reaction analysing one or few genes at a time. The large sequencing projects provided the content for detailed expression studies under a variety of stimuli and conditions. The human genome project identified around 30 000 human genes. Estimated number of protein products is, however, 10-30 times higher, mainly due to the alternative splicing and post-translational modifications. The identification of gene functions requires both genomic and proteomic approaches, including protein microarrays, and numerous current microarray projects focus on deciphering gene expression patterns under a variety of conditions. Establishing the key genes and gene products for particular conditions opens the way for diagnostic applications using multiparameter, high-throughput assays. This format can also accommodate existing blood screening assays, potentially providing a single testing platform. This review considers the progress in diagnostic microarrays in a wider context of in vitro diagnostics field.

High-throughput molecular profiling of blood donors for minor red blood cell and platelet antigens

BACKGROUND

ABO and D phenotyping of both blood donors and patients receiving transfusions is routinely performed by blood banks to ensure compatibility. These analyses are performed by antibody-based agglutination assays. Blood is not tested for minor blood group antigens on a regular basis, however, because of cost and time constraints. This can result in alloimmunization of the patient against one to several minor antigens and may complicate future transfusions.

STUDY DESIGN AND METHODS

To address this problem, an assay has been generated on the GenomeLab SNPstream genotyping system to test simultaneously polymorphisms linked to 22 different blood antigens with donor's DNA isolated from minute amounts of white blood cells.

RESULTS

The results showed that both the error rate of the assay, as measured by the strand concordance rate, and the no-call rate were very low (0.1%). The concordance rate with the actual red blood cell (RBC) and platelet (PLT) serology data varied from 97 to 100 percent. Experimental or database errors as well as rare polymorphisms contributing to antigen conformation could explain the observed differences. These rates, however, are well above requirements because phenotyping and cross-matching will always be performed before transfusion.

CONCLUSION

Molecular profiling of blood donors for minor RBC and PLT antigens will give blood banks instant access to many different matched donors through the setup of a centralized data storage system.

Molecular genetics of RH and its clinical application

BACKGROUND

The RH genes RHD and RHCE encode two proteins that represent the clinically most important blood group system defined by the sequences of red cell membrane proteins. In the last five years the field has been moving from defining the underlying molecular genetics to applying the molecular genetics in clinical practice.

MATERIALS AND METHODS

The state of the current knowledge is briefly summarized using recent reviews and original work since 2000.

RESULTS

The RHD and RHCE genes are strongly homologous and located closely adjacent at the human chromosomal position 1p36.11. Part of the genetic complexity is explained by the clustered orientation of both genes with their tail ends facing each other. The SMP1 gene is located interspersed between both RH genes. Using additional genetic features of the RH gene locus, RHCE was shown to represent the ancestral RH position, while RHD is the duplicated gene. More than 150 alleles have been defined for RHD alone. They were classified based on antigenic and clinical properties into phenotypes like partial D, weak D and DEL. Among the D negative phenotype a large variety of non-functional alleles were found. The frequencies of these distinct alleles vary widely among human populations, which has consequences for clinical practice.

CONCLUSION

Rhesus is a model system for the correlation of genotype and phenotype, facilitating the understanding of underlying genetic mechanisms in clustered genes. With regard to clinical practice, the genetic diagnostics of blood group antigens will advance the cost-effective development of transfusion medicine.

Rapid and/or high-throughput genotyping for human red blood cell, platelet and leukocyte antigens, and forensic applications

BACKGROUND

Traditionally, transfusion medicine, platelet and human leukocyte antigen (HLA) typing, and forensic medicine relied on serologic studies.

METHODS

In recent years, molecular testing on nucleic acids has been increasingly applied to these areas. Although conventional molecular diagnostic methods such as PCR-sequence-specific priming, PCR-restriction fragment-length polymorphism, PCR-single-strand conformation polymorphism, sequence-based typing, and DNA fingerprinting have been shown to perform well, their use is limited by long turnaround times, high cost, labor-intensiveness, the need for special technical skills, and/or the high risk of amplicon contamination. With advance of fast and/or high-throughput methods and platforms that often combine amplification and detection, a new era of molecular genotyping is emerging in these fields dominated by serology for a century. As new targets, short tandem repeats, mitochondrial DNA and Y-chromosome sequences were introduced for forensic applications. This article reviews the current status of the application of rapid and/or high-throughput genotyping methods to these areas.

RESULTS

The results are already promising with real-time PCR, pyrosequencing, microarrays, and mass spectrometry and show high concordance rates with classic serologic and earlier manual molecular diagnostic methods. Exploration of other emerging methodologies will likely further enhance the diagnostic utility of molecular testing in these areas.