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. 2015 Oct 29;14(2):160–167. doi: 10.2450/2015.0124-15

Evaluation of red blood cell and platelet antigen genotyping platforms (ID CORE XT/ID HPA XT) in routine clinical practice

Kirstin Finning 1, Radhika Bhandari 2, Fiona Sellers 2, Nicoletta Revelli 3, Maria Antonietta Villa 3, Eduardo Muñiz-Díaz 4, Núria Nogués 4,
PMCID: PMC4781785  PMID: 26674823

Abstract

Background

High-throughput genotyping platforms enable simultaneous analysis of multiple polymorphisms for blood group typing. BLOODchip® ID is a genotyping platform based on Luminex® xMAP technology for simultaneous determination of 37 red blood cell (RBC) antigens (ID CORE XT) and 18 human platelet antigens (HPA) (ID HPA XT) using the BIDS XT software.

Materials and methods

In this international multicentre study, the performance of ID CORE XT and ID HPA XT, using the centres’ current genotyping methods as the reference for comparison, and the usability and practicality of these systems, were evaluated under working laboratory conditions. DNA was extracted from whole blood in EDTA with Qiagen methodologies. Ninety-six previously phenotyped/genotyped samples were processed per assay: 87 testing samples plus five positive controls and four negative controls.

Results

Results were available for 519 samples: 258 with ID CORE XT and 261 with ID HPA XT. There were three “no calls” that were either caused by human error or resolved after repeating the test. Agreement between the tests and reference methods was 99.94% for ID CORE XT (9,540/9,546 antigens determined) and 100% for ID HPA XT (all 4,698 alleles determined). There were six discrepancies in antigen results in five RBC samples, four of which (in VS, N, S and Doa) could not be investigated due to lack of sufficient sample to perform additional tests and two of which (in S and C) were resolved in favour of ID CORE XT (100% accuracy). The total hands-on time was 28–41 minutes for a batch of 16 samples. Compared with the reference platforms, ID CORE XT and ID HPA XT were considered simpler to use and had shorter processing times.

Discussion

ID CORE XT and ID HPA XT genotyping platforms for RBC and platelet systems were accurate and user-friendly in working laboratory settings.

Keywords: BLOODchip® ID, genotyping, platelets, red blood cells

Introduction

Knowledge of the molecular bases of most blood group systems has given rise to the development of DNA-based methods for blood group determination1. In recent years, several multiplex molecular testing platforms have become available to predict phenotypes based on blood group genetics2. DNA-based techniques can provide blood typing results in cases in which antisera are not available, predict weak and variant antigens and help resolve ABO discrepancies3. High-throughput tools have the potential for application in mass-scale testing of donor blood1,4,5.

Immunohematology reference laboratories currently employ a variety of techniques for blood group typing, ranging from classical serology to polymerase chain reaction (PCR)-based assays to DNA biosensor/microarray-based platforms1. Given that novel mutations are continually being identified, test kits must be upgraded regularly to detect the more relevant genetic variations as new information becomes available. Blood group genotyping techniques are winning their place in blood and transfusion centres, not only by helping to resolve serology discrepancies but by overcoming the limitations of haemagglutination assays610. Moreover, the use of DNA-based techniques may be particularly important in the management of multi-transfused patients who become alloimmunised due to incomplete matching of blood groups11,12.

BLOODchip® ID (Progenika Biopharma, a Grifols Company, Derio, Spain) is the second-generation version of a molecular genotyping platform that uses Luminex® xMAP technology (Luminex Corporation, Austin, TX, USA) to identify red blood cell (RBC) antigens (ID CORE XT) and human platelet antigens (HPA) (ID HPA XT). With respect to the capabilities of previous generation platforms1316, BLOODchip® ID has an optimised kit configuration, expanded antigen coverage, improved software and reduced processing time. ID CORE XT uses purified genomic DNA for simultaneous identification of multiple allelic variants encoding the most important RBC antigens of the Rh, Kell, Kidd, Duffy, MNS, Diego, Dombrock, Colton, Cartwright and Lutheran systems; 29 single nucleotide polymorphisms are analysed that determine 37 antigens of these ten blood group systems. ID HPA XT uses purified genomic DNA for simultaneous identification of multiple allelic variants of the major human platelet systems HPA-1-11 and HPA-15; 13 single nucleotide polymorphisms are analysed for identification of 18 HPA. The BLOODchip® ID platform also includes BIDS XT software for data interpretation, storage, search and retrieval. BLOODchip® ID was recently shown to have similar accuracy as the OpenArray® real-time PCR system (100 vs 99.93%), while offering advantages in terms of results interpretation and processing capabilities17.

Here we report on a European multicentre study conducted in immunohematology reference laboratories in which the performance of ID CORE XT and ID HPA XT was compared with the centres’ current genotyping methods for identification of human erythrocyte/platelet antigens.

Materials and methods

This multicentre study was conducted over a 4-week period in May-June 2013 at four European immunohaematology reference laboratories in Italy (Milan), Spain (Barcelona) and the United Kingdom (Bristol, Aberdeen). All participating centres had broad experience of blood group genotyping using diverse molecular techniques and platforms.

The objectives of the study were: (i) to evaluate the performance of ID CORE XT and ID HPA XT, taking as the reference for comparison the centres’ current genotyping methods used previously to determine human erythrocyte/platelet antigens; and (ii) to evaluate the practicality and usability of ID CORE XT and ID HPA XT under actual usage conditions.

Reference methods for comparison with ID CORE XT included: HEA BeadChip® (BioArray Solutions, Warren, NJ, USA), BLOODchip® Reference (Progenika Biopharma, a Grifols company, Derio, Spain), IDCore+ (Progenika Biopharma, a Grifols Company, Derio, Spain), in-house TaqMan assays, in-house PCR-sequence-specific priming (PCR-SSP) and serology.

Reference methods for comparison with ID HPA XT included HPA BeadChip®, ID HPA (Progenika Biopharma), BLOODchip® Reference, and in-house or commercial PCR-SSP.

Sample handling procedures

All equipment and materials required for evaluations were used according to the manufacturers’ instructions. Samples that had been previously genotyped/phenotyped using the centres’ reference methods were tested using ID CORE XT and ID HPA XT. Depending on the laboratory, samples were processed using either a Veriti or GeneAmp 9700 thermocycler from Applied Biosystems (Life Technologies Corporate, NY, USA), and were analysed in the Luminex® 100/200 System.

DNA specimens were obtained from whole blood in EDTA (or from buffy coat for some ID HPA XT tests). Methods of DNA extraction were QIAamp Blood columns or the automated extractors Qiacube and QiaSymphony (all from Qiagen, Hilden, Germany) depending on the centre, with DNA elution buffer: AE (10 mM Tris Cl; 0.5 mM EDTA pH 9.0); ATE (10 mM Tris-HCl, 0.1 mM EDTA, 0.04% sodium azide pH 8.3); or water. Extracted DNA was kept under storage conditions (usually −20 ºC) until testing. Up to three thaws/freezes were allowed. Samples older than those obtained during the study period were eligible for use, either because they carried a rare phenotype or because they corresponded to a population potentially carrying polymorphisms of interest.

Within the study setting, samples selected for DNA testing had previously been typed for as many RBC and/or HPA systems as possible and the cohort of samples had to cover as many antigen specificities and/or genotypes as possible, including low frequency rare variants as well as heterozygous and homozygous specimens. Data collected for each sample included: the specimen from which DNA was extracted, method of DNA extraction, date of extraction, storage conditions (temperature, dilution media-buffer or water, number of thaws/freezes), DNA purity (OD260/280 and OD260/230), DNA concentration and type of sample (patient or donor).

A total of 96 samples were processed per assay: 87 testing samples plus five positive controls (DNA from cell lines provided by the manufacturer) and four negative controls (DNA-free water). The reference laboratories in Milan and Barcelona evaluated both ID CORE XT and ID HPA XT. In the UK, the Bristol laboratory evaluated ID CORE XT and the Aberdeen laboratory evaluated ID HPA XT. An initial batch of eight samples was tested as a training exercise; these samples included two positive controls and one negative control. The remaining 88 samples were processed in three batches as follows: 1×16 samples, 1×24 samples and 1×48 samples. Each batch included one positive control and one negative control.

Evaluation parameters

For each sample, the following data were collected for each RBC and HPA system analysed: the reference method used and associated result; the genotype result obtained with ID CORE XT and ID HPA XT and the predicted phenotype; the presence/absence of discrepancies between the reference method and ID CORE XT or ID HPA XT. Comparisons between methods were collated by antigen within each RBC or HPA system and reported as the number of “no calls” (inability of the genotyping platform to assign a phenotype; % calls), discrepancy with reference method, predicted phenotype result, and percentage of agreement (based on the number of samples tested per phenotype). Possible contamination was assessed on the basis of the number of correct/incorrect negative controls.

Samples with a “no call” result were tested again when possible, and both results were reported. Samples associated with “no call” results and discrepancies were sent to the manufacturer’s reference laboratory for further investigation.

The hands-on time to process a sample batch was recorded for each individual step of the procedure: amplification, hybridisation, labelling, Luminex® processing, and data analysis.

The usability and practicality of the ID CORE XT and ID HPA XT platforms were evaluated at the Bristol, Aberdeen and Barcelona sites by means of a questionnaire which covered aspects relating to the test procedure, kit shipment and storage conditions, software analysis (other than BIDS XT), BIDS XT (CD and configuration, process, reports, data and graphics), database information and registration, and a general overview of the products.

Results

In total, 522 tests were performed, 261 with ID CORE XT (to determine 37 RBC antigens per sample, equating to 9,546 antigens in total) and 261 with ID HPA XT (to determine 18 allelic variants per sample, equating to 4,698 alleles in total). The DNA concentration range was 12–200 ng/μL for ID CORE XT and 9-319 ng/μL for ID HPA XT. As three ID CORE XT samples could not be evaluated because of low DNA concentration, results for 258 samples are presented.

No cross contamination occurred during sample processing with ID CORE XT and ID HPA XT. Positive and negative controls were correct in all batches tested at the participating centres. Global agreement between ID CORE XT/ID HPA XT and the reference methods was close to 100%. The two discrepancies investigated were resolved in favour of the tested system.

ID CORE XT assay

Of the 258 evaluable samples tested with ID CORE XT, 55% were derived from blood donors and 45% from patients. The array of tested samples included a number of low frequency antigen variants and uncommon phenotypes such as Coa−, CW+, Dib−, Joa−, Lub−, Mia+ and RHCE*CeRN (1 sample); k−, Kpa+, r’s, GYPB*S_ null(230T), GYPB*deletion, GYPB*S_null(IVS5+5T) and RHCE*ceAR (2–5 samples); Cob+, Dia+, K+, Jsa+, hrB−, Lua+, Yta−, FY*X and RHCE*ce[733G,1006T] (6–15 samples); Dob−, Ytb+, s−, V+, VS+, FY*B_GATA and RHCE*ce[733G] (>15 samples). Details of all RBC antigens detected are shown in Table I.

Table I.

ID CORE XT: antigens and percent agreement (N=258 evaluable samples).

Red blood cell system Antigens Discrepancy (n) Predicted phenotype
Positive Negative
n % agreement n % agreement
Rh C (RH:2) * 1 137 100 121 99.2
E (RH:3) * 0 38 100 220 100
c (RH:4) * 0 184 100 74 100
e (RH:5) * 0 240 100 18 100
CW (RH:8) 0 1 100 257 100
V (RH:10) 0 24 100 234 100
hrS (RH:19) 0 258 100 0 100
VS (RH:20) 1 29 100 229 99.6
hrB (RH:31) 0 245 100 13 100
Kell K (KEL:1) 0 11 100 247 100
k (KEL:2) 0 256 100 2 100
Kpa (KEL:3) 0 5 100 253 100
Kpb (KEL:4) 0 258 100 0 100
Jsa (KEL:6) 0 12 100 246 100
Jsb (KEL:7) 0 258 100 0 100
Kidd Jka (JK:1) 0 213 100 45 100
Jkb (JK:2) 0 168 100 90 100
Duffy Fya (FY:1) 0 136 100 122 100
Fyb (FY:2) 0 161 100 97 100
MNS M (MNS:1) 0 196 100 62 100
N (MNS:2) 1 185 99.5 73 100
S (MNS:3) 1, 1 129 100 129 98.4
s (MNS:4) 0 227 100 31 100
U (MNS:5) 0 254 100 4 100
Mia (MNS:7) 0 1 100 257 100
Diego Dia (DI:1) 0 6 100 252 100
Dib (DI:2) 0 257 100 1 100
Dombrock Doa (DO:1) 1 163 100 95 98.9
Dob (DO:2) 0 223 100 35 100
Hy (DO:4) 0 258 100 0 100
Joa (DO:5) 0 257 100 1 100
Colton Coa (CO:1) 0 257 100 1 100
Cob (CO:2) 0 11 100 247 100
Cartwright Yta (YT:1) 0 251 100 7 100
Ytb (YT:2) 0 27 100 231 100
Lutheran Lua (LU:1) * 0 15 100 243 100
Lub (LU:2) * 0 257 100 1 100
*

No previous antigen typing information;

discrepancy could not be confirmed due to lack of sufficient sample to perform additional tests (not taken into account in the accuracy calculation).

The reference method used for comparison with ID CORE XT was HEA BeadChip® in 42% of samples, TaqMan assays (26%), BLOODchip® Reference (15%), IDCore+ (10%) and PCR-SSP/serology (7%).

No substantial differences were observed in the results obtained using ID CORE XT and the reference methods; percent agreement was 99.94% (9,540 concordant antigens out of 9,546), with a 99.2% rate of calls (256 out of 258 samples) (Table I). There were two “no call” signals in Rh that were attributed to human error (preparing the DNA concentration or in the pre-PCR stage).

For ten samples non-concordances were observed between ID CORE XT and the reference methods. Five of these were not taken into account in the percent agreement and correct calls calculations because three were caused by human and/or methodological errors (involving multiple antigens), which could be furtherly corrected, and two were caused by an incorrect predicted phenotype output algorithm (involving Dob antigen) which was corrected by updating the software.

For five samples there were discrepancies between ID CORE XT and the reference methods. Three of these samples (involving VS, N, S and Doa antigens; see Table I) could not be investigated due to lack of sufficient sample to perform additional tests and were not, therefore, taken into account in the accuracy calculation. In the two discrepancies that were investigated, ID CORE XT provided the correct result (100% accuracy); one in S antigen typing and one in C antigen typing (Table I). DNA sequencing of the sample with the discrepant S typing result indicated that the sample’s genotype was heterozygous Ss. The S+s+ predicted phenotype agreed with the ID CORE XT result, in contrast to the original S− result obtained with the reference method (HEA BeadChip®). The sample with the discrepant C result yielded a homozygous RHc/RHc genotype in ID CORE XT and a C+c+ predicted phenotype, in contrast to the C−c+ predicted phenotype obtained with the reference method (TaqMan assay) which analyses a C-specific intron 2 insert and the c-specific exon 2 sequence. ID CORE XT found this sample negative for a RHCE*C allele but positive for RHD*r’s, a variant known to encode a form of C antigen. The correct predicted phenotype of the sample was thus C+c+.

ID HPA XT assay

Of the 261 samples tested with ID HPA XT, most were from blood donors (78%) or were patients’ samples (21%) that had been referred to the laboratories for diagnostic purposes (e.g. neonatal alloimmune thrombocytopenia or platelet refractoriness). A few workshop samples (1%) carrying infrequent alleles were also used. Several samples (around 10%) with uncommon genotypes such as HPA1b/1b, HPA2b/2b, HPA4a/4b, HPA6a/6b, HPA6b/6b and HPA9a/9b were included in the evaluation. Details of all HPA alleles detected are shown in Table II.

Table II.

ID HPA XT: alleles and percent agreement (N=261 samples).

HPA Alleles Discrepancy (n) Predicted phenotype

Positive Negative


n % agreement n % agreement
HPA-1 HPA1-a 0 236 100 25 100
HPA1-b 0 92 100 169 100

HPA-2 HPA2-a 0 251 100 10 100

HPA2-b 0 54 100 207 100

HPA-3 HPA3-a 0 216 100 45 100

HPA3-b 0 161 100 100 100

HPA-4 HPA4-a 0 261 100 0 100

HPA4-b 0 2 100 259 100

HPA-5 HPA5-a 0 251 100 10 100

HPA5-b 0 56 100 205 100

HPA-6 HPA6-bw 0 3 100 258 100

HPA-7 HPA7-bw 0 0 100 261 100

HPA-8 HPA8-bw 0 0 100 261 100

HPA-9 HPA9-bw 0 6 100 255 100

HPA-10 HPA10-bw 0 1 100 260 100

HPA-11 HPA11-bw 0 0 100 261 100

HPA-15 HPA15-a 0 155 100 106 100

HPA15-b 0 197 100 64 100

The reference method used for comparison was PCR-SSP in 52% of samples (18% in-house and 34% commercial), HPA BeadChip® (33%), ID HPA (8%) and BLOODchip® Reference (7%).

Two samples known to carry mutations that can interfere with some HPA genotyping approaches, (262T>C) in the ITGB3 gene and (468C>G) in the GPIb alpha gene, were tested and the ID HPA XT genotyping results were correct in each instance.

There were no significant differences in the results obtained using ID HPA XT and the reference methods; the results were 100% concordant (all 4,698 alleles concordant), with a 99.6% rate of calls (260 out of 261 samples) (Table II). There was a “no call” result in HPA-3 that was resolved according to protocol when a repeat test using the same assay showed a valid result that agreed with the historical result.

There were three samples for which there was non-concordance between ID HPA XT and the reference methods (observed in HPA-1 and HPA-2), all of which were due to technical, protocol or processing errors that could be furtherly corrected and were not, therefore, considered for the percent agreement calculations.

Usability and practicality of the ID CORE XT and ID HPA XT platforms

Depending on the number of samples in the batch, the total hands-on time required to process a batch ranged from 28–41 minutes (16 samples) to 68–91 minutes (48 samples) (Table III).

Table III.

Hands-on time (in minutes; range) to process batches using the ID HPA XT and ID CORE XT platforms.

Procedural step Batch size

16 samples 24 samples 48 samples
Amplification 10–12 15–16 25–30
Hybridisation 5–6 5–7 10–12
Labelling 2–8 3–5 6–8
Luminex® set up 6–10 10–15 15–25
Data analysis 5 10 15–16

The laboratories were generally uniformly satisfied with the usability and practicality of the ID CORE XT and ID HPA XT platforms and their fit within the normal laboratory routine (Table IV). No system malfunctions were reported. In particular, exclusion of the filtration step in the newer-generation assay was viewed as an improvement as it simplified the procedure and reduced overall assay time. The processing time of less than 4 hours to obtain results was shorter with the ID CORE XT and ID HPA XT platforms than with the reference platforms and was considered useful for diagnostic purposes. Laboratories commented that a batch run of 96 samples is beyond current requirements, but may be appropriate if the type of services offered were to change (e.g. to include donor typing). A delayed connection between the Luminex® and BIDS XT software occurred in one batch and results were obtained through a Product Specialist. The problem was fixed in the subsequent version of the software. Otherwise the software was considered to be user-friendly overall and superior to previous versions.

Table IV.

Usability and practicality of ID CORE XT and ID HPA XT platforms. Survey results from participating centres.

Topic Questions included Answers from users

N % positive % negative
Procedure 12 60 96.7 3.3
Kit shipment and storage conditions 5 25 92.0 8.0
Software analysis 6 30 83.3 16.7
BIDS XT - CD and configuration 8 40 92.5 7.5
Database information and registration 6 30 100 0
BIDS XT process 8 40 92.5 7.5
BIDS XT reports, data and graphics 8 40 82.5 17.5
Luminex® interface 2 10 60.0 40.0

Discussion

The current study was conducted in four European immunohaematology laboratories to assess the performance of the ID CORE XT and ID HPA XT genotyping platforms and to evaluate their usability and practicality under working conditions. A total of 522 tests were performed and 519 were evaluable: 258 with ID CORE XT to determine 9,546 RBC antigens and 261 with ID HPA XT to determine 4,698 alleles. Both platforms were accurate and user-friendly having taken the centres’ current genotyping methods as reference for comparison.

In Europe, the BLOODchip® Reference system (based on glass microarray technology) has been assessed for comprehensive genotyping of individuals for all clinically significant blood groups. BLOODchip® Reference was determined to be more accurate than serology, especially when applied to the Rh system, and may be applied as a replacement technology for blood grouping18,19. The results obtained in this study using BLOODchip® ID based on Luminex® xMAP technology (ID CORE XT and ID HPA XT) were accurate, with near 100% agreement with respect to the reference methods and 100% of correct results in the cases of discrepancy.

The discrepancy that was encountered in S antigen typing was resolved by sample sequencing in favour of ID CORE XT. In another sample with a C antigen typing discrepancy, ID CORE XT was superior to the reference method in predicting a C+c+ phenotype for RhCE, although it was expected to give a C+ with a comment on the altered C antigen expression, rather than simply a C+ call. ID CORE XT found this sample to carry RHD*r’s, which explains the apparent discrepancy between the C− genotype and the C+ phenotype. The reference method does not look at position RHCE1006 (associated with r’s) and it is accepted that some patients are mistyped C− and not C+(wk)20 because this is the preferable call to prevent them from receiving C+ blood.

In addition to accuracy, both simplicity and processing time are important aspects to ensure that a blood group typing methodology is practical for laboratories to work with routinely. It is known that, compared with serology, genotyping takes a longer time to perform21. In addition, automated high-throughput genotyping methods require test-specific technical expertise22. The ID CORE XT and ID HPA XT platforms have simplified and shortened the overall assay procedure as confirmed by the participating laboratories. A processing time of approximately four hours, inclusive of hands-on time of about 30–40 minutes for a batch of 16 samples, is suitable for diagnostic purposes and fits in with laboratory workflow, freeing up time to perform other assays. The ID CORE XT and ID HPA XT platforms had flexibility to accommodate the different number of samples that may need to be processed simultaneously and the various levels of throughput offer scope for laboratories to match their services provided with the needs of the community.

The near 100% global concordance indicated that differences among laboratories in terms of how samples were extracted, stored and prepared had no influence on the results. Although the concentration of DNA required in the study was relatively high, the satisfactory results achieved when samples with a lower concentration were tested indicated that ID CORE XT and ID HPA XT are robust over a wide range of DNA concentrations and purity. Inclusion of DNA samples that carried a rare phenotype or that corresponded to a population potentially carrying a polymorphism of interest resulted in consistent and robust results with both ID CORE XT and ID HPA XT.

Conclusions

In conclusion, the new ID CORE XT and ID HPA XT platforms provided broader coverage than previous versions and were found to be highly accurate in comparison with the centres’ current reference methods in a working laboratory setting. The ID CORE XT and ID HPA XT platforms also had improved functionality, including a shorter processing time, compared with the reference methods. The system software (BIDS XT) was generally considered user-friendly, with some features, such as sample traceability and database searches, highlighted as being particularly useful for some blood centres.

Acknowledgements

Elisenda Farssac and Montserrat Ibañez from the Banc de Sang i Teixits are acknowledged for their technical support.

Footnotes

Funding and resources

This study was supported by Grifols. Writing and editorial assistance was provided by Content Ed Net (with funding from Grifols) and Jordi Bozzo, PhD CMPP (Grifols).

Authorship contributions

KF, RB, FS, NR, MAV, and NN contributed to the design of the work and acquisition of data; EMD and NN analysed and interpreted the data; KF, RB, FS, NR, MAV, and NN drafted the work; EMD and NN critically revised the work for intellectual content. All Authors approved the final version of the manuscript to be published.

The Authors declare no conflicts of interest.

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