Simultaneous genotyping of human platelet antigen-1 to 17w by polymerase chain reaction sequence-based typing

Establishment and Application of a Multiplex PCR NGS Method for the Genotyping of HLA-Class I and HPA

Selecting compatible HLA-Class I and/or HPA platelets based on genotyping could alleviate immune platelet transfusion refractoriness (PTR). A fast and reliable method of HLA-Class I and HPA genotyping is necessary to construct a platelet donor bank with known HLA-Class I and HPA genotypes. Ten pairs of specific primers for HLA-A, HLA-B, HLA-C, HPA-1 through HPA-6w, HPA-15 and HPA-21w were designed. The appropriate fragments were optimised for amplification in a single multiplex reaction. After a cleanup step using paramagnetic beads, the amplicon library was prepared and sequenced. To validate the accuracy of the developed method, commercial NGS kits for the genotyping of HLA-A, HLA-B and HLA-C and the TaqMan real-time PCR method in-house for the genotyping of HPA-1 through HPA-6w, HPA-15 and HPA-21w were used to detect all the specimens in parallel. A total of 386 specimens were detected and the results of genotyping HLA-A, HLA-B, HLA-C and HPA-1 through HPA-6w, HPA-15 and HPA-21w were obtained simultaneously, which is 100% consistent between the two methods. Four new HLA alleles, HLA-A*11:451, HLA-A*30:01:26, HLA-B*39:201 and HLA-B*40:538, were also reconfirmed. Two novel SNVs, c.2671C > T and c.2681T > G, in the coding region of ITGA2B were detected, all of which are heterozygous in individuals. A novel NGS method based on multiplex PCR was established to detect HLA-Class I and HPA simultaneously, which is high-throughput, rapid and accurate and could be applied to build a platelet donor bank.

Human Platelet Antigens in Brazilian Multiethnic Populations: Occurrence of Regional Variation and Frequency in a Large Urban Center (Belo Horizonte)

Background

The frequency of human platelet antigens (HPA) varies according to ethnicity, which causes differences in the morbidity of alloimmune and autoimmune thrombocytopenic disorders in different populations. Studies on HPA frequencies in Brazil have reported differences among Brazilian populations produced by the diverse degrees of admixture throughout the country.

Methods

In the present study, we investigated the variation of HPA distribution in Brazil, compared with worldwide populations, and describe the frequencies of HPA-1, -2, -3, -5, and -15 in a large urban center in Southern Brazil (Belo Horizonte) based on a sample of blood donors.

Results

The principal component analysis and the dendrogram based on genetic distance revealed a clear relationship between Brazilian populations and the groups formed by European and African populations. The coefficients of variation for HPA allele frequencies suggest that Brazilian populations presented variations for HPA alleles comparable with the populations from continental groups. In Belo Horizonte, the allele a frequencies for HPA-1, -2, -3, -5 and -15 were 0.8575, 0.8400, 0.6225, 0.8525 and 0.5825 respectively. The genotypes with higher frequencies were a/a (72-74%), except for HPA-3 and -15, whose heterozygous a/b genotypes were shown to be more prevalent (43.5 and 44.5%, respectively).

Conclusion

We confirmed the heterogeneity of HPA antigens in Brazilian populations, reinforcing the importance of HPA panels composed of regional blood donors, or a national panel that contemplates the specificities of the different regions of the country, in order to provide support in platelet transfusions and to minimize the risks associated with HPA alloimmunization. The evaluation of HPA data from Belo Horizonte represents the initial step toward the development of a genotyped platelet donor registry in order to treat HPA alloimmunized patients in this region.

Assessment of HNA alloimmunisation risk in Northeastern Thais, Burmese and Karen

OBJECTIVES

This study aimed to determine human neutrophil antigen (HNA) frequency, estimate possible HNA incompatibilities and predict the risk of HNA alloimmunisation in the Northeastern Thai, Burmese and Karen populations.

BACKGROUND

Alloantibodies against HNA are implicated in a number of clinical conditions, including immune-mediated neutropenia and transfusion reactions.

METHODS

A total of 400 unrelated healthy Thais, 261 Burmese and 249 Karen was included in this study. DNA samples were typed for HNA-1, -3, -4 and -5 systems using polymerase chain reactions with sequence-specific primers (PCR-SSP).

RESULTS

In this cohort, HNA-1a was more prevalent than HNA-1b. Accordingly, the possible risk of HNA-1a alloimmunisation against HNA-1a is lower than HNA-1b (0·0802-0·1351 vs 0·2293-0·2497). This is in contrast to the situation reported in Caucasian and African populations. The predicted risk of HNA-3 incompatibility in Thais, Burmese and Karen were 28·09%, 30·66% and 22·77%, respectively. The possible risks of HNA-3a alloimmunisation were 0·0493 in Thais, 0·0608 in Burmese and 0·0196 in Karen, respectively. No individuals were found to be homozygous for HNA-4bb. The probability of developing alloantibodies against HNA-4a was low in these populations and every population in Asia. In contrast, the overall frequency of HNA-5bb homozygous individuals was high in this study, peaking at 0·192.

CONCLUSIONS

This is the first study that reported the allele frequencies of HNA-1, -3, -4, and -5 in a large sample of healthy unrelated individuals from ethnic Thais, Burmese and Karen. Our results indicated the high possible risk of HNA-1, -3 and -5 alloimmunisation in these populations.

Simultaneous genotyping of human platelet alloantigen-1 to 28bw systems by multiplex polymerase chain reaction sequence-based typing

BACKGROUND AND OBJECTIVES

Human platelet alloantigen (HPA) genotyping is important for the diagnosis and prevention the alloimmune platelet disorders. In this study, a simultaneous genotyping method for HPA-1 to -28bw systems was established using multiplex PCR-SBT and the frequencies of genotypes and alleles of HPA-1 to -28bw systems in the Zhejiang Han population were analysed.

MATERIALS AND METHODS

The specific primers were designed according to the nucleotide sequences of HPA-1 to 28bw systems which are located in ITGB3, GP1BA, ITGA2B, ITGA2, GP1BB and CD109, respectively. The multiplex PCR amplification systems were used, and then, the amplicons were purified and sequenced. A total of 335 healthy volunteer blood donors were detected.

RESULTS

The genotypes of ten reference samples from Platelet Immunology Workshop of ISBT were in concordance with the known genotypes. Among the 28 HPA systems, HPA a and b alleles were found in HPA-1 to 6w, HPA-15 and HPA-21w systems in the Chinese Han population, while only HPA aa genotype was detected in the other HPA systems. The frequencies of HPA-1a and HPA-1b were 0·993 and 0·007, with 0·943 and 0·057 for HPA-2a and HPA-2b, 0·527 and 0·473 for HPA-3a and HPA-3b, 0·997 and 0·003 for HPA-4a and HPA-4b, 0·991 and 0·009 for HPA-5a and HPA-5b, 0·980 and 0·020 for HPA-6wa and HPA-6wb, 0·508 and 0·492 for HPA-15a and HPA-15b and 0·994 and 0·006 for HPA-21wa and HPA-21wb.

CONCLUSIONS

One multiplex PCR-SBT method for HPAs was established and the data of the study could help to prevent and treat for alloimmune thrombocytopenia.

Simultaneous human platelet antigen genotyping and detection of novel single nucleotide polymorphisms by targeted next-generation sequencing

BACKGROUND

Twenty-nine human platelet antigen systems have been described to date, but the majority of current genotyping methods are restricted to the identification of those most commonly associated with alloantibody production in a clinical context. This can result in a protracted investigation if causative human platelet antigens are rare or novel. A targeted next-generation sequencing approach was designed to detect all known human platelet antigens with the additional capability of identifying novel mutations in the encoding genes.

STUDY DESIGN AND METHODS

A targeted enrichment, high-sensitivity HaloPlex assay was designed to sequence all exons and flanking regions of the six genes known to encode human platelet antigens. Indexed DNA libraries were prepared from 47 previously human platelet antigen-genotyped samples and subsequently combined into one of three pools for sequencing on an Illumina MiSeq platform. The generated FASTQ files were aligned and scrutinized for each human platelet antigen polymorphism using SureCall data analysis software.

RESULTS

Forty-six samples were successfully genotyped for human platelet antigens 1 through 29bw, with an average per base coverage depth of 1144. Concordance with historical human platelet antigen genotypes was 100%. A putative novel mutation in Exon 10 of the integrin β-3 (ITGB3) gene from an unsolved case of fetal neonatal alloimmune thrombocytopenia was also detected.

CONCLUSION

A next-generation sequencing-based method that can accurately define all known human platelet antigen polymorphisms was developed. With the ability to sequence up to 96 samples simultaneously, our HaloPlex design could be used for high-throughput human platelet antigen genotyping. This method is also applicable for investigating fetal neonatal alloimmune thrombocytopenia when rare or novel human platelet antigens are suspected.

Sequence-Based Typing for Platelet alloantigens

Human platelet antigen (HPA) typing is largely performed by use of DNA-based techniques in patients that require assessing the risk of HPA alloimmunization. In this chapter, HPA typing by sequencing-based typing (SBT) techniques is described.

Sequence analysis of the human fucosyltransferase 1 and 2 genes in Tibetan blood donors: identification of three novel alleles

BACKGROUND

The α(1,2)-fucosyltransferase gene 1 (FUT1) and 2 (FUT2), respectively, regulate H antigen synthesis in red blood cells and body fluids. Genetic polymorphisms of FUT1 and FUT2 are ethnically and geographically specific.

STUDY DESIGN AND METHODS

Healthy unrelated Tibetan blood donors (n = 200) from the Tibet Autonomous Region of China were recruited for this study. The entire FUT1 and FUT2 coding regions were amplified and sequenced. The haplotypes including novel single-nucleotide polymorphisms (SNPs) were determined by clone sequencing.

RESULTS

In Tibetans, the major FUT1 allele was wild-type allele with a frequency of 97.75%. One novel FUT1 allele was defined by a novel synonymous mutation (846T>G). The two most common FUT2 alleles were functional allele Se(357) with a frequency of 32.75% and nonfunctional allele se(357,385) with a frequency of 55%. Two new FUT2 alleles were found at low frequency. They were characterized by two novel SNPs on the basis of se(357,385) : 617 T>G (V206G) and 841 G>A (G281R).

CONCLUSION

Three new alleles in FUT1 and FUT2 genes were identified in the study. The allelic polymorphisms of FUT1 and FUT2 in Tibetans show a population-specific manner.

Comparison of a simple-probe real-time PCR and multiplex PCR techniques for HPA-1 to HPA-6 and HPA-15 genotyping

BACKGROUND

We aimed to compare HPA-1 to HPA-6 and HPA-15 genotyping results obtained by a simple-probe real-time polymerase chain reaction (PCR) technique with the multiplex PCR technique.

METHODS

Five hundred DNA samples from the Thai National Stem Cell Donor Registry (TSCDR) of the National Blood Centre, Thai Red Cross Society were included. Human platelet antigen (HPA) genotyping was performed by simple-probe real-time PCR and multiplex PCR techniques.

RESULTS

HPA-1, HPA-2, HPA-3, and HPA-4 genotyping results obtained by both techniques were in agreement. The misinterpretation of HPA-5, HPA-6, and HPA-15 genotypes was found in eight samples by simple-probe real-time PCR and HPA genotypes were confirmed by DNA sequencing. Two samples of HPA-5 were misinterpreted as HPA-5a5a instead of HPA-5a5b due to an NM_002203.3:c.1594A>C mutation (rs199808499) near the HPA-5 polymorphism (5' side). Five samples of HPA-6a6b were misinterpreted as HPA-6b6b because of an NM_000212.2:c.1545G>A mutation (rs4634) adjacent to the HPA-6 polymorphism (3' side). Interestingly, one sample of HPA-15a15b was misinterpreted as HPA-15b15b due to an NM_133493.1:c.2118C>A mutation near the HPA-15 polymorphism (3' side).

CONCLUSIONS

HPA genotyping results by two PCR techniques were compared. Incorrect assignments were found due to genetic variations near each HPA single nucleotide polymorphism. Therefore, to avoid false assignation, the use of two genotyping techniques is recommended.

Genotyping of human neutrophil antigens by polymerase chain reaction sequence-based typing

BACKGROUND

Genotyping for human neutrophil antigen (HNA) systems is required in the investigation of disorders involving alloimmunisation to HNA. We established a polymerase chain reaction sequence-based typing method for genotyping HNA and determined the genotype and allele frequencies of HNA in the Zhejiang Han population of China.

MATERIALS AND METHODS

Four hundred, healthy unrelated Zhejiang Han individuals were recruited. Specific primers for HNA were designed and the polymerase chain reaction amplification conditions were optimised. Amplification amplicons were purified with enzyme digestion and then sequenced.

RESULTS

The frequencies of the FCGR3B*01 and FCGR3B*02 alleles were 0.613 and 0.387; no FCGR3B*03 allele was found. The frequencies of the SLC44A2*1 and SLC44A2*2 alleles were 0.654 and 0.346, respectively, while the frequencies of the ITGAL*1 (HNA-5a) and ITGAL*2 (HNA-5b) alleles were 0.896 and 0.104. Only ITGAM*1 (HNA-4a) allele was found in this study. Six single nucleotide polymorphisms were confirmed on sequenced regions separate from HNA polymorphisms, including FCGR3B (IVS3+39G>A and IVS3+52G>A), CD177(172A>G), SLC44A2 (IVS5-44A>G and IVS7-15T>C) and ITGAM (IVS3+118T>C).

DISCUSSION

The polymerase chain reaction sequence-based typing method for genotyping HNA is reliable. These data of HNA alleles frequencies could contribute to the analysis of alloimmunisation to HNA in China.

Frequency of human platelet antigens in oncohematological patients with thrombocytopenia and the probability of incompatibility to platelet transfusions

OBJECTIVE

The objective of this study was to evaluate the frequencies of human platelet antigens in oncohematological patients with thrombocytopenia and to analyze the probability of their incompatibility with platelet transfusions.

METHODS

Platelet antigen genotyping was performed by sequence-specific primer polymerase chain reaction (SSP-PCR) for the HPA-1a, HPA-1b, HPA-2a, HPA-2b, HPA-3a, HPA-3b, HPA-4a, HPA-4b, HPA-5a, HPA-5b; HPA-15a, HPA-15b alleles in 150 patients of the Hematology Service of the Hospital das Clínicas (FMUSP).

RESULTS

THE ALLELE FREQUENCIES FOUND WERE: HPA-1a: 0.837; HPA-1b: 0.163; HPA-2a: 0.830; HPA-2b: 0.170; HPA-3a: 0.700; HPA-3b: 0.300; HPA-4a: 1; HPA-4b: 0; HPA-5a: 0.887; HPA-5b: 0.113; HPA-15a: 0.457 and HPA-15b: 0.543.

CONCLUSIONS

Data from the present study showed that the A allele is more common in the population than the B allele, except for HPA-15. This suggests that patients homozygous for the B allele are more predisposed to present alloimmunization and refractoriness to platelet transfusions by immune causes. Platelet genotyping could be of great value in the diagnosis of alloimmune thrombocytopenia and to provide compatible platelet concentrates for these patients.

High-throughput simultaneous genotyping of human platelet antigen-1 to -16 by using suspension array

BACKGROUND

Comprehensive and accurate detection of human platelet antigens (HPAs) plays a significant role in diagnosis and prevention of the platelet (PLT) alloimmune syndromes and ensuring clinical safety of patients undergoing PLT transfusion. The majority of the available methods are incapable of performing high-throughput simultaneous detection of HPA-1 to -16, and the accuracy of many methods needs to be further enhanced.

STUDY DESIGN AND METHODS

We have developed a new HPA-genotyping method for simultaneous detection of HPA-1 to -16 based on suspension array technology. A total of 216 samples from Chinese Han donors in Xi'an were genotyped using the developed method, and all the samples again were genotyped using polymerase chain reaction (PCR) sequence-based typing (PCR-SBT), which is considered the gold standard.

RESULTS

All 216 samples were successfully genotyped for HPA-1 to -16 using both our method and PCR-SBT. Results showed that the genotype and allele frequencies obtained using our method were fully consistent with those obtained using PCR-SBT.

CONCLUSION

Our method provides accurate, high-throughput, and simultaneous genotyping of HPA-1 to -16 and will serve as the foundation for large-scale clinical genotyping of HPAs and for the establishment of an HPA-typed PLT donor registry.

Human platelet antigen genotyping and expression of CD109 (human platelet antigen 15) mRNA in various human cell types

CD109 gene encodes a glycosylphosphatidylinositol-linked glycoprotein found in a subset of platelets and endothelial cell, and human platelet antigen (HPA) 15 is found on CD109. We evaluated the HPA genotype and/or the CD109 mRNA expression on two peripheral blood stem cells (PBSC), two peripheral bloods (PB), 12 granulocyte products, natural killer (NK)-92, B-lymphocyte (CO88BV59-1), K-562 leukemia cell line, human embryonic stem cell (hESC), and human fibroblasts (HF). HPA genotyping was performed by SNaPshot assay and CD109 mRNA expression was evaluated by real-time PCR with SYBR green and melting curve analysis. Genotype HPA-15a/-15a was found in PBSC#1 and two granulocyte products, and HPA-15a/-15b was found in PBSC#2, eight granulocyte products, NK-92, K-562, hESC, and HF, and HPA-15b/-15b was found in two granulocyte products. CD109 mRNA expression was highly increased in HF and increased in CD34+ and CD34- PBSCs and some granulocyte products, compared to the PB. However, the increase of expression level varied among the PBSC and granulocyte products. The CD109 mRNA expression of NK-92, K-562, hESC, and CO 88BV59-1 was not detected. HPA genotype was evaluated in various cells and the expression of CD109, which contains HPA 15, was different among cell lines and high in HF and PBSCs.

Prevalence of the HPA-18w to -21w alleles in the Chinese Han population

Recently, four new platelet alloantigen (HPA) systems HPA-18w to-21w were identified. However, genotyping for HPA-18w to -21w alleles was rarely reported. Here, we established a polymerase chain reaction sequence-based typing (PCR-SBT) method and investigated the distribution of HPA-18w to -21w alleles in the Chinese Han population. The specific primers of HPA-18w, -19w, -20w and -21w were designed, and the PCR products were bidirectionally sequenced. 855 randomly selected platelet donors were genotyped for HPA-18w to -21w with the PCR-SBT method. The results showed that all individuals were monomorphic for HPA-18w to HPA-20w with a/a homozygous frequency of 1.0 and absence of HPA-18bw to -20bw alleles. The frequencies of the HPA-21a/21a and HPA-21a/21b genotypes were 0.981(839/855) and 0.019(16/855), respectively. Seven mutations were confirmed on sequenced region separate from HPA polymorphisms, including ITGA2 (IVS17+48G>A and IVS17+72G>A), ITGA2B (IVS19-26C>G) and ITGB3 (IVS4+234C>T, IVS11-19 T>C, IVS11-104T>C and GT repeats from IVS11-131 to IVS11-109). These data will provide useful information for diagnosis, prevention and treatment of alloimmune thrombocytopaenia.

Human platelet antigen allele frequencies and new mutations on platelet glycoprotein genes in the Chinese Han population

BACKGROUND AND OBJECTIVES

The frequencies of human platelet antigens (HPAs) vary between different populations. In this study, we determined the HPA allele frequencies in the Chinese Han population and identified situation of incompatibility possibly leading to alloimmunisation.

METHODS

A total of 750 volunteer blood donors of the Chinese Han population were genotyped for HPA-1 to -17w systems. HPA genotyping was determined by polymerase chain reaction sequence-based typing.

RESULTS

Among the 17 HPA systems, the allele frequency is different from other populations. We noted the absence of HPA-7bw to HPA-14bw, HPA-16bw and HPA-17bw alleles in the population. The estimated incompatibility probabilities regarding platelet antigens 1 to 6w and 15 systems after transfusion of random donor platelet were from 0·004 to 0·373. Thirteen glycoprotein alleles were observed in the population. In addition, we identified 16 novel mutations on the glycoprotein genes separated from HPA polymorphisms, including GP1BA (517-525delAAC), ITGA2B (2722C>T and IVS26+85T>C), ITGA2 (1521C>T, 2474T>G and IVS20+10 G>C), ITGB3 (1476G>A, IVS10+19C>A, 1813G>A, IVS11+21G>A, IVS11+152A>G and IVS11-104T>C), GP1BB (IVS1-79G>A, IVS1-27C>T and 129G>A) and CD109 (2139A>G). Five of them could lead to amino acid deletion, substitution or premature stop codon in corresponding glycoprotein.

CONCLUSIONS

There was a high degree of polymorphism of the membrane glycoprotein genes related to human platelet alloantigen-1 to -17w systems in the Chinese Han population. These data could have some impact on the diagnosis, prevention and treatment of alloimmune thrombocytopenia.