Single PCR multiplex SNaPshot reaction for detection of eleven blood group nucleotide polymorphisms: optimization, validation, and one year of routine clinical use

Assessing the efficacy of an innovative diagnostic method for identifying 5 % variants in somatic ctDNA

BACKGROUND

Liquid biopsy is considered a complementary and recently also an alternative method to surgical biopsy. It allows for the acquisition of valuable information regarding the potential presence of tumors, particularly through the analysis of circulating tumor DNA (ctDNA). CtDNA is a fraction of circulating free DNA (cfDNA) that can be extracted from various tissues, with blood being the most readily available.

RESULTS

To maximize the yield of plasma separation, specific Streck tubes are recommended for blood collection. The MagPurix CFC DNA Extraction Kit can be used for cfDNA extraction, and the TWIST Library Preparation protocol can be optimized for further analysis. Next-generation sequencing (NGS) can be employed to compare somatic and germline lineages, enabling the identification of somatic variants with a Variant Allele Frequency (VAF) of 5 % or higher, which are absent in the germline lineage.

CONCLUSION

This analysis helps in the assessment of recurrence, analysis, and monitoring of cancer tissue.

Malignancy following solid organ transplantation: Current techniques for determination of donor versus recipient origin

Among the post-transplantation complications that patients may encounter, the transmission of a donor-derived malignant neoplasm is uncommon but potentially life threatening. The determination of donor versus recipient origin is essential particularly in the setting of multiple transplant recipients from the donor. Advances in molecular biology now allow accurate discrimination utilizing routine tissue samples in a timely and cost-effective manner. The techniques are routinely performed in hospital molecular biology laboratories and are also available in commercial labs. The current methodologies are discussed and future possibilities are presented for clinicians caring for solid organ recipients.

Blood Group Testing

Red blood cell (RBC) transfusion is one of the most frequently performed clinical procedures and therapies to improve tissue oxygen delivery in hospitalized patients worldwide. Generally, the cross-match is the mandatory test in place to meet the clinical needs of RBC transfusion by examining donor-recipient compatibility with antigens and antibodies of blood groups. Blood groups are usually an individual's combination of antigens on the surface of RBCs, typically of the ABO blood group system and the RH blood group system. Accurate and reliable blood group typing is critical before blood transfusion. Serological testing is the routine method for blood group typing based on hemagglutination reactions with RBC antigens against specific antibodies. Nevertheless, emerging technologies for blood group testing may be alternative and supplemental approaches when serological methods cannot determine blood groups. Moreover, some new technologies, such as the evolving applications of blood group genotyping, can precisely identify variant antigens for clinical significance. Therefore, this review mainly presents a clinical overview and perspective of emerging technologies in blood group testing based on the literature. Collectively, this may highlight the most promising strategies and promote blood group typing development to ensure blood transfusion safety.

Blood group typing from whole-genome sequencing data

Many questions can be explored thanks to whole-genome data. The aim of this study was to overcome their main limits, software availability and database accuracy, and estimate the feasibility of red blood cell (RBC) antigen typing from whole-genome sequencing (WGS) data. We analyzed whole-genome data from 79 individuals for HLA-DRB1 and 9 RBC antigens. Whole-genome sequencing data was analyzed with software allowing phasing of variable positions to define alleles or haplotypes and validated for HLA typing from next-generation sequencing data. A dedicated database was set up with 1648 variable positions analyzed in KEL (KEL), ACKR1 (FY), SLC14A1 (JK), ACHE (YT), ART4 (DO), AQP1 (CO), CD44 (IN), SLC4A1 (DI) and ICAM4 (LW). Whole-genome sequencing typing was compared to that previously obtained by amplicon-based monoallelic sequencing and by SNaPshot analysis. Whole-genome sequencing data were also explored for other alleles. Our results showed 93% of concordance for blood group polymorphisms and 91% for HLA-DRB1. Incorrect typing and unresolved results confirm that WGS should be considered reliable with read depths strictly above 15x. Our results supported that RBC antigen typing from WGS is feasible but requires improvements in read depth for SNV polymorphisms typing accuracy. We also showed the potential for WGS in screening donors with rare blood antigens, such as weak JK alleles. The development of WGS analysis in immunogenetics laboratories would offer personalized care in the management of RBC disorders.

Molecular profiling of non-small cell lung cancer

Lung cancer is generally treated with conventional therapies, including chemotherapy and radiation. These methods, however, are not specific to cancer cells and instead attack every cell present, including normal cells. Personalized therapies provide more efficient treatment options as they target the individual’s genetic makeup. The goal of this study was to identify the frequency of causal genetic mutations across a variety of lung cancer subtypes in the earlier stages. 833 samples of non-small cell lung cancer from 799 patients who received resection of their lung cancer, were selected for molecular analysis of six known mutations, including EGFR, KRAS, BRAF, PIK3CA, HER2 and ALK. A SNaPshot assay was used for point mutations and fragment analysis searched for insertions and deletions. ALK was evaluated by IHC +/- FISH. Statistical analysis was performed to determine correlations between molecular and clinical/pathological patient data. None of the tested variants were identified in most (66.15%) of cases. The observed frequencies among the total samples vs. only the adenocarcinoma cases were notable different, with the highest frequency being the KRAS mutation (24.49% vs. 35.55%), followed by EGFR (6.96% vs. 10.23%), PIK3CA (1.20% vs. 0.9%), BRAF (1.08% vs. 1.62%), ALK (0.12% vs. 0.18%), while the lowest was the HER2 mutation (0% for both). The statistical analysis yielded correlations between presence of a mutation with gender, cancer type, vascular invasion and smoking history. The outcome of this study will provide data that helps stratify patient prognosis and supports development of more precise treatments, resulting in improved outcomes for future lung cancer patients.

Assessment for familial pattern and association of polymorphisms in KIAA0319 gene with specific reading disorder in children from North India visiting a tertiary care centre: A case-control study

Genetic association studies have identified KIAA0319 gene as a possible susceptibility locus for reading disorder; however, very few studies are available from India. The study was planned to investigate the familial pattern and association of KIAA0319 polymorphisms among children with reading disorder visiting a tertiary centre in North India. This is a case-control, familial, and genetic association study on 30 children diagnosed with reading disorder (ICD-10) and 30 matched healthy controls and their families. The Aggregate Neurobehavioral Student Health and Educational Review System was administered on parents of probands and controls for reading problems in their siblings, and Adult Reading Questionnaire was administered for parents of both groups. The blood sample was taken from probands, and DNA was isolated. Four KIAA0319 coding sequence single nucleotide polymorphisms (SNPs; rs4504469, rs6935076, rs2038137, and rs2179515) were genotyped using SNaPshot single nucleotide extension. The incidence of reading problem was significantly higher in families of probands as compared with families of controls. There were no significant differences in both groups regarding the frequency of alleles of four SNPs. The reading disorder showed a significant familial pattern, but KIAA0319 gene did not appear to be a susceptibility factor. Future replications with larger samples and whole genome studies are warranted.

Extended Donor Typing by Pooled Capillary Electrophoresis: Impact in a Routine Setting

Background

PCR with sequence-specific priming using allele-specific fluorescent primers and analysis on a capillary sequencer is a standard technique for DNA typing. We aimed to adapt this method for donor typing in a medium-throughput setting.

Methods

Using the Extract-N-Amp PCR system, we devised a set of eight multiplex allele-specific PCR with fluorescent primers for Fy^a/Fy^b, Jk^a/Jk^b, M/N, and S/s. The alleles of a gene were discriminated by the fluorescent color; donor and polymorphism investigated were encoded by product length. Time, cost, and routine performance were collated. Discrepant samples were investigated by sequencing. The association of new alleles with the phenotype was evaluated by a step-wise statistical analysis.

Results

On validation using 312 samples, for 1.1% of antigens (in 5.4% of samples) no prediction was obtained. 99.96% of predictions were correct. Consumable cost per donor were below EUR 2.00. In routine use, 92.2% of samples were successfully predicted. Discrepancies were most frequently due to technical reasons. A total of 11 previously unknown alleles were detected in the Kell, Lutheran, and Colton blood group systems. In 2017, more than 20% of the RBC units prepared by our institution were from donors with predicted antigen status. A steady supply of Yt(a-), Co(a-) and Lu(b-) RBC units was ensured.

Conclusions

Pooled capillary electrophoresis offers a suitable alternative to other methods for extended donor DNA typing. Establishing a large cohort of typed donors improved transfusion support for patients.

Rapid rare ABO blood typing using a single PCR based on a multiplex SNaPshot reaction

BACKGROUND

ABO subgroups would be considered when discrepancies in ABO grouping occur. Serological methods including adsorption-elution test, salivary ABH inhibition test, and anti-A1 (lectin) saline method could be used. However, these serological methods are laboring and obscure. Therefore, reliable and affordable method to assess the ABO subgroups is of particular interest.

METHODS

To solve this problem, the multiplex SNaPshot-based assays were designed to determine rare A and B subgroups. Primers used as probes for determination of rare ABO blood groups known in Taiwanese population were designed. Many ABO subtype samples were used to validate the accuracy and reproducibility of our SNaPshot panel.

RESULTS

A panel of primer probes were successfully designed in determining 8 SNP sites (261, 539, 838, 820, 745, 664, IVS6 +5, and 829 in exon 6 and 7) for A phenotype and 6 SNP sites (261, 796, IVS3 +5, 247, 523, and 502 in exon 2, 6 and 7 and intron 3) for B phenotype. SNaPshot analysis for defining blood group A alleles (A₁, A₂, A₃, A_m and A_el) and blood group B alleles (B₁, B₃, B_w and B_el) was therefore available.

CONCLUSION

SNaPshot analysis could be used in reference laboratories for typing known rare subgroups of A and B without DNA cloning and traditional sequencing. Moreover, this method would help to construct databases of genotyped blood donors, and it potentially plays a role in determining fetal-maternal ABO incompatibility.

Identification of Forensically Important Calliphoridae and Sarcophagidae Species Collected in Korea Using SNaPshot Multiplex System Targeting the Cytochrome c Oxidase Subunit I Gene

Estimation of postmortem interval (PMI) is paramount in modern forensic investigation. After the disappearance of the early postmortem phenomena conventionally used to estimate PMI, entomologic evidence provides important indicators for PMI estimation. The age of the oldest fly larvae or pupae can be estimated to pinpoint the time of oviposition, which is considered the minimum PMI (PMI_min). The development rate of insects is usually temperature dependent and species specific. Therefore, species identification is mandatory for PMI_min estimation using entomological evidence. The classical morphological identification method cannot be applied when specimens are damaged or have not yet matured. To overcome this limitation, some investigators employ molecular identification using mitochondrial cytochrome c oxidase subunit I (COI) nucleotide sequences. The molecular identification method commonly uses Sanger's nucleotide sequencing and molecular phylogeny, which are complex and time consuming and constitute another obstacle for forensic investigators. In this study, instead of using conventional Sanger's nucleotide sequencing, single-nucleotide polymorphisms (SNPs) in the COI gene region, which are unique between fly species, were selected and targeted for single-base extension (SBE) technology. These SNPs were genotyped using a SNaPshot® kit. Eleven Calliphoridae and seven Sarcophagidae species were covered. To validate this genotyping, fly DNA samples (103 adults, 84 larvae, and 4 pupae) previously confirmed by DNA barcoding were used. This method worked quickly with minimal DNA, providing a potential alternative to conventional DNA barcoding. Consisting of only a few simple electropherogram peaks, the results were more straightforward compared with those of the conventional DNA barcoding produced by Sanger's nucleotide sequencing.

Associations between thromboxane A synthase 1 gene polymorphisms and the risk of ischemic stroke in a Chinese Han population

Thromboxane A synthase 1 (TBXAS1) catalyses the synthesis of thromboxane A2 (TXA2), which plays an important role in the pathogenesis of ischemic stroke. Thus, the TBXAS1 gene was investigated as a candidate gene involved in the formation of atherosclerosis. This case-control study collected peripheral blood specimens and clinical data of 370 ischemic stroke patients and 340 healthy controls in the Northern Chinese Han population from October 2010 to May 2011. Two TBXAS1 single-nucleotide polymorphisms, rs2267682 and rs10487667, were analyzed using a SNaPshot Multiplex sequencing assay to explore the relationships between the single-nucleotide polymorphisms in TBXAS1 and ischemic stroke. The TT genotype frequency and T allele frequency of rs2267682 in the patients with ischemic stroke were significantly higher than those in the controls (P < 0.01 and P = 0.02). Furthermore, compared with the GG + GT genotype, the TT rs2267682 genotype was associated with increased risk of ischemic stroke (odds ratio (OR) = 1.80, 95% confidence interval (CI): 1.16–2.79, P < 0.01). Multivariate logistic analysis with adjustments for confounding factors revealed that rs2267682 was still associated with ischemic stroke (OR = 1.94, 95% CI : 1.13–3.33, P = 0.02). The frequency of the T-G haplotype in the patients was significantly higher than that in the controls according haplotype analysis (OR = 1.49, 95% CI: 1.10–2.00, P < 0.01). These data reveal that the rs2267682 TBXAS1 polymorphism is associated with ischemic stroke. The TT genotype of TBXAS1 and T allele of rs2267682 increase susceptibility to ischemic stroke in this Northern Chinese Han population. The protocol has been registered with the Chinese Clinical Trial Registry (registration number: ChiCTR-COC-17013559).

Addressing the challenges of applying precision oncology

Precision oncology is described as the matching of the most accurate and effective treatments with the individual cancer patient. Identification of important gene mutations, such as BRCA1/2 that drive carcinogenesis, helped pave the way for precision diagnosis in cancer. Oncoproteins and their signaling pathways have been extensively studied, leading to the development of target-based precision therapies against several types of cancers. Although many challenges exist that could hinder the success of precision oncology, cutting-edge tools for precision diagnosis and precision therapy will assist in overcoming many of these difficulties. Based on the continued rapid progression of genomic analysis, drug development, and clinical trial design, precision oncology will ultimately become the standard of care in cancer therapeutics.

Vitamin D receptor polymorphisms in immune thrombocytopenic purpura

BACKGROUND

Vitamin D receptor (VDR) polymorphisms have been studied in immune-mediated disorders, but not yet in immune thrombocytopenic purpura (ITP). We investigated whether VDR variants were associated with ITP in children.

METHODS

The study included 44 children with a diagnosis of ITP and 100 healthy controls. Five VDR polymorphisms (Cdx-2, FokI, BsmI, ApaI and TaqI) were genotyped and used to evaluate the association of VDR variants with ITP.

RESULTS

The distribution of the three Cdx-2 genotype groups (GG, GA, and AA) was significantly different between ITP patients and controls (P = 0.025); the homozygous GG genotype of Cdx-2 was overrepresented in ITP patients. The frequency of the A allele of Cdx-2 was significantly different between patients and controls (P = 0.01). The A allele of Cdx-2 was associated with a decreased risk of ITP (OR, 0.343; 95% CI: 0.150-0.782). No statistically significant difference was found between the ITP group and control group for Fok1, Bsm1, Apa1, and Taq1 polymorphisms (P > 0.5).

CONCLUSION

There appears to be an interaction between the Cdx-2 variant of VDR and childhood immune thrombocytopenia.

Vitamin D Receptor (VDR) Polymorphisms in Pediatric Patients Presenting With Hodgkin's Lymphoma

Vitamin D receptor (VDR) polymorphisms are found more commonly in some tumor types than in healthy individuals, suggesting that some polymorphisms (Cdx2, Fok1, Bsm1, Apa1, Taq1) contribute to tumor development. There is no previous report on VDR polymorphism in Hodgkin's lymphoma (HL) patients. VDR polymorphism patterns in 95 pediatric HL cases with 100 healthy controls were compared. No statistically significant difference was found between the patient group and control group in terms of Cdx2, Fok1, Bsm1, Apa1, and Taq1 polymorphisms (P>0.5). Our findings suggest that VDR polymorphisms may not play a role in HL development.

Mini-SNaPshot multiplex assays authenticate elephant ivory and simultaneously identify the species origin

Illegal trading of ivory is mainly responsible for the dramatic decline in elephant populations. Thailand is one of the largest laundering hotspots for African ivory, as the domestic Asian elephant ivory can be legally traded. So, to help combat ivory poaching and smuggling, an efficient method is needed to identify the elephant species from its ivory and ivory products. In this study, a mini-SNaPshot^® multiplex assay was developed and fully validated for the identification of confiscated ivory and low DNA template ivory products. Elephantid- and elephant species-specific mitochondrial single nucleotide polymorphisms (SNPs) were identified from 207 mammalian and 1705 elephant/mammoth cytochrome b sequence alignments. Seven informative SNPs were used for assay development. The assay unambiguously and accurately identified authentic elephant ivory and its species of origin on the basis of peak size and color observed in the haplotype profile. The assay was highly efficient for analysis of confiscated ivory and low-template ivory products with a 99.29% success rate (N=140). It was highly reproducible, exhibited no cross-reaction with eight other mammalian DNA; and had 100% identification accuracy. In addition, nested and direct PCR amplification were also compatible with the developed assay. This efficient assay should benefit wildlife forensic laboratories and aid in the prosecution of elephant-related crimes.

Polymorphisms in the 5-hydroxytryptamine receptor 3B gene are associated with heroin dependence in the Chinese Han population

Previous studies suggested that the 5-hydroxytryptamine receptor 3B (HTR3B) is involved in heroin dependence by modulating dopamine (DA) release in the reward pathway and that the genetic polymorphisms in HTR3B play plausible role in modulating the risk of developing heroin addiction. To identify markers that contribute to the genetic susceptibility to heroin dependence, we examined the potential associations between heroin dependence and 7 single nucleotide polymorphisms (SNPs) of the HTR3B gene using multiplex SNaPshot technology in a Chinese Han population. Participants included 418 heroin-dependent subjects and 422 healthy controls. The results suggested that the genotype distribution of HTR3B rs1176746 and rs1185027 were significantly different between heroin dependent subjects and healthy controls (both p=0.004). The frequency of the GG of rs1176746 and AA of rs1185027 genotype in heroin-dependent subjects were significantly higher than that of healthy controls, while the GA of rs1176746 and AT of rs1185027 genotype distributions were much lower. Another SNP, rs10789970, showed a nominally significant p-value in the genotype distribution between heroin dependent subjects and controls (p=0.022). These findings indicate the important role of HTR3B polymorphisms in heroin dependence among the Chinese Han population and provide valuable information for further genetic and neurobiological investigations of heroin dependence.

Single-Nucleotide Polymorphism rs17611 of Complement Component 5 Shows Association with Ischemic Stroke in Northeast Chinese Population

BACKGROUND

Complement component 5 (C5) has been described to play an important role in the development and progression of atherosclerosis and cardiovascular disease. Our aim was to determine whether genetic variation of C5 was associated with ischemic stroke (IS) in northeast Chinese population.

METHODS

We used a case-control study involving 386 IS patients and 386 non-IS controls from a rural population and determined the genotypes of five polymorphisms (rs12237774, rs17611, rs4837805, rs7026551, and rs1017119) of C5 gene by Snapshot single-nucleotide polymorphism genotyping assays to assess any links with IS.

RESULTS

In univariate analysis, rs17611 was significantly associated with IS in the additive model, the dominant model, and recessive model (additive p 0.031, dominant p 0.034, and recessive p 0.027). After adjustment for Binary Logistic Regression, rs17611 polymorphism was still significant in three models (adjusted odds ratio (OR) = 1.306, 95% confidence interval (CI) = 1.069-1.595, p-value = 0.009 in an additive model; OR = 1.378, 95% CI = 1.024-1.856, p-value = 0.035 in a dominant model; and OR = 1.511, 95% CI = 1.048-2.18, p-value = 0.027 in a recessive model).

CONCLUSION

In this sample of patients, genetic variation of rs17611 in C5 is associated with higher prevalence of IS.

Serum and red-blood-cell folate demonstrate differential associations with BMI in pregnant women

Objective

To examine the association between BMI and folate concentrations in serum and red blood cells (RBC) in pregnant women.

Design

A cross-sectional comparison of folate concentrations in serum and RBC sampled simultaneously from the same individual.

Setting

The Ottawa Hospital and Kingston General Hospital, Ontario, Canada.

Subjects

Pregnant women recruited between 12 and 20 weeks of gestation.

Results

A total of 869 pregnant women recruited from April 2008 to April 2009 were included in the final analysis. Serum folate was inversely associated and RBC folate positively associated with BMI, after adjusting for folic acid supplementation, age, gestational age at blood sample collection, race, maternal education, annual income, smoking and MTHFR 677C→T genotype. In stratified analyses, this differential association was significant in women with the MTHFR CC variant. In women with the CT and TT variants, the differential associations were in the same direction but not significant. Folic acid supplementation during pregnancy did not alter the differential association of BMI with serum and RBC folate concentration. This indicates that the current RBC folate cut-off approach for assessing risk of neural tube defects in obese women may be limited.

Conclusions

BMI is inversely associated with serum folate and positively associated with RBC folate in pregnant women, especially for those with the MTHFR CC variant.

Clinical Potential of Effective Noninvasive Exclusion of KEL1-Positive Fetuses in KEL1-Negative Pregnant Women

Background: The clinical importance of assessing the fetal KEL genotype is to exclude ‘K'-positive fetuses (genotype KEL1/KEL2) in ‘K'-alloimmunized pregnant women (genotype KEL2/KEL2). Noninvasive assessment of the fetal KEL genotype is not yet available in the Czech Republic. Objective: The aim of this study was to assess the fetal KEL1/KEL2 genotype from cell-free fetal DNA in the plasma of KEL2/KEL2 pregnant women. Methods: The fetal genotype was assessed by minisequencing (a dilution series including control samples). A total of 138 pregnant women (between the 8th and 23rd gestational week) were tested by minisequencing. The fetal genotype was further verified by analysis of a buccal swab from the newborn. Results: Minisequencing proved to be a reliable method. In 2.2% (3/138) of the examined women, plasma sample testing failed; 94.8% (128/135) had the KEL2/KEL2 genotype, and a total of 3.1% of fetuses (4/128) had the KEL1/KEL2 genotype. Sensitivity and specificity reached 100% (p < 0.0001). Conclusion: Minisequencing is a reliable method for the assessment of the fetal KEL1 allele from the plasma of KEL2/KEL2 pregnant women.

Efficient detection of frequent eIF2B mutations for the rapid molecular diagnosis of CACH/VWM syndrome

OBJECTIVES

The aim of this study was to develop a reliable, rapid and cost-effective molecular diagnostic assay allowing widespread routine investigation of eIF2B-related disorders (CACH/VWM syndrome). This heterogeneous disease is caused by autosomal recessive mutations in the genes encoding the five subunits of the translation-initiation factor eIF2B. Such a diagnostic method would be particularly adapted to the apparently acute presentation of the disease.

DESIGN AND METHODS

We developed a multiplex PCR amplification method for 7 genomic regions of the eIF2B genes in a single run. This method targeted the 8 most frequent mutations representing 61.4% of all mutations identified to date in our laboratory. These mutations affected eIF2B2 exon 5, eIF2B3 exon 2, eIF2B4 exons 8 and 11 and eIF2B5 exons 5, 7 and 8. PCR products were then pooled and subjected to a primer-extension assay validated using previously genotyped samples.

RESULTS

The results were compared to screening and/or direct sequencing methods: 100% agreement between methods confirmed equivalent sensitivity and specificity. The new assay was highly superior in terms of cost, time to results and robustness despite sample heterogeneity.

CONCLUSIONS

This genotyping strategy allows the detection of all eIF2B mutations targeted. A second multiplex primer-extension assay is in development to detect the 11 next-most frequent mutations, thus raising the global detection rate to 76.8%. Our approach is widely applicable as it involves standard techniques and equipment. Moreover, it can easily be further adapted to the clinical and genetic heterogeneity of eIF2B-related disorders by including or excluding mutations.

A simple genotyping procedure without DNA extraction to identify rare blood donors

BACKGROUND

Transfusion-induced alloimmunization has severe clinical consequences including haemolytic transfusion reactions, impaired transfused RBCs longevity and greater difficulty in finding compatible blood. Molecular analysis of genomic DNA now permits prediction of blood group phenotypes based on identification of single nucleotide polymorphisms. Implementation of molecular technologies in donor centres would be helpful in finding RBC units for special patient populations, but DNA extraction remains an obstacle to donor genotyping.

MATERIALS AND METHODS

We propose a simple method compatible with high throughput that allows blood group genotyping using a multiplex commercial kit without the need for DNA extraction. The principle relies on pre-PCR treatment of whole blood using heating/cooling procedure in association with a recombinant hotstart polymerase.

RESULTS

In a prospective analysis, we yielded 5628 alleles identification and designated 63 donors with rare blood, that is either negative for a high-frequency antigen or with a rare combination of common antigens.

CONCLUSION

The procedure was optimized for simplicity of use in genotyping platform and would allow not only to supply antigen-matched products to recipients but also to find rare phenotypes. This methodology could also be useful for establishing a donor repository for human platelet antigens (HPA)-matched platelets since the same issues are involved for patients with neonatal alloimmune thrombocytopenia or post-transfusion purpura.

[Contribution of red blood group genotyping for recipients in immune-hematology through three years of activity at the EFS Alpes-Méditerranée]

AIM OF THE STUDY

Current knowledge of the molecular basis of most blood groups enables genetic testing for blood groups to overcome the limitations of agglutination. A retrospective review was carried out on genotyping assays performed between 2011 and 2013.

METHODS AND PATIENTS

The Molecular Hematology Laboratory of the EFS Alpes-Méditerranée implements commercially available tools (BioArray, Gen-Probe) and other techniques (TaqMan, tetra-primer ARMS-PCR, sequencing). It provides a high-level of expertise in molecular biology, complying with regulatory requirements and standards.

RESULTS

A total of 2382 genotyping assays was performed including 764 extended typings and 115 large extended typings essentially in cases involving multiple transfusion and suspected rare blood type. Phenotype discrepancies linked to the RH system accounted for 1501 genotypings. Discrepancies linked to the D and E were mainly related to an allele coding for weak antigen (weak D type 1, 2, 3 and EIV) while those linked to C, c and e antigens were related to an allele coding for a partial antigen (RN, ces(340), ceMo). A high prevalence of (C)ces haplotype in trans of a DAR allele was observed in Afro-Caribbean (54/62).

CONCLUSION

In transfusion medicine, red-cell genotyping can overcome the limitations of hemagglutination. It must be used only in situations where it provides a benefit either for the patient or resource management. For implementation of appropriate transfusional practices, this technique requires a sound knowledge of the genetic characteristics of blood groups and clinically relevant variants. It also requires competency with molecular biology tools and continuously updated scientific data.

PCR-free blood group genotyping using a nanobiosensor

BACKGROUND AND OBJECTIVES

The last two decades have seen major developments in genotyping assays to facilitate the procurement of red blood cell units to alloimmunized patients. To make genotyping faster, simpler and less costly, a nanotechnology approach based on metal/silica fluorescent nanoparticles and a polymer-based hybridization optical transducer was designed. The objectives of this study were (1) to verify whether this nanobiosensor has the ability to discriminate single nucleotide polymorphisms in non-amplified genomic DNA and (2) to establish whether the signal generated by the nanobiosensor is sufficiently intense to be detected by standard flow cytometry.

MATERIALS AND METHODS

Silver-core silica-shell fluorescent nanoparticles (Ag@SiO₂) were prepared, and amine-modified DNA probes were grafted to their surface. A cationic conjugated polymer was electrostatically bound to the surface probes to become optically active upon hybridization with a target. Two nanobiosensor formulations specific to DO*01 and DO*02 alleles were prepared. DNA was extracted from whole blood and mixed with the nanobiosensor for hybridization. The nanobiosensor fluorescence was measured by flow cytometry.

RESULTS

Nine volunteers were typed for Dombrock blood group antigens DO*01 and DO*02. A statistically significant increase in the optical transduction signal was observed for sequence-specific samples. All nine genotypes were correctly identified when compared to standardized PCR assays.

CONCLUSION

The nanobiosensor provides rapid and simple genotyping of blood group antigens from unamplified genomic DNA and can be measured using standard flow cytometers. This PCR-free approach could be applied to any known genetic polymorphism.

HLA-DPB1 Variant Effect on Hepatitis B Virus Clearance and Liver Cirrhosis Development Among Southwest Chinese Population

BACKGROUND

Previous studies have shown that genetic variants in HLA-DP genes affect disease progression in hepatitis B virus (HBV) infection.

OBJECTIVES

We aimed to evaluate possible association between HLA-DPB1 rs9277534 polymorphism and different clinical complications of hepatitis B virus (HBV) infection.

MATERIALS AND METHODS

Snapshot assay was used to investigate the association of rs9277534 polymorphism in 342 patients with persistent HBV infection and 342 age and gender-matched HBV spontaneous clearance controls. Patients were categorized into asymptomatic HBV carriers (AsC, n = 104), chronic hepatitis B (CHB, n = 116), and liver cirrhosis (LC, n = 122) subgroups.

RESULTS

There was a significantly higher proportion of the rs9277534 minor allele A in HBV spontaneous clearance control than that in HBV persistent infection group (OR = 0.58, 95%CI = 0.46-0.73, P < 0.0001). Genotypic analysis showed that GA and AA genotypes were associated with HBV spontaneous clearance (GA: OR = 0.56, 95%CI = 0.40-0.79, P = 0.019; AA: OR = 0.24, 95%CI = 0.14-0.44, P < 0.0001). A significant difference was found between AsC and LC groups in the distribution of AA genotype (OR = 9.32, 95%CI = 1.293-67.14, P = 0.027).

CONCLUSIONS

Variant at rs9277534 could affect both the spontaneous clearance of HBV infection and progression from asymptomatic HBV carriers to HBV-related liver cirrhosis in Southwest Han Chinese population.

Polymorphisms in CISH gene are associated with persistent hepatitis B virus infection in Han Chinese population

BACKGROUND AND AIM

Cytokine-inducible SRC homology 2 domain protein (CISH) is the first member of the suppressors of cytokine signaling (SOCS) protein family. An association between multiple CISH polymorphisms and susceptibility to infectious diseases has been reported. This study aimed to investigate the possible association of these single nucleotide polymorphisms (SNPs) in CISH gene with different outcomes of Hepatitis B virus (HBV) infection.

METHODS

1019 unrelated Chinese Han subjects, including 240 persistent asymptomatic HBV carriers, 217 chronic hepatitis B patients, 137 HBV-related liver cirrhosis patients, and 425 cases of spontaneously recovered HBV as controls, were studied. Four SNPs (rs622502, rs2239751, rs414171 and rs6768300) in CISH gene were genotyped with the snapshot technique. Transcriptional activity of the CISH promoter was assayed in vitro using the dual-luciferase reporter assay system.

RESULTS

At position rs414171, A allele and AA genotype frequencies were significantly higher in the HBV-resolved group as compared to the persistent HBV infection group. At position rs2239751, TT genotype was further observed in the HBV-resolved group. Using asymptomatic HBV carriers as controls, our results indicated that the rs414171 and rs2239751 polymorphisms were unrelated to HBV progression. The other two SNPs (rs622502 and rs6768300) showed no association with persistent HBV infection. Haplotype analysis revealed that the GGCA haplotype was associated with spontaneous clearance of HBV in this population. Moreover, luciferase activity was significantly higher in the PGL3-Basic-rs414171T construct as compared to the PGL3-Basic-rs414171A construct (p<0.001).

CONCLUSION

Two SNPs (rs414171 and rs2239751) in the CISH gene were associated with persistent HBV infection in Han Chinese population, but not with HBV progression.

Flexible automated platform for blood group genotyping on DNA microarrays

The poor suitability of standard hemagglutination-based assay techniques for large-scale automated screening of red blood cell antigens severely limits the ability of blood banks to supply extensively phenotype-matched blood. With better understanding of the molecular basis of blood antigens, it is now possible to predict blood group phenotype by identifying single-nucleotide polymorphisms in genomic DNA. Development of DNA-typing assays for antigen screening in blood donation qualification laboratories promises to enable blood banks to provide optimally matched donations. We have designed an automated genotyping system using 96-well DNA microarrays for blood donation screening and a first panel of eight single-nucleotide polymorphisms to identify 16 alleles in four blood group systems (KEL, KIDD, DUFFY, and MNS). Our aim was to evaluate this system on 960 blood donor samples with known phenotype. Study data revealed a high concordance rate (99.92%; 95% CI, 99.77%-99.97%) between predicted and serologic phenotypes. These findings demonstrate that our assay using a simple protocol allows accurate, relatively low-cost phenotype prediction at the DNA level. This system could easily be configured with other blood group markers for identification of donors with rare blood types or blood units for IH panels or antigens from other systems.

Association of interleukin-33 gene single nucleotide polymorphisms with ischemic stroke in north Chinese population

Background

IL-33, an IL-1-like cytokine, is a ligand for IL1RL1, which is an important effector molecule of type 2 T helper responses. Although IL-33/IL1RL1 interaction has been suggested to be important in the development of atherosclerosis, genetic influences of the polymorphisms of IL33 in human ischemic stroke are unclear. The aim of this study was to examine whether the single nucleotide polymorphisms in IL33 are associated with ischemic stroke in Northern Chinese population.

Methods

We used a nested case–control study involving 90 ischemic stroke patients and 270 age-matched, sex-matched and blood pressure-matched non-ischemic stroke controls from a rural population and determined the genotypes of four polymorphisms (rs1929992, rs10975519, rs4742170, rs16924159) in IL33 by Snapshot SNP genotyping assays to assess any links with ischemic stroke.

Results

Univariate analysis showed two single nucleotide polymorphisms (rs1929992, rs4742170) in IL33 were associated with ischemic stroke in additive, dominant, and recessive model. Binary Logistic Regression shows that rs4742170 variation is the most important factor associated with ischemic stroke (adjusted odds ratio (OR) = 1.880, 95% confidence interval (CI) = 1.316-2.686 in an additive model; OR = 2.091, CI = 1.249-3.498 in a dominant model; OR = 2.623, CI = 1.366-5.036 in a recessive model).

Conclusion

In this sample of patients, genetic variation of rs4742170 in IL33 is significantly associated with the developing of ischemic stroke.

DNA biosensor/biochip for multiplex blood group genotyping

At present, 33 blood groups representing over 300 antigens are listed by the International Society of Blood Transfusion (ISBT). Most of them result from a single nucleotide polymorphism (SNP) in the corresponding DNA sequence, i.e. approx. 200 SNPs. In immunohematology laboratories, blood group determination is classically carried out by serological tests, but these have some limitations, mostly in term of multiplexing and throughput. Yet, there is a growing need of extended blood group typing to prevent alloimmunization in transfused patients and transfusion accidents. The knowledge of the molecular bases of blood groups allows the use of molecular biology methods within immunohematology laboratories. Numerous assays focused on blood group genotyping were developed and described during the last 10 years. Some of them were real biochips or biosensors while others were more characterized by the particular molecular biology techniques they used, but all were intending to produce multiplex analysis. PCR techniques are most of the time used followed by an analytical step involving a DNA biosensor, biochip or analysis system (capillary electrophoresis, mass spectrometry). According to the method used, the test can then be classified as low-, medium- or high-throughput. There are several companies which developed platforms dedicated to blood group genotyping able to analyze simultaneously various SNPs or variants associated with blood group systems. This review summarizes the characteristics of each molecular biology method and medium-/high-throughput platforms dedicated to the blood group genotyping.

Comprehensive genotyping for 18 blood group systems using a multiplex ligation-dependent probe amplification assay shows a high degree of accuracy

BACKGROUND

In recent years genotyping methods have been implemented in blood banks as alternative to comprehensive serologic typing. We evaluated a newly developed assay for convenient and comprehensive genotyping of blood group alleles based on multiplex ligation-dependent probe amplification (MLPA) technology.

STUDY DESIGN AND METHODS

We analyzed 103 random and 150 selected samples to validate the specificity of the blood-MLPA assay that is able to determine the presence, absence, and copy number of 48 blood group and 112 variant alleles of 18 blood group systems. A total of 4038 serologic typing results, including 52 different antigens, were available for these samples.

RESULTS

In 4018 (99.5%) of the 4038 serologic typing results the predicted phenotypes by the blood-MLPA were in concordance with serologic typing. Twenty discordant results were due to false-positive serologic results (n = 2), false-negative serologic results (n = 1), inability of routine serologic typing to detect variant antigens (n = 14), or false-positive prediction from the blood-MLPA due to the presence of a null allele (n = 3).

CONCLUSION

The blood-MLPA reliably predicts the presence or absence of blood group antigens, including almost all clinically relevant blood group antigens, except ABO, in patients and donors. Furthermore, it is the first assay that determines copy numbers of blood group alleles in the same test. It even provides more detailed and accurate information than serologic typing, because most variant alleles are immediately recognized. Since only standard laboratory equipment is needed, this assay finally offers the possibility to comprehensively type recipients and makes extensive matching for selected patients groups more feasible.

Association between microRNA polymorphisms and humoral immunity to hepatitis B vaccine

To investigate whether selected single nucleotide polymorphisms (SNPs) in miR-146a, miR-196a2, miR-27a, miR-26a-1, miR-124 and miR-149 genes are associated with immune response to hepatitis B vaccine. The genotype and allele frequencies of SNPs were compared between the non-responders (n=77) and responders (n=207). The associations of the genotypes with antibody levels were assessed in the responders. Significant associations were observed between SNPs in miR-146a and miR-26a-1 genes and non-response to hepatitis B vaccine (p<0.05). In addition, SNPs in miR-146a and miR-27a genes were associated with variations in levels of antibodies to hepatitis B antigen. Thus, specific SNPs in microRNAs (miRNAs) genes may affect status of the hepatitis B vaccine induced protective humoral immune response. They also suggest that the three miRNAs play a role in modulating antibody responses to hepatitis B vaccine.

Association of three polymorphisms in ARID5B, IKZF1 and CEBPE with the risk of childhood acute lymphoblastic leukemia in a Chinese population

Recent genome-wide association studies (GWAS) that focus on childhood acute lymphoblastic leukemia (ALL), the most common malignancy in children younger than 15 years old, have found evidence that single nucleotide polymorphisms (SNPs) in IKZF1 (7p12.2), ARID5B (10q21.2) and CEBPE (14q11.2) are strongly related to the risk of childhood ALL. These polymorphisms may lead to abnormal expression and dysfunction of the corresponding transcription factors and are likely to increase the risk of ALL. To validate the relationship between these SNPs and the risk of childhood ALL in Chinese population, we conducted a case-control study of 570 ALL cases and 673 controls. We determined that the SNP rs10821936 in ARID5B was statistically significantly associated with the risk of childhood ALL (P<0.0001). The results were also significant for the subgroup analysis of high-risk, medium-risk and low-risk ALL as well as B-lineage ALL. Statistically significant differences were not found in the SNPs for IKZF1 and CEBPE. In conclusion, ARID5B rs10821936 could serve as a potential biomarker for assessing the risk of childhood ALL in Chinese children.

A new strategy to identify rare blood donors: single polymerase chain reaction multiplex SNaPshot reaction for detection of 16 blood group alleles

BACKGROUND

As an alternative to phenotyping, large-scale DNA-based assays, which are feasible for high-throughput donor red blood cell typing, were developed for determination of blood group polymorphisms. However, high-throughput genotyping platforms based on these technologies are still expensive and the inclusion of single nucleotide polymorphisms and analysis of the alleles depend on the manufacturer's determination. To overcome this limitation and in order to develop an assay to enable the screening of rare donors, we developed a SNaPshot assay for analysis of nine single nucleotide polymorphisms related to antigens that are difficult to assess using conventional serology.

MATERIALS AND METHODS

The single polymerase chain reaction multiplex SNaPshot reaction was optimized to identify nine single nucleotide polymorphisms determining 16 alleles: KEL*3/KEL*4, KEL*6/KEL*7, DI*1/DI*2, DI*3/DI*4, YT*1/YT*2, CO*1/CO*2, DO*1/DO*2, DO*4, DO*5. We designed a single multiplex PCR with primers encompassing the blood group single nucleotide polymorphisms and performed an internal reaction with probe primers able to discriminate the alleles after fragment analysis. The SNaPshot assay was validated with 140 known alleles previously determined by PCR restriction fragment length polymorphism.

RESULTS

We were able to simultaneous detect nine single nucleotide polymorphisms defining 16 blood group alleles on an assay based on a multiplex PCR combined with a single base extension using genomic DNA.

DISCUSSION

This study demonstrates a robust genotyping strategy for conducting rare donor screening which can be applied in blood centers and could be an important tool for identifying antigen-negative donors and, therefore, for providing rare blood.

Improved allele-specific PCR technique for Kidd blood group genotyping

BACKGROUND

We developed an allele-specific polymerase chain reaction (AS-PCR) technique for Kidd blood group genotyping.

METHODS

Altogether, 340 blood samples from Thai blood donors at the National Blood Centre, Thai Red Cross Society, were tested with anti-Jk(a) and anti-Jk(b) using the gel technique and the direct urea lysis test was used for screening Jk(a-b-) phenotype. For AS-PCR technique, different types of primers were used for JK*01 and JK*02 allele detections in known DNA controls.

RESULTS

Regarding JK*02 allele detection, the pseudopositve amplification products were found when using correctly matched forward primer and a single mismatch forward primer. Interestingly, one type of two mismatch pairing at the 3' end of the forward primer can be used together with the newly designed reverse primer for Kidd blood group genotyping. It was found that the typing results in all samples obtained by serological techniques and newly developed AS-PCR technique were in agreement and this PCR technique also gave 100% concordance of results in 30 samples randomly tested twice and demonstrated reproducible results.

CONCLUSION

This study shows that the in-house AS-PCR is simple, cost-effective, and convenient for Kidd blood group genotyping in routine laboratories, especially, in resolving serologic investigations.

Association of Fcγ receptor IIB polymorphism with cryptococcal meningitis in HIV-uninfected Chinese patients

BACKGROUND

As important regulators of the immune system, the human Fcγ receptors (FcγRs) have been demonstrated to play important roles in the pathogenesis of various infectious diseases. The aim of the present study was to identify the association between FCGR polymorphisms and cryptococcal meningitis.

METHODOLOGY/PRINCIPAL FINDINGS

In this case control genetic association study, we genotyped four functional polymorphisms in low-affinity FcγRs, including FCGR2A 131H/R, FCGR3A 158F/V, FCGR3B NA1/NA2, and FCGR2B 232I/T, in 117 patients with cryptococcal meningitis and 190 healthy controls by multiplex SNaPshot technology. Among the 117 patients with cryptococcal meningitis, 59 had predisposing factors. In patients with cryptococcal meningitis, the FCGR2B 232I/I genotype was over-presented (OR = 1.652, 95% CI [1.02-2.67]; P = 0.039) and the FCGR2B 232I/T genotype was under-presented (OR = 0.542, 95% CI [0.33-0.90]; P = 0.016) in comparison with control group. In cryptococcal meningitis patients without predisposing factors, FCGR2B 232I/I genotype was also more frequently detected (OR = 1.958, 95% CI [1.05-3.66]; P = 0.033), and the FCGR2B 232I/T genotype was also less frequently detected (OR = 0.467, 95% CI [0.24-0.91]; P = 0.023) than in controls. No significant difference was found among FCGR2A 131H/R, FCGR3A 158F/V, and FCGR3B NA1/NA2 genotype frequencies between patients and controls.

CONCLUSION/SIGNIFICANCE

We found for the first time associations between cryptococcal meningitis and FCGR2B 232I/T genotypes, which suggested that FcγRIIB might play an important role in the central nervous system infection by Cryptococcus in HIV-uninfected individuals.

Identification of RHCE and KEL alleles in large cohorts of Afro-Caribbean and Comorian donors by multiplex SNaPshot and fragment assays: a transfusion support for sickle cell disease patients

To lower the alloimmunization risk following transfusion in blacks, we developed two genotyping assays for large-scale screening of Comorian and Afro-Caribbean donors. One was a multiplex SNaPshot assay designed to identify ce(s) (340), ceMO/AR/EK/BI/SM, ce(s) , ce(s) (1006) and KEL*6/*7 alleles. The other was a multiplex fragment assay designed to detect RHD, RHDψ and RHCE*C and 455A>C transversion consistent with (C)ce(s) Type 1 and DIII Type5 ce(s) . Variant RHCE*ce alleles or RH haplotypes were detected in 58·69% of Comorians and 41·23% of Afro-Caribbeans. The ce(s) allele, (C)ce(s) Type 1, and DIII Type 5 ce(s) haplotypes were identified respectively in 39·13%, 14·67% and 4·88% of Comorians and 32·23%, 5·28% and 1·76% of Afro-Caribbeans. Genotypes consistent with partial D, C, c and/or e antigen expression were observed in 26·08% of Comorians and 14·69% of Afro-Caribbeans. No homozygous genotype corresponding to the RH:-18, -34, and -46 phenotypes were found. However, over 50% of genotypes produced low-prevalence antigens at risk for negative recipients, i.e., V, VS, JAL, and/or KEL6. One new variant RHCE*ce(s) (712) allele was identified. This is the first determination of variant RHCE and KEL allele frequencies. Results indicate the most suitable targets for molecular assay screening to optimize use of compatible blood units and lower immunization risk.