A(1,2)BO(1,2) genotyping by multiplexed allele-specific PCR

Evolution of technology for molecular genotyping in blood group systems

The molecular basis of the blood group antigens was identified first in the 1980s and 1990s. Since then the importance of molecular biology in transfusion medicine has been described extensively by several investigators. Molecular genotyping of blood group antigens is one of the important aspects and is successfully making its way into transfusion medicine. Low-, medium- and high-throughput techniques have been developed for this purpose. Depending on the requirement of the centre like screening for high- or low-prevalence antigens where antisera are not available, correct typing of multiple transfused patients, screening for antigen-negative donor units to reduce the rate of alloimmunization, etc. a suitable technique can be selected. The present review discusses the evolution of different techniques to detect molecular genotypes of blood group systems and how these approaches can be used in transfusion medicine where haemagglutination is of limited value. Currently, this technology is being used in only a few blood banks in India. Hence, there is a need for understanding this technology with all its variations.

A new method for ABO genotyping using fluorescence melting curve analysis based on peptide nucleic acid probes

ABO genotyping has been routinely used to identify suspects or unknown remains in crime investigations. Probe-based fluorescence melting curve analysis (FMCA) is a powerful tool for mutation detection and is based on melting temperature shifts due to thermal denaturation. In the present study, we developed a new method for ABO genotyping using peptide nucleic acid (PNA) probe-based FMCA. This method allowed for the simultaneous detection of three single nucleotide polymorphism (SNP) sites in the ABO gene (nucleotide positions 261, 526, and 803) and the determination of 14 ABO genotypes (A/A, A/O01 or A/O02, A/O03, B/B, B/O01 or B/O02, B/O03, O01/O01 or O01/O02 or O02/O02, O01/O03 or O02/O03, O03/O03, A/B, cis-AB01/A, cis-AB01/B, cis-AB01/O01 or cis-AB01/O02, and cis-AB01/cis-AB01). Using this method, we analyzed 80 samples and successfully identified ABO genotypes (A/A [n=5], A/O01 or A/O02 [n=23], B/B [n=3], B/O01 or B/O02 [n=18], A/B [n=9], O01/O01 or O01/O02 or O02/O02 [n=20], cis-AB01/A [n=1], and cis-AB01/O01 or cis-AB01/O02 [n=1]). In addition, all steps in the method, including polymerase chain reaction, PNA probe hybridization, and FMCA, could be performed in one single closed tube in less than 3h. Since no processing or separation steps were required during analysis, this method was more convenient and rapid than traditional methods and reduced the risk of contamination. Thus, this method may be an effective and helpful tool in forensic investigations.

A simple ABO genotyping by PCR using sequence-specific primers with mismatched nucleotides

In forensics, the specific ABO blood group is often determined by analyzing the ABO gene. Among various methods used, PCR employing sequence-specific primers (PCR-SSP) is simpler than other methods for ABO typing. When performing the PCR-SSP, the pseudo-positive signals often lead to errors in ABO typing. We introduced mismatched nucleotides at the second and the third positions from the 3'-end of the primers for the PCR-SSP method and examined whether reliable typing could be achieved by suppressing pseudo-positive signals. Genomic DNA was extracted from nail clippings of 27 volunteers, and the ABO gene was examined with PCR-SSP employing primers with and without mismatched nucleotides. The ABO blood group of the nail clippings was also analyzed serologically, and these results were compared with those obtained using PCR-SSP. When mismatched primers were employed for amplification, the results of the ABO typing matched with those obtained by the serological method. When primers without mismatched nucleotides were used for PCR-SSP, pseudo-positive signals were observed. Thus our method may be used for achieving more reliable ABO typing.

A₁A₂BO and Rh gene frequencies among six populations of Jammu and Kashmir, India

A study was undertaken to record gene frequencies of ABO blood groups, their subtypes and Rh antigen for six different endogamous groups including a tribal population. The ABO phenotypic frequency varies among six different populations showing significant difference (p<0.0005). Gujjar and Bakarwal (a tribal population) shows highest (42.29%) of B blood phenotypes. A1 is the highest among Syeds (39.31%), O blood group frequency highest among Mughals (43.23%) and A1B and A2B are rare phenotypes showing very low frequency among all populations. The pattern of allele frequencies (p<0.025) is in order of I(O)>I(B)>I(A1)>I(A2), except Syeds (I(O)>I(A1)>I(B)>I(A2)). The rhesus protein (Rh) phenotypic frequency (p<0.01) shows significant increase in Rh(D) positive (87.86% in Syed to 96.03% in Khan) among all populations. The Rh allele (p<0.05) and genotype (p<0.02) frequencies shows a significant difference. Heterozygosity for Rh protein is less than homozygosity among six populations. The result from this study provides information on the genetic variation in blood antigens and rhesus protein among human populations inhabiting Jammu and Kashmir.

ABO genotyping by capillary electrophoresis

Single-strand conformation polymorphism by capillary electrophoresis (SSCP-CE) has been developed to detect single nucleotide mutations. This method is used to identify the ABO alleles A(1), A(1v), B, O(1), O(1v), and O(2) in this chapter. Four amplicons (112, 121, 123, and 160 bp) labeled with fluorescence are separately amplified by polymerase chain reaction from exons 6 and 7 of ABO gene. These four fragments are combined into a single tube for SSCP-CE analysis using native gel to identify their single nucleotide polymorphism. This method can fast screen ABO genotypes from unknown samples and will be valuable in clinical transfusion or forensic applications.

An integrated system of ABO typing and multiplex STR testing for forensic DNA analysis

A new amplification system for ABO and STR genotyping in a single reaction has been successfully developed. Two types of information can be obtained from a biological sample at one time. One is the classical information of ABO blood group typing for screening suspects and the other is STR information for individual identification. The system allows for the simultaneous detection of 15 autosomal STR loci (containing all CODIS STR loci as well as Penta D and Penta E), six ABO genotypes (O/O, B/B, A/A, A/O, A/B, and B/O) and the gender-determining locus Amelogenin. Primers are designed so that the amplicons are distributed ranging from 75bp to 500bp within a four-dye fluorescent design, leaving a fourth dye for the internal size standard. With 30 cycles, the results showed that the optimal amount of DNA template for this multiplex ranges from 250pg to 2ng and the lowest detection threshold is 125pg (as low as 63pg for ABO loci). For the DNA template outside the optimal detection range, we could adjust the number of cycles to obtain the robust profiles. Mixture studies showed that over 83% of minor alleles were detected at 1:9 ratios. The full profiles were still observed when 4ng of degraded DNA was digested by DNase I and 1ng undegraded DNA was added to 40μM haematin. Polymerase chain reaction (PCR)-based conditions including the concentrations of primers, magnesium and the Taq polymerase as well as volume, cycle numbers and annealing temperature were examined and optimised. In addition, the system was validated by 364 bloodstain samples and 32 common casework samples. According to the Chinese National Standards and Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, our system demonstrates good detection performance and is an ideal tool for forensic DNA typing with potential application.

Determination of ABO genotypes by real-time PCR using allele-specific primers

ABO grouping of biological specimens is informative for identifying victims and narrowing down suspects. In Japan and elsewhere, ABO grouping as well as DNA profiling plays an essential role in crime investigations. In the present study, we developed a new method for ABO genotyping using allele-specific primers and real-time PCR. The method allows for the detection of three single nucleotide polymorphisms (SNPs) at nucleotide positions 261, 796, and 803 in the ABO gene and the determination of six major ABO genotypes. This method required less than 2 h for accurate ABO genotyping using 2.0 ng of DNA. This method could be applicable for rapid and simple screening of forensic samples.

Rapid direct PCR for ABO blood typing

Many different molecular typing methods have been reported to complement routine serological ABO blood typing in forensics. However, these ABO genotyping methods are often time-consuming and call for an initial DNA isolation step that requires the use of expensive kits or reagents. We report here a rapid direct ABO genotyping method that eliminates the need for DNA extraction from fresh blood, hair, and body fluid stains before PCR. Using a fast PCR instrument and an optimized polymerase, the genotyping method-which employs a multiplex allele-specific primer set for the simultaneous detection of three single-nucleotide polymorphism (SNP) sites (nucleotides 261, 526, and 803)-identifies A, B, O01/O02, O03, and cis-AB01 alleles in around 70 min from sample collection to electropherogram. Not only will this ABO genotyping method be efficiently used in forensic practice for rapid screening of samples before full-blown multilocus short tandem repeat profiling, but it will also demonstrate an example of rapid direct genotyping of SNPs that offers the advantages of time- and cost-efficiency, convenience, and reduced contamination during DNA analysis.

Multicolor real-time PCR genotyping of ABO system using displacing probes

Rapid and informative ABO genotyping has become increasingly popular in forensic use. We developed a multiplex real-time polymerase chain reaction (PCR) approach to genotype ABO major groups and subgroups. Seven differently fluorophor-labeled displacing probes for O(1)(261delG), A(261G), A(796C/803C), B(796A/803C), O(2) (802G>A), A(2) (1059delC), and A(2) (1009A>G) were combined in one or two PCRs to determine either ABO major groups or subgroups. The method correctly detected 13 reference DNA samples. A blind test of 237 samples resulted in complete agreement with their phenotypes, and 110 of these 237 samples as well as with PCR-SSP method. The whole analysis could be finished in less than 100 min at substantially low material cost and the template DNA ranging from 0.16 to 500 ng per reaction could be quantitatively detected. Despite the limited informativeness of ABO genotyping, the developed methods could find application in rapid and inexpensive screening of forensic settings.

Development of a laboratory project to determine human ABO genotypes-Limitations lead to further student explorations

A multiplex allele-specific PCR analysis was developed to identify six "common" genotypes: AA, AO, BB, BO, OO, and AB. This project included a pre-laboratory exercise that provided active learning experiences and developed critical thinking skills. This laboratory resulted in many successful analyses, which were verified by student knowledge of their phenotypes. However, the design was found to be deficient for the analysis of variants. The limitations in the original allied-health multiplex design were verified through a student designed problem-based laboratory project in an advanced level biochemistry class. Variants were further analyzed in an undergraduate research project using SSCP analyses. The topic of ABO genotyping provides several opportunities for student-centered explorations.

ABO genotyping by single strand conformation polymorphism--using CE

This study describes a novel method of ABO genotyping using amplicons generated by PCR-SSCP and separated by CE. We describe four amplicons with sizes of 112, 121, 123 and 160 bp based on SSCP analysis. These amplicons are amplified from exons 6 and 7 and include polymorphic sites of cDNA 261, 297, 467, 526, 646, 657, 681, 703, 1061 and 1096 generated from the ABO gene. The positions of the SSCP alleles, when rescaled using SSCP pattern as the mobility values based on an internal standard ranged, ranged from 146 to 210. The mobility variations of alleles with 1-4 SNPs within the same amplicons were from 1.88 to 12.01. These wide mobility differences allow for unambiguous allele determination. The use of different fluorescent dyes allows for the identification of two fragments with overlapping size ranges. The validity of the test was confirmed based on the SD of the mobility values from the eleven fragments of allelic ladder and it never exceeded 0.37. The mean values of the mobility variation between the samples and the ladders for the four amplicons ranged only from 0.05 to 0.39. This method was shown to successfully identify alleles A(1), A(1v), B, O(1), O(1v) and O(2) in tested samples. Since the largest amplicons are only 160 bp, this method is ideal for the fast screening ABO genotypes from trace, or seriously, degraded samples and may be valuable in clinical transfusion or forensic applications.

Biologic response to subcutaneous and intranasal therapy with desmopressin in a large Amish kindred with Type 2M von Willebrand disease

The aim of this study was to characterize the adequacy and longevity of biological response to desmopressin (DDAVP) in a large Amish kindred of Type 2M von Willebrand disease (VWD) possessing C-to-T transition at nucleotide 4120 in exon 28 of A1 domain of von Willebrand factor (VWF) gene. Response to both intranasal (Stimate) and subcutaneous DDAVP administration was assessed. Rise in ristocetin cofactor activity (VWF:RCo) > or = 40% at 90-min post-Stimate and 1-2 h after subcutaneous DDAVP was defined as initial response; response longevity was assessed only after subcutaneous dosing by measuring VWF:RCo levels at time-points 1, 2, 4 and 6 h. Eleven patients (five males, six females; age range: 20-56 years) participated in intranasal and 9/11 (four males, five females) in subcutaneous testing. Baseline haemostatic profiles included: VWF:RCo < 15%, VWF:Ag < 40% and normal VWF multimers. Initial response was comparable by both intranasal (6/11; 54.5%) and subcutaneous (4/9; 44%) routes; sustained response (VWF:RCo > 40% for 2 h) was observed in only one in nine (11%) patients tested. Median VWF:RCo peak levels after intranasal (40%) and subcutaneous (39%) routes were equivalent. Peak VWF:Ag levels were significantly higher after subcutaneous than intranasal DDAVP (94% vs. 54%; P = 0.03). Area under the curve for VWF:RCo was significantly decreased (170 microg h mL(-1)) compared with VWF:Ag (471 microg h mL(-1)) and FVIII:C (624.60 microg h mL(-1)). This study suggests that in this population: (i) intra-individual DDAVP response is consistent with subcutaneous and intranasal administration; and (ii) extending DDAVP challenge test up to at least 6 h is required to characterize adequacy and longevity of biologic response prior to using DDAVP as a sole haemostatic intervention.

Molecular genotyping and frequencies of A1, A2, B, O1 and O2 alleles of the ABO blood group system in a Kuwaiti population

Expression of the highly polymorphic ABO gene cluster is commonly investigated for blood transfusion and analysis, but little information is available for Middle Eastern populations. This study determined the major ABO allele frequency in a Kuwaiti Arab cohort using a multiplex PCR-RFLP technique; 355 unrelated blood donors of phenotype A1 (46), A2 (31), A1B (6), A2B (4), B (97) and O (171) were genotyped. DNA fragments of 252 (251 for O1) and 843 (842 for A2) bp spanning the two major exons, 6 and 7, of the ABO gene were amplified and digested with HpaII and KpnI. Thirteen different genotypes could be identified when combining the A1, A2, B, O1 and O2 alleles from the digestion patterns: 1 A1 A1 (0.28%), 6 A1 A2 (1.69%), 38 A1 O1 (10.71%), 1 A1 O2 (0.28%), 1 A2 A2 (0.28%), 30 A2 O1 (8.45%), 6 A1 B (1.69%), 4 A2 B (1.13%), 12 BB (3.38%), 79 BO1 (22.25%), 6 BO2 (1.69%), 167 O1 O1 (47.04%) and 4 O1 O2 (1.13%). Two of the combinations (A2 O2, O2 O2) were not found. All genotypes determined were consistent with the serotypes. The frequencies of the five alleles in the Kuwaiti sample population were ABO*A1 = 0.0746, ABO*A2 = 0.0592, ABO*B = 0.1676, ABO*O1 = 0.6831 and ABO*O2 = 0.0155. These results are discussed with reference to gene frequencies reported for other ethnic groups.

What a difference 2 nucleotides make: a short review of ABO genetics

ABO is the most important blood group system for transfusion and solid organ transplantation, but it is only over the past 15 years that the techniques for studying its molecular basis became mainstream. Many of its common and rare alleles are now well characterized and by using various expression systems, their effects on the resulting glycosyltransferases are being appreciated. As progress has been made in genetics and glycobiology, so too do reagents used to routinely type red blood cells in the clinical laboratory evolve. Monoclonal reagents are now widely used. This has created difficulties in nomenclature to describe subtype phenotypes as the names of some of these uncommon phenotypes were based on the red blood cell agglutination pattern using polyclonal reagents. In this brief review a discussion of the wild-type ABO allele and the enzymes it encodes is followed by a description of a selection of unusual and fascinating alleles-some that encode enzymes that create both A and B antigens and others that result from hybridization events. A short section on the techniques of ABO allele investigation describes some of the current methodologies used in both research and clinical laboratories.

ABO blood group alleles and genetic recombination

The ABO blood group gene is known to code for a glycosyltransferase, which acts at the last step of sequential extension of oligosaccharide chains attached to glycoproteins or glycolipids. Since the first delineation of the molecular basis of ABO blood group, genotype-phenotype relationship of various ABO alleles has been extensively studied. Major differences between the coding sequences of them were found to reside in exons 6 and 7. Over 70 alleles have been analyzed for their sequences, more than half of which were found to exhibit hybrid nature in their sequence motifs. These alleles seem to result not from recurrent mutation but most likely from intragenic recombination due to crossing-over or genetic conversion. Occurrence of reciprocal products and de novo recombinant support the idea. The aim of this article is to outline the genetic mechanism underlying the ABO allelic diversity with a speculative model for genesis of an allele.

A new method for ABO genotyping using a multiplex single-base primer extension reaction and its application to forensic casework samples

We developed a new method for ABO genotyping using a multiplex single-base primer extension reaction. The method allows for the simultaneous detection of six SNP sites in the ABO gene (nt 261, 297, 681, 703, 802, and 803) and the determination of ABO genotypes from their combinations. It enabled ABO genotyping of all samples of peripheral blood DNA extracted from 103 Japanese individuals, and had a highly satisfactory detection sensitivity being capable of genotyping 0.1 ng of genomic DNA. Using this method, we were able to determine ABO genotypes of minute stain samples, heated bloodstains, aged bloodstains and mixed samples. Experiments with samples from 26 animal species and bacterial samples to test the species-specificity of the method showed that genotyping was possible in the chimpanzee and gorilla, but their genotypes were extremely rare in humans. In addition, we applied this method to casework samples, and successfully determined ABO genotypes of bones, teeth, muscles, organs, nails, and semen-contaminated vaginal fluid in which ABO grouping by conventional serological techniques was not possible. This new method enables the sensitive, simultaneous detection of six SNP sites in the ABO gene by two specific reactions, i.e. PCR and a primer extension reaction. Therefore, it holds promise as an effective method of ABO genotyping particularly for forensic samples.

ABO locus O1 allele and risk of myocardial infarction

An association between ABO blood group and myocardial infarction (MI) has been described. One probable mechanism underlying this association is the influence of ABO blood group on plasma von Willebrand factor (vWF) levels. We conducted this genetic study to test whether the ABO O1 allele is associated with low vWF plasma levels and with a reduced risk of MI. Cases consisted of 793 consecutive, angiographically examined patients with either acute or prior MI. As controls served 340 angiographically examined patients with neither coronary artery disease nor signs of MI. ABO1 locus alleles (A1, A2, B, O1, O2) were identified with polymerase chain reaction and fluorogenic probes. The distribution of O1 alleles in the MI group versus the control group was: no O1 allele (15.4%/10.0%), one O1 allele (49.7%/50.0%) and two O1 alleles (34.9%/40.0%) (P = 0.035). O1 allele carriage was associated with a 39% reduction in the risk of MI unadjusted odds ratio, 0.61; 95% confidence interval, 0.41-0.91). The significant association was maintained after adjustment for other cardiovascular risk factors. vWF antigen levels correlated with the number of O1 alleles (P = 0.00003) in a separate control group (n = 164). Carriage of the O1 allele is associated with a decreased risk of myocardial infarction, with homozygosity providing the greatest protection.

Relationship between ABO and Secretor genotype with plasma levels of factor VIII and von Willebrand factor in thrombosis patients and control individuals

In contrast to earlier reports, this study examined the relationship between plasma levels of factor VIII (FVIII) and von Willebrand factor (VWF) and ABO blood group and secretor status at the genetic level in 355 patients with venous thrombosis as well as in 236 controls. ABO glycosyl transferase alleles A(1) and B were more frequent in the thrombosis collective and alleles O(1), O(2) and A(2) were more frequent in the controls. A low-risk group for venous thrombosis of individuals with genotypes O(1)O(1), O(1)O(2) and O(1)A(2) (H-antigen rich) could be distinguished from a high-risk group with genotypes A(1)A(1), A(1)B, O(1)A(1) and O(1)B (H-antigen poor). In both the thrombosis and control groups, the H-antigen rich group showed significantly lower levels of FVIII coagulant activity (FVIII:C) and VWF antigen (VWF:Ag) than the H-antigen poor group. The frequency of the different secretor genotypes in the thrombosis group was not different from that in the control group. No significant differences of FVIII:C and VWF:Ag levels were seen between SeSe, Sese and sese individuals in the thrombosis and in the control group. Thus the risk of venous thrombosis is associated with the ABO blood group genotype but not with secretor status.

A modified PCR-SSP method for the identification of ABO blood group antigens

The ABO blood group antigens are carbohydrate molecules synthesized by the glycosyltransferases encoded by the ABO gene on chromosome 9. Kidney transplantation across the ABO barrier generally leads to rapid humoral graft rejection due to the presence of naturally occurring antibodies to the A and B antigens. We have developed a method for ABO typing our cadaveric organ donors by the polymerase chain reaction using sequence-specific primers (PCR-SSP). The method uses 12 primers in eight PCR mixtures and is performed under the same conditions as our routine HLA-A, B, C PCR-SSP typing. The PCR-SSP-based types of 166 regular blood donors and 148 cadaveric organ donors all showed total concordance with their serologically assigned ABO groups. Six individuals possessing the ABO A subgroups (A3, Ax and Aend) all typed as A1 by PCR-SSP, as expected. PCR-SSP is an appropriate method for ABO typing of cadaveric organ donors and, importantly, enables both ABO and HLA typing to be performed on the same DNA material.

Systematic analysis of the ABO gene diversity within exons 6 and 7 by PCR screening reveals new ABO alleles

BACKGROUND

Mutations critical for ABO blood group phenotypes have predominantly been found in exons 6 and 7 of the ABO gene, both of which encode the catalytic domain of ABO glycosyltransferase. To design rapid and reliable ABO genotyping assays, a profound knowledge of the prevalent alleles is required and a reliable sequence database needs to be established.

STUDY DESIGN AND METHODS

A PCR screening system was established consisting of 102 different PCRs, each specific for a single nucleotide (nt) variation. The primer mixes were developed to walk from the 5' to the 3' end of exons 6 and 7 of the ABO gene to screen for nt mutations at 50 known polymorphic sites. A total of 109 unrelated individuals with common and rare ABO characteristics were screened. All blood samples in which the PCR results were inconclusive or inconsistent with the ABO phenotypes were subjected to sequence analysis of exons 6 and 7.

RESULTS

The results of PCR screening were conclusive and consistent with the ABO phenotypes in 90 cases. In the remaining 19 cases, PCR screening revealed unusual allele combinations or amplification results that were incompatible with known ABO allele combinations or subgroups predicted by serologic analysis. In these 19 cases, sequencing revealed new ABO alleles (one ABO*Ael allele, one ABO*B(A) allele and two ABO*O alleles) in two individuals with common and seven individuals with variant ABO phenotypes.

CONCLUSION

This PCR screening strategy is an effective tool for obtaining deeper insight into the ABO gene diversity and diversification and may be useful to increase the quality of the ABO sequence database.

Genomic analysis of clinical samples with serologic ABO blood grouping discrepancies: identification of 15 novel A and B subgroup alleles

Since the cloning in 1990 of complementary DNA corresponding to messenger RNA transcribed at the blood group ABO locus, polymorphisms and phenotype-genotype correlations have been reported by several investigators. Exons 6 and 7, constituting 77% of the gene, have been analyzed previously in samples with variant phenotypes but for many subgroups the molecular basis remains unknown. This study analyzed 324 blood samples involved in ABO grouping discrepancies and determined their ABO genotype. Samples from individuals found to have known subgroup alleles (n = 53), acquired ABO phenotypes associated with different medical conditions (n = 65), probable chimerism (n = 3), and common red blood cell phenotypes (n = 109) were evaluated by ABO genotype screening only. Other samples (n = 94) from apparently healthy donors with weak expression of A or B antigens were considered potential subgroup samples without known molecular background. The full coding region (exons 1-7) and 2 proposed regulatory regions of the ABO gene were sequenced in selected A (n = 22) or B (n = 12) subgroup samples. Fifteen novel ABO subgroup alleles were identified, 2 of which are the first examples of mutations outside exon 7 associated with weak subgroups. Each allele was characterized by a missense or nonsense mutation for which screening by allele-specific primer polymerase chain reaction was performed. The novel mutations were encountered in 28 of the remaining 60 A and B subgroup samples but not among normal donors. As a result of this study, the number of definable alleles associated with weak ABO subgroups has increased from the 14 previously published to 29.

Genotyping of Factor V G1691A (Leiden) without the Use of PCR by Invasive Cleavage of Oligonucleotide Probes

Background: The factor V G1691A Leiden (FVL) mutation is the most common known hereditary risk factor for venous thrombosis.

Methods: Third Wave Technologies, Inc. (Madison, WI) has developed a new microtiter plate-based assay that does not require PCR, restriction digestion, or gel electrophoresis. This technology system, termed the InvaderTM assay, utilizes a 5′ “invading” oligonucleotide and a partially overlapping 3′ “signal” oligonucleotide, which together form a specific structure when bound to a complementary genomic DNA template. A thermostable flap endonuclease cleaves this structure, releasing the 5′ flap from the signal oligonucleotide. Increased temperature and an excess of the signal probe enable multiple probes to be cleaved for each target sequence present without temperature cycling. The cleaved probes then direct cleavage of a secondary probe, which is 5′ end-labeled with fluorescein but is quenched by an internal dye. Upon cleavage, the fluorescein-labeled product is detected using a standard fluorescence plate reader. Genotypes are determined by net wild-type/mutant signal ratio.

Results: Complete concordance was observed, after resolution of four discordances, when 1369 individuals (1264 wild type, 102 heterozygous, 3 homozygous) were FVL genotyped by both the Invader assay and by allele-specific PCR.

Conclusion: We conclude that FVL genotyping using invasive cleavage of oligonucleotide probes is a rapid and reliable alternative to genotyping by more traditional PCR-based methods.

Single-tube multiplex PCR-SSCP analysis distinguishes 7 common ABO alleles and readily identifies new alleles

The ABO blood group is clinically the most important blood group system. Elucidation of the molecular basis of the ABO polymorphism allows genotype determination without family studies. Described here is a new method based on the simultaneous amplification by polymerase chain reaction (PCR) of 3 fragments from exon 6, and 5′ and 3′ ends of exon 7 of the ABO gene, followed by single-strand conformation polymorphism (SSCP) analysis. This multiplex PCR-SSCP protocol allows the well-established base changes at 9 nucleotide positions 261, 297, 467, 526, 646, 657, 681, 1059, and 1096 to be assayed simultaneously so that 7 common alleles (A1, A1v, A2, B, O1, O1v, and O2) can be distinguished in a single-tube single-lane format. Each allele was characterized by a set of 3 haplotype-specific SSCP patterns. Chinese (n = 125) and white European (n = 98) samples were analyzed, and their genotypes were found consistent with the serologic phenotypes or could be deduced unambiguously. Fifteen samples (2 Chinese and 13 white European) were each found carrying at least 1 rare allele. Most of these alleles were new and some might be generated by intragenic recombination. This technique is the simplest, quickest, and most informative method reported to date and also readily identifies new alleles.

Rapid identification of the ABO genotypes by their single-stand conformation polymorphism

The ABO locus on chromosome 9 contains many more alleles than are currently used routinely in forensic science. The use of single-strand conformation polymorphism (SSCP) can separate sequence polymorphisms that differ by only one base. The SSCP process used allows for both single- and double-stranded polymerase chain reaction (PCR) products to be visualized. The six ABO genotypes can be differentiated by the allele-specific B and O SSCP patterns. The double-stranded DNA produced 'hybrid' bands due to heterozygous samples and allowed sequence diversity to be detected between alleles of heterozygotes. These 'hybrid' bands are valid markers to confirm genotypes of specimens.

Prenatal genotyping of the Duffy blood group system by allele-specific polymerase chain reaction

Maternal allo-immunization to antigens of the Duffy blood group system can result in haemolytic disease of the newborn (HDN), therefore, the application of allele-specific polymerase chain reaction (ASPCR) for prenatal genotyping of the Duffy antigen system to identify pregnancies at risk for HDN was evaluated. Oligonucleotide primers were designed for ASPCR of FYA, FYB and nullFY alleles. A validation study was performed using DNA isolated from 94 serotyped whole blood samples and 8 amniocentesis samples. A concordance rate of 100 per cent was observed between serotyping and ASPCR detection of the FYA, FYB and nullFY alleles. This assay is particularly useful for rapid genotyping of fetal amniotic cells to identify pregnancies at risk for HDN due to maternal fetal incompatibilities within the Duffy blood group system.