Introduction of new alternative pipeline using multiplexed fast COLD­PCR together with sequencing approach highlighting pharmacoeconomics by detection of CYP variants.

In precision medicine, multiple factors are involved in clinical decision-making because of ethnic and racial genetic diversity, family history and other health factors. Although advanced techniques have evolved, there is still an economic obstacle to pharmacogenetic (PGx) implementation in developing countries. The aim of the present study was to provide an alternative pipeline that roughly estimate patient carrier type and prescreen out wild-type samples before sequencing or genotyping to determine genetic status. Fast co-amplification at lower denaturation temperature (COLD)-PCR was used to differentiate genetic variant non-carriers from carriers. The majority of drugs are hepatically cleared by cytochrome P450 (CYP) enzymes and genes encoding CYP enzymes are highly variable. Of all the CYPs, CYP2 family of CYP2C9, CYP2C19, and CYP2D6 isoforms have clinically significant impact on drugs of PGx testing. Therefore, five variants associated with these CYPs were selected for preliminary testing with this novel pipeline. For fast COLD-PCR, the optimal annealing temperature and critical denaturation temperature were determined and evaluated via Sanger sequencing of 27 randomly collected samples. According to precise Tc, to perform in a single-reaction is difficult. However, in this study, this issue was resolved by combination of precise Tc using 10+10+20 cycles. The results showed 100% sensitivity and specificity, with perfect agreement (κ=1.0) compared with Sanger sequencing. The present study provides a prescreening platform by introducing multiplex fast COLD-PCR as a pharmacoeconomic implementation. Our study just present in five variants which are not enough to describe patient metabolic status. Therefore, other actional genetic variants are still needed to cover the actual patient's genotypes. Nevertheless, the proposed method can well-present its efficiency and reliability for serving as a PGx budget platform in the future.

HLA-DRB1*04:05 and HLA-DQB1*04:01: Alleles Potentially Associated with Vogt-Koyanagi-Harada in Northern Thai Patients.

PURPOSE: To determine the frequency and association of alleles at human leukocyte antigen (HLA)-DRB1 and HLA-DQB1 loci in VKH disease patients from Northern Thailand. METHODS: A case-control study was conducted with three subject groups: 23 VKH patients, 20 patients with other uveitis entities, and 40 healthy blood donors. HLA-DRB1 and HLA-DQB1 loci were analyzed and the frequency of HLA-DRB1 and HLA-DQB1 alleles was calculated by direct counting. The measure of association was calculated by odds ratio (OR) and 95% confidence interval. RESULTS: In VKH patients, the most prevalent allele was HLA-DRB1*04:05, found in 35% of patients and with the highest OR (42.13). HLA-DQB1*04:01 was the next most prevalent, found in 23.91% of VKH patients. HLA-DQB1*05:02 was also detected in 23.91% of patients; however, a higher prevalence was observed in non-VKH and healthy controls (30% and 35%, respectively). CONCLUSION: HLA-DRB1*04:05 and HLA-DQB1*04:01 could be potential genetic markers for VKH.

Mixed-field agglutination observed in column agglutination testing is not always associated with the A3 subgroup.

CONCLUSIONS: Mixed-field agglutination (MFA) can be observed in forward typing of samples from A3 individuals with serologic ABO typing methods. The results of column agglutination testing (CAT) and tube agglutination testing using different antibody clones can be discordant. In this report, we reveal our experience using polymerase chain reaction-sequence-based typing (PCR-SBT) of ABO exon 7 to clarify serologic method discordance of A subgroup blood typing in Northern Thai donors. A total of 21 group A blood donors with either MFA or weak agglutination on routine ABO CAT were recalled. CAT was repeated with human and monoclonal anti-A, and tube agglutination testing with monoclonal anti-A and PCR-SBT of ABO exon 7 was performed. A total of 13 of the 21 donors returned, and ABO CAT with human anti-A was repeated. Eleven samples showed MFA suspected to be the A3 subgroup, and two samples showed 2+ strength suspected to be the Aweak subgroup. When tube agglutination testing using monoclonal antibody was performed, MFA was not observed in 9 of 11 samples with previously observed MFA from routine CAT, which were then interpreted as A2. From PCR-SBT performed in only exon 7 of the ABO gene, 7 of 13 sample results were consistent with ABO*A2 or ABO*AW alleles. Two samples suspected to be A2 or A3 had an ABO*AW allele. In two samples suspected to be Aweak, no mutation was detected in ABO exon 7, suggesting genetic variation elsewhere in the gene. Although other coding exons were not examined, in the alleles that could be assigned, ABO*A3 alleles were found less frequently than would be predicted from the serologic findings. These findings suggest that when MFA in routine CAT is observed, an A3 subgroup cannot be presumed. Caution should be exercised when MFA is noted in routine CAT.

Detection of blood group genes using multiplex SNaPshot method.

BACKGROUND: The determination of blood group antigens in patients and donors is of primary importance in transfusion medicine. Blood group antigens are inherited and are polymorphic in nature. The majority of polymorphic blood group antigens arise from single-nucleotide polymorphisms (SNPs) in the blood group genes. Many DNA-based assays, such as species-specific polymerase chain reaction (PCR), PCR-restriction fragment length polymorphism, and microchips, have been described to study variant blood group genes. In this study, the SNaPshot (Applied Biosystems) method was adapted to detect SNPs in 10 common blood group systems. STUDY DESIGN AND METHODS: DNA regions of interest were amplified in multiplex PCR and annealed to specific oligonucleotide probe primers of different lengths. AmpliTaq DNA polymerase extended the primers by adding only a single fluorescent ddNTP to its 3' end and was detected by differential mobility in capillary electrophoresis in a genetic analyzer. Results were analyzed using computer software in SNaPshot default analysis method. RESULTS: Seventeen SNP sites in 29 blood samples, previously phenotyped and/or genotyped, were used to test the accuracy and reproducibility of multiplex SNaPshot assays. The results were compared with the previously analyzed types. SNaPshot analyses predicted the 17 SNP sites accurately for all the 29 blood samples. Both homozygous and heterozygous blood groups were detected with equal confidence. CONCLUSION: Blood group detection by SNaPshot method is a practical alternative to antibody-dependent phenotype prediction. Starting with DNA, this method is fast with a turnaround time of 24 hours with mean reagent cost around $2 per SNP detected.

Prevalence of CYP2C9 and VKORC1 mutation in patients with valvular heart disease in northern Thailand.

BACKGROUND: Warfarin has been widely used for the prevention and treatment of thromboembolism. Warfarin therapy depends on interaction between physiological, environmental, and genetic factors. Vitamin K epoxide reductase (VKORC1) and cytochrome P450 2C9 (CYP2C9) enzyme conjointly determine the warfarin maintenance dose. The prevalence of CYP2C9 and VKORC1 variants varies among ethnic groups. The purpose of the present study was to investigate the prevalence of CYP2C and VKORC1 in the Northern Thai population. MATERIAL AND METHOD: Patients with valvular heart disease who regularly took a steady maintenance warfarin dose for at least one month were recruited into the present study. Patients who had taken amiodarone or an anti-inflammatory drug were excluded Clinical data were obtained from medical records. Five milliliters of whole blood was drawn from each patient for gene analysis and prothrombin time with international normalized ratio (INR) measurement. RESULTS: From 242 patients, CYP2C9 *1/*1 was found in 230 patients (95%) and CYP2C9 *1/*3 was found in 12 patients (5%). Neither mutant CYP2C9*2 allele nor individuals homozygous for CYP2C9*3 were observed. Regarding VKORC1, haplotype AB was found in 83 patients (34.3%) and haplotype AA was found in 154 patients (63.6%). Haplotype BB (wild type) was found in five patients (2.1%). CONCLUSION: The prevalence of CYP2C9 *1/*1 is high while the prevalence of CYP2C9*2 and CYP2C9*3 is very low. VKORC1 haplotype AA is the most common among the Northern Thai population. Further study regarding pharmacogenetic and non-genetic factors to develop warfarin-dosing algorithm is warranted

Novel GYP(A-B-A) hybrid gene in a DANE+ person who made an antibody to a high-prevalence MNS antigen.

BACKGROUND: The glycophorin (GP) molecule associated with the GP.Dane phenotype is a GP(A-B-A) hybrid that contains some amino acids encoded by the Pseudoexon 3 of GYPB and Asn(45) of GPA and carries the low-prevalence MNS antigens DANE and Mur. Serum from a woman of English ancestry contained an immunoglobulin M alloantibody to a high-prevalence MNS antigen, and the purpose of this study was to identify the molecular basis of her phenotype. STUDY DESIGN AND METHODS: Hemagglutination, Western blotting, and DNA analyses were performed by standard methods. RESULTS: Tests of the proband's RBCs with monoclonal antibodies indicated a change of amino acids between positions 27 and 55 of GPA. Her RBCs expressed M, s, Mur, and DANE antigens and were M(g)-negative. The antigen recognized by her antibody was sensitive to treatment with papain, ficin, and trypsin and resistant to alpha-chymotrypsin and dithiothreitol. Sequencing of DNA from the proband revealed a sequence of nucleotides identical to the GYP(A-B-A) encoding GP.Dane but without the adenyl nucleotide substitution, which has been predicted to change Ile(46) of GPA to Asn(45). Testing of her immediate family revealed the presence of an M(k) gene. CONCLUSION: The proband had a novel GYP(A-B-A) encoding a DANE+ GP that is in cis to GYPB(s) and in trans to M(k). The high-prevalence antigen lacking from this GP.Dane phenotype and recognized by the proband's serum is called ENDA (ISBT Number MNS44). Our results indicate that the change of Ile(46) of GPA to Asn(45) of GP.Dane is not required for expression of the DANE antigen.