Enabling routine ß-thalassemia Prevention and Patient Management by scalable, combined Thalassemia and Hemochromatosis Mutation Analysis.

BACKGROUND: Beta (ß)-thalassemia is one of the most common inherited disorders worldwide, with high prevalence in the Mediterranean, the Middle East and South Asia. Over the past 40 years, awareness and prevention campaigns in many countries have greatly reduced the incidence of affected child births. In contrast, much remains to be done in South-Asia. Thus, for Pakistan, an estimated ~ 7000 children annually are born with thalassemia, with no sign of improvement. Although there is good agreement that intermarriage of carriers significantly contributes to the high prevalence of the disorder, effective tools for molecular screening and diagnosis on which to base prevention programs are not readily available. METHODS: Here, we present results for a novel LeanSequencing™ process to identify a combination of 18 ß-thalassemia mutations (including the sickle cell anemia mutation, HbS, and structural variants HbC and HbE) and 2 hemochromatosis mutations in a multi-ethnic population of 274 pediatric and adolescent patients treated at Afzaal Memorial Thalassemia Foundation in Karachi, Pakistan. RESULTS: We found substantial differences in the predominance of disease-causing mutations among the principal ethnic groups in our cohort. We also found the hemochromatosis mutation H63D C > G in 61 (or 22.1%) of our patients including 6 (or 2.2%) homozygotes. CONCLUSIONS: To our knowledge, this is the first screen combining a large set of ß-thalassemia and hemochromatosis mutations, so as to facilitate the early identification of patients who may be at increased potential risk for complications from iron overload and thereby to improve the prospective management of thalassemia patients.

Mononuclear cells from a rare blood donor, after freezing under good manufacturing practice conditions, generate red blood cells that recapitulate the rare blood phenotype.

BACKGROUND: Cultured red blood cells (cRBCs) from cord blood (CB) have been proposed as transfusion products. Whether buffy coats discarded from blood donations (adult blood [AB]) may be used to generate cRBCs for transfusion has not been investigated. STUDY DESIGN AND METHODS: Erythroid progenitor cell content and numbers and blood group antigen profiles of erythroblasts (ERYs) and cRBCs generated in human erythroid massive amplification (HEMA) culture by CB (n = 7) and AB (n = 33, three females, three males, one AB with rare blood antigens cryopreserved using CB protocols) were compared. RESULTS: Variability was observed both in progenitor cell content (twofold) and number of ERYs generated (1 log) by CB and AB in HEMA. The average progenitor cell contents of the subset of AB and CB analyzed were similar. AB generated numbers of ERYs three times lower (p < 0.01) than CB in HEMA containing fetal bovine serum but similar to CB in HEMA containing human proteins. Female AB contained two times fewer (p < 0.05) erythroid progenitor cells but generated numbers of ERYs similar to those generated by male AB. Cryopreserved AB with a rare blood group phenotype and shipped to another laboratory generated great numbers of ERYs, 90% of which matured into cRBCs. Blood group antigen expression was consistent with the donor genotype for ERYs generated both by CB and AB but concordant with that of native RBCs only for cells derived from AB. CONCLUSION: Buffy coats from regular donors, including a donor with rare phenotypes stored under conditions established for CB, are not inferior to CB for the generation of cRBCs.

Toward extended phenotype matching: a new operational paradigm for the transfusion service.

BACKGROUND: Conventional pretransfusion testing uses hemagglutination to ensure donor-recipient compatibility for ABO/D status and recipient alloantibodies. While screening large numbers of donor units for multiple antigens by hemagglutination is impractical, novel methods of DNA analysis permit the rapid determination of an extended human erythrocyte antigen (xHEA) phenotype. A prospective observational study was conducted at four hospital transfusion services to test an alternative paradigm of identifying xHEA-typed units for patients in three cohorts by utilizing DNA analysis and a novel inventory management model. STUDY DESIGN AND METHODS: xHEA typing of recipient samples and donor units of known ABO/D status was performed by HEA analysis (BeadChip, BioArray Solutions). xHEA-typed units were assigned to pending transfusion requests using an inventory management system designed to simulate blood order processing. The fraction of requests fulfilled, or "fill fraction" (FF) was determined at four levels of matching stringency. RESULTS: For alloimmunized patients, all but one participating site observed an FF of more than 95% when matching for ABO, D, and known alloantibodies and an FF of more than 90% when additionally matching for C, c, E, e, and K; the site handling the most challenging requests still observed FFs of 62 and 51%, respectively. FF was found to correlate positively with the ratio of available donor units to units requested and negatively with the degree of recipient alloimmunization. CONCLUSION: This study demonstrates that substantial fill fractions can be achieved by selecting existing donor units for xHEA analysis and operating an inventory management system for efficient allocation of units to recipients.

Elevated thrombopoietin levels in patients with myelofibrosis may not be due to enhanced production of thrombopoietin by bone marrow.

Thrombopoietin (TPO) is recognized as the primary regulator of megakaryocyte and platelet production. Two alternative hypotheses for the mechanism of regulation have been proposed: (1) platelet and/or megakaryocyte mass regulate circulating TPO levels by binding to TPO through TPO receptors (c-MPL), with subsequent internalization and degradation of the protein; (2) TPO mRNA produced by bone marrow (BM) stromal cells or BM cells modulates blood TPO levels or platelet counts. In myeloproliferative disorders (MPD), including primary myelofibrosis (MF) and essential thrombocythemia (ET), elevated blood TPO levels occur despite increased platelet and megakaryocyte mass. Therefore, in these diseases, elevated blood TPO levels cannot be explained by the first mechanism. The present study, was designed to measure TPO mRNA production by BM mononuclear cells and BM stromal cells using a relative RT-PCR technique, to verify the second mechanism. We found no increase of TPO mRNA production in either BM cells or in BM stromal cells in patients with MF and ET. Furthermore, in those patients with MF who had elevated plasma TPO levels, TPO mRNA levels in bone marrow fibroblasts (BMFs) or BM cells were not elevated as compared with controls. Therefore, we concluded that in patients with MF, the elevated plasma TPO levels are not due to enhanced production of TPO mRNA either by BMF, or BM cells. The TPO receptor (c-MPL) abnormalities including reduced MPL protein levels or defective TPO induced signal transduction pathways are the likely mechanisms.

Competitive hybridization models.

Microarray technology, in its simplest form, allows one to gather abundance data for target DNA molecules, associated with genomes or gene-expressions, and relies on hybridizing the target to many short probe oligonucleotides arrayed on a surface. While for such multiplexed reactions conditions are optimized to make the most of each individual probe-target interaction, subsequent analysis of these experiments is based on the implicit assumption that a given experiment yields the same result regardless of whether it was conducted in isolation or in parallel with many others. It has been discussed in the literature that this assumption is frequently false, and its validity depends on the types of probes and their interactions with each other. We present a detailed physical model of hybridization as a means of understanding probe interactions in a multiplexed reaction. Ultimately, the model can be derived from a system of ordinary differential equations (ODE's) describing kinetic mass action with conservation-of-mass equations completing the system. We examine pairwise probe interactions in detail and present a model of "competition" between the probes for the target--especially, when the target is effectively in short supply. These effects are shown to be predictable from the affinity constants for each of the four probe sequences involved, namely, the match and mismatch sequences for both probes. These affinity constants are calculated from the thermodynamic parameters such as the free energy of hybridization, which are in turn computed according to the nearest neighbor (NN) model for each probe and target sequence. Simulations based on the competitive hybridization model explain the observed variability in the signal of a given probe when measured in parallel with different groupings of other probes or individually. The results of the simulations can be used for experiment design and pooling strategies, based on which probes have been shown to have a strong effect on each other's signal in the in silico experiment. These results are aimed at better design of multiplexed reactions on arrays used in genotyping (e.g., HLA typing, SNP, or CNV detection, etc.) and mutation analysis (e.g., cystic fibrosis, cancer, autism, etc.).

Determination of 24 minor red blood cell antigens for more than 2000 blood donors by high-throughput DNA analysis.

BACKGROUND: A "BeadChip" array permits reliable simultaneous DNA typing of single-nucleotide polymorphisms for minor blood groups. A high-throughput DNA analysis was studied as a routine method of phenotype prediction and software was developed to interpret and analyze the large volume of data points. STUDY DESIGN AND METHODS: DNA was extracted from whole blood of donors of known phenotypes and self-identified ethnicity. Analysis of single-nucleotide polymorphisms (SNPs) associated with 24 antigens of 10 blood group systems was performed with BeadChips (BioArray Solutions), and the results were compared to historical serologic typings. Phenotypes were predicted for individual samples, and phenotype prevalence was determined for ethnicities. The BeadChip was expanded to incorporate SNPs that silence the S antigen, validated, and tested with 369 DNA samples. A time-motion analysis was conducted. RESULTS: Results of BeadChip analyses were concordant with prediction of antigen negativity for 4,510 antigens. Eight discordant results were due to silencing of GYPB(S) and 16 were likely errors in recording serological results or data entry. The analyses produced 19,457 antigen-negative typings not serologically defined, identified 21 rare donors (Co(a-b+) [n = 1], Jo(a-) [n = 6], S-s-[n = 12], and K+k-[n = 2]), and determined allele frequencies and antigen prevalence for four ethnicities. The expanded panel detected 30 SS, 235 ss, 100 Ss, and 4 U- samples. The format processes 192 DNA samples (two plates) per 8-hour shift per technician, including automated data analysis and report generation. CONCLUSION: DNA analysis with BeadChip format, combined with computerized data entry and analysis, permits the prediction of minor blood group antigens.

A flexible array format for large-scale, rapid blood group DNA typing.

BACKGROUND: Typing for blood group antigens is currently performed by hemagglutination. The necessary reagents are becoming costly and limited in availability, and the methods are labor-intensive. The purpose of this study was to determine the feasibility of the use of large-scale DNA analysis in a microarray as a substitute for blood group typing. STUDY DESIGN AND METHODS: DNA, extracted from blood samples that had been phenotyped for some of the red blood cell antigens, was analyzed for selected blood group alleles by bead array (BeadChip, (BioArray Solutions Ltd., Warren, NJ) Illumina) [corrected] and by manual polymerase chain reaction (PCR)-based assays. Selected alleles were identified by enzyme-mediated elongation of probes, which were on color-encoded beads assembled into arrays on silicon chips. The performance of a prototype BeadChip (BioArray Solutions Ltd., Warren, NJ) [corrected] (BLOOD-1) containing single-nucleotide polymorphisms (SNPs) for FYA/B, FY-GATA, DOA/B, COA/B, LWA/B, DIA/B, and SC1/SC2 was verified with DNA from serologically characterized donors. It was then used to analyze more than 400 samples of partially defined phenotype. Samples from Chinese, Ashkenazi, and Thai donors (total n = 227) were tested with BLOOD-1. An expanded BeadChip (BioArray Solutions Ltd., Warren, NJ) [corrected] with a total of 18 SNPs (36 alleles; SNPs in BLOOD-1 and M/N, S/s, Lu(a)/Lu(b), K/k, FY265[for the Fy(X) polymorphism], Jk(a)/Jk(b), DO323[for Hy], DO350[for Jo(a)], and HgbS) was then evaluated with a subset of previously tested samples from Chinese, Ashkenazi, and New York blood donors (127) and an additional set of samples from Israeli donors (total n = 188). RESULTS: Results obtained by BeadChip (BioArray Solutions Ltd., Warren, NJ) [corrected] analysis were concordant with those obtained with the manual PCR-restriction fragment length polymorphism, allele-specific PCR, and hemagglutination assays. The frequencies of the alleles in the samples from different ethnic panels were within the expected ranges; however, two new DO alleles were discovered. CONCLUSION: It has been shown that microarray technology can be used to type DNA and detect new alleles in donor cohorts.

Cystic fibrosis carrier screening: validation of a novel method using BeadChip technology.

PURPOSE: To validate a novel BeadChip assay system for cystic fibrosis (CF) mutation testing using the panel of 25 ACMG recommended mutations and D1152H. METHODS: DNA from 519 individuals originally tested for CF mutation status by allele specific oligonucleotide hybridization (ASOH) were blindly analyzed by the BeadChip assay and the results were compared. The elongation mediated multiplexed analysis of polymorphisms (eMAP) protocol, which combines multiplex amplification of genomic DNA and multiplex detection of mutations on color-coded bead arrays, was used to analyze 26 CF mutations in two separate groups. RESULTS: The system accurately distinguished the 26 CF genotypes and had 100% concordance with the ASOH technique with an assay failure rate of 1.7%. Benign variants of exon 10 codons 506, 507, and 508 did not interfere with mutation identification and reflex testing for the 5/7/9T IVS8 polymorphism was performed on a separate array. CONCLUSIONS: The BeadChip assay system provided accurate and rapid identification of the ACMG recommended CF mutations.