ABSTRACT
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.
Subject(s)
Blood Donors , Blood Group Antigens/genetics , DNA/genetics , Algorithms , Alleles , DNA/isolation & purification , Erythrocytes , Gene Frequency , Genotype , Haplotypes , Humans , Mutation , Phenotype , Polymorphism, Single Nucleotide , Sequence Analysis, DNA/methodsABSTRACT
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.
