Multiplex single nucleotide extension: a robust and high throughput method for HLA-A locus typing.
This report describes a typing method that can identify all known human leukocyte antigen A (HLA-A) alleles by determining nucleotides present at polymorphic sites using single nucleotide extension. Allele specific primers are bound to capture oligonucleotides which allows for a multiplex approach during single nucleotide extension (SNE) reactions. Eleven group-specific polymerase chain reaction amplifications were performed to obtain the templates to be analyzed with sets of primers designed to investigate the polymorphisms. Extension of biotin-labeled ddNTPs onto allele-specific primers was catalyzed by a DNA polymerase and each primer was hybridized to a specific capture oligonucleotide covalently bound to a bead. After staining with streptavidin-PE, incorporated fluorescence was determined with a flow cytometer. Fluorescence intensities were interpreted by computer and the nucleotide sequence was translated into HLA-A genotypes. Group-specific amplification reactions and primer sets for SNE were validated with 42 reference samples of known HLA-A alleles. In addition, 296 samples from three populations (N. A. Caucasian, African-American, Terena S. A. Indian) were analyzed and results compared to previous typing by SSOP. Reproducibility between repeated typings was 100% and ambiguities were quite rare. The method has been found to be accurate, relatively simple to perform and fast. It is our method of choice for high resolution clinical HLA-A typing.
Han
Mei
M
Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8886, USA.
Tan
Yue Qing
YQ
Zhang
Yanzheng
Y
Tsai
Jeannette
J
Vorhaben
Rob
R
Moraes
J Roberto
JR
Moraes
M Elisa
ME
Stastny
Peter
P
D000483:Alleles; D001483:Base Sequence / Q000235:genetics; D015234:HLA-A Antigens / Q000235:genetics*; D006650:Histocompatibility Testing; D006801:Humans; D007962:Leukocytes / Q000276:immunology*; D015345:Oligonucleotide Probes / Q000737:chemistry; D016133:Polymerase Chain Reaction; D018807:Polymorphism, Single-Stranded Conformational; D015203:Reproducibility of Results
D015234:HLA-A Antigens; D015345:Oligonucleotide Probes