Polymorphism analysis within the HLA-A locus by universal oligonucleotide array.
作者： Clarissa Consolandi , Andrea Frosini , Cinzia Pera , Gian Battista Ferrara , Roberta Bordoni
DOI: 10.1002/HUMU.20098
关键词:
摘要: Human leukocyte antigen (HLA) class I genes present some of the most complex single nucleotide polymorphism (SNP) patterns in human genome. HLA typing is therefore extremely challenging. In this article, we use ligation detection reaction (LDR) combined with a universal array (UA) as robust and efficient method to analyze SNPs within HLA-A region that includes alleles interest for immunotherapy tumor diseases. The LDR, UA platform, has been optimized 27 distributed exons 2 3 HLA-A. assay involves amplification by PCR genomic (1,900 bp), cycled reaction, followed capture ligated products through hybridization onto UA. Each slide was designed allow up eight samples parallel. PCR/LDR/UA evaluated analyzing 62 individuals (31 homozygous 31 heterozygous) previously typed direct sequencing. We demonstrate microarray genotyping procedure described here unambiguous alleles. perfect agreement obtained Our results clearly combination enzymatic processing demultiplexing tool SNP discrimination highly polymorphic region. specificity efficiency such an approach, suggesting feasibility low resolution procedure.
elsevier.com
sci-hub.se 参考文章(11)
Reyna Favis, Joseph P. Day, Norman P. Gerry, Catherine Phelan, Steven Narod, Francis Barany, Universal DNA array detection of small insertions and deletions in BRCA1 and BRCA2 Nature Biotechnology. ,vol. 18, pp. 561- 564 ,(2000) , 10.1038/75452
Ulrika Liljedahl, Julia Karlsson, Hakan Melhus, Lisa Kurland, Marie Lindersson, Thomas Kahan, Fredrik Nystrom, Lars Lind, Ann-Christine Syvanen, A microarray minisequencing system for pharmacogenetic profiling of antihypertensive drug response. Pharmacogenetics. ,vol. 13, pp. 7- 17 ,(2003) , 10.1097/00008571-200301000-00003
Jingwen Chen, Marie A Iannone, May-Sung Li, J David Taylor, Philip Rivers, Anita J Nelsen, Kimberly A Slentz-Kesler, Allen Roses, Michael P Weiner, A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Research. ,vol. 10, pp. 549- 557 ,(2000) , 10.1101/GR.10.4.549
C. Pera, L. Delflno, A. Morabito, A. Longo, L. Johnston-Dow, C. B. White, M. Colonna, G. B. Ferrara, HLA-A typing: comparison between serology, the amplification refractory mutation system with polymerase chain reaction and sequencing. Tissue Antigens. ,vol. 50, pp. 372- 379 ,(1997) , 10.1111/J.1399-0039.1997.TB02890.X
M. Schaffer, O. Olerup, HLA-AB typing by polymerase-chain reaction with sequence-specific primers: more accurate, less errors, and increased resolution compared to serological typing. Tissue Antigens. ,vol. 58, pp. 299- 307 ,(2001) , 10.1034/J.1399-0039.2001.580503.X
Clarissa Consolandi, Elena Busti, Cinzia Pera, Laura Delfino, Gian Battista Ferrara, Roberta Bordoni, Bianca Castiglioni, Luigi Rossi Bernardi, Cristina Battaglia, Gianluca De Bellis, Detection of HLA polymorphisms by ligase detection reaction and a universal array format: a pilot study for low resolution genotyping. Human Immunology. ,vol. 64, pp. 168- 178 ,(2003) , 10.1016/S0198-8859(02)00685-7
R. Ramakrishnan, An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. Nucleic Acids Research. ,vol. 30, ,(2002) , 10.1093/NAR/30.7.E30
Elena Busti, Roberta Bordoni, Bianca Castiglioni, Paolo Monciardini, Margherita Sosio, Stefano Donadio, Clarissa Consolandi, Luigi Rossi Bernardi, Cristina Battaglia, Gianluca De Bellis, Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction) BMC Microbiology. ,vol. 2, pp. 27- 38 ,(2002) , 10.1186/1471-2180-2-27
Norman P Gerry, Nancy E Witowski, Joseph Day, Robert P Hammer, George Barany, Francis Barany, Universal DNA microarray method for multiplex detection of low abundance point mutations. Journal of Molecular Biology. ,vol. 292, pp. 251- 262 ,(1999) , 10.1006/JMBI.1999.3063
R. Mendez, A. Serrano, E. Jäger, I. Maleno, F. Ruiz-Cabello, A. Knuth, F. Garrido, Analysis of HLA class I expression in different metastases from two melanoma patients undergoing peptide immunotherapy. Tissue Antigens. ,vol. 57, pp. 508- 519 ,(2001) , 10.1034/J.1399-0039.2001.057006508.X