Construction of microarrays for genotyping of DQA using unmodified 45-mer oligonucleotide

Yin, Bin‐Cheng; Fei, Yue; Ye, Bang‐Ce

doi:10.1007/s12033-007-0011-7

Cited by 5 publications

(3 citation statements)

References 13 publications

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“…For each allele, we only consider the amino acids located from the “start marker” to the “end marker” since this region constitutes the whole of exon 2. The class II MHC gene exon 2 encodes the peptide-binding sites, thereby contributing to the diversity in antigen presentation [ 23 , 24 , 25 ]. The DRA (HLA-DR

-chain) allele is very monomorphic; in contrast, both the DQA (HLA-DQ

-chain) and DPA (HLA-DP

-chain) alleles contain the polymorphisms specifying the peptide binding specificities [ 26 ], so we therefore considered the polymorphisms of both the

and

chains in the superMHC model development.…”

Section: Methodsmentioning

confidence: 99%

The Utility of Supertype Clustering in Prediction for Class II MHC-Peptide Binding

Shen

Zhang

et al. 2018

Molecules

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Motivation: Extensive efforts have been devoted to understanding the antigenic peptides binding to MHC class I and II molecules since they play a fundamental role in controlling immune responses and due their involvement in vaccination, transplantation, and autoimmunity. The genes coding for the MHC molecules are highly polymorphic, and it is difficult to build computational models for MHC molecules with few know binders. On the other hand, previous studies demonstrated that some MHC molecules share overlapping peptide binding repertoires and attempted to group them into supertypes. Herein, we present a framework of the utility of supertype clustering to gain more information about the data to improve the prediction accuracy of class II MHC-peptide binding. Results: We developed a new method, called superMHC, for class II MHC-peptide binding prediction, including three MHC isotypes of HLA-DR, HLA-DP, and HLA-DQ, by using supertype clustering in conjunction with RLS regression. The supertypes were identified by using a novel repertoire dissimilarity index to quantify the difference in MHC binding specificities. The superMHC method achieves the state-of-the-art performance and is demonstrated to predict binding affinities to a series of MHC molecules with few binders accurately. These results have implications for understanding receptor-ligand interactions involved in MHC-peptide binding.

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-chain) allele is very monomorphic; in contrast, both the DQA (HLA-DQ

-chain) and DPA (HLA-DP

-chain) alleles contain the polymorphisms specifying the peptide binding specificities [ 26 ], so we therefore considered the polymorphisms of both the

and

chains in the superMHC model development.…”

Section: Methodsmentioning

confidence: 99%

The Utility of Supertype Clustering in Prediction for Class II MHC-Peptide Binding

Shen

Zhang

et al. 2018

Molecules

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“…The MBMS was also employed to identify genotypes of the DQA1 gene. The design of the probe set corresponding to all alleles of exon2 of DQA1 gene, primers, and PCR amplification were described in detail in our previous papers . The microbeads attached with the DQA probe set were arranged in PDMS microchannels with an order of A1, A2, B1, B2, B3, C1, C2, D1, D2, D3, E1, E2, F1, F2, F3, F4, G1, G2, G3, H1, H2, H3, H4, H5, I1, I2, I3, I4, J1, J2, and Pos (Table S2 in the Supporting Information).…”

Section: Methodsmentioning

confidence: 99%

Multiplexed Bead-Based Mesofluidic System for Gene Diagnosis and Genotyping

Jin

Huo

et al. 2010

Anal. Chem.

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We have developed a novel multiplexed bead-based mesofluidic system (MBMS) based on the specific recognition events on the surface of a series of microbeads (diameter 250 μm) arranged in polydimethylsiloxane (PDMS) microchannels (diameter 300 μm) with the predetermined order and assembled an apparatus implementing automatically the high-throughput bead-based assay and further demonstrated its feasibility and flexibility of gene diagnosis and genotyping, such as β-thalassemia mutation detection and HLA-DQA genotyping. The apparatus, consisting of bead-based mesofluidic PDMS chip, liquid-processing module, and fluorescence detection module, can integrate the procedure of automated-sampling, hybridization reactions, washing, and in situ fluorescence detection. The results revealed that MBMS is fast, has high sensitivity, and can be automated to carry out parallel and multiplexed genotyping and has the potential to open up new routes to flexible, high-throughput approaches for bioanalysis.

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“…After hydration, the slides were exposed to UV light at 950 mJ/cm 2 in Stratalinker 2400 (Stratagene, CA, USA), then rinsed in boiling water for 2 min to denature the PCR product followed by rinsing in 100% alcohol for 1 min, dried by centrifugation at 1000 r.p.m. for 1 min, and stored in a vacuum oven [ 31 ].…”

Section: Methodsmentioning

confidence: 99%

Microarray-based estimation of SNP allele-frequency in pooled DNA using the Langmuir kinetic model

Yin

2008

BMC Genomics

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Background: High throughput genotyping of single nucleotide polymorphisms (SNPs) for genome-wide association requires technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. In this work, we have developed a theoretical approach to estimate allele frequency in pooled DNA samples, based on the physical principles of DNA immobilization and hybridization on solid surface using the Langmuir kinetic model and quantitative analysis of the allelic signals.

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Construction of microarrays for genotyping of DQA using unmodified 45-mer oligonucleotide

Cited by 5 publications

References 13 publications

The Utility of Supertype Clustering in Prediction for Class II MHC-Peptide Binding

The Utility of Supertype Clustering in Prediction for Class II MHC-Peptide Binding

Multiplexed Bead-Based Mesofluidic System for Gene Diagnosis and Genotyping

Microarray-based estimation of SNP allele-frequency in pooled DNA using the Langmuir kinetic model

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