Search

Your search keyword '"Yin, Yuxin"' showing total 969 results
Start Over Author "Yin, Yuxin"
969 results on '"Yin, Yuxin"'

76. Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples.

Author

Yin, Yuxin, Lan, James H, Nguyen, David, Valenzuela, Nicole, Takemura, Ping, Bolon, Yung-Tsi, Springer, Brianna, Saito, Katsuyuki, Zheng, Ying, Hague, Tim, Pasztor, Agnes, Horvath, Gyorgy, Rigo, Krisztina, Reed, Elaine F, and Zhang, Qiuheng

Subjects
Mouth Mucosa, Humans, HLA Antigens, Histocompatibility Testing, Sequence Analysis, DNA, Gene Frequency, Genotype, Alleles, Exons, Tissue Donors, Workflow, High-Throughput Nucleotide Sequencing, Multiplex Polymerase Chain Reaction, Sequence Analysis, DNA, General Science & Technology
Abstract

BackgroundUnambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA.MethodsMultiplex long-range PCR primers amplified the full-length of HLA class I genes (A, B, C) from promotor to 3' UTR. Class II genes (DRB1, DQB1) were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2×250 bp paired-end sequencing on the Illumina MiSeq. HLA typing was assigned using Omixon Twin software that combines two independent computational algorithms to ensure high confidence in allele calling. Consensus sequence and typing results were reported in Histoimmunogenetics Markup Language (HML) format. All homozygous alleles were confirmed by Luminex SSO typing and exon novelties were confirmed by Sanger sequencing.ResultsUsing this automated workflow, over 10,063 NMDP registry donors were successfully typed under high-resolution by NGS. Despite known challenges of nucleic acid degradation and low DNA concentration commonly associated with buccal-based specimens, 97.8% of samples were successfully amplified using long-range PCR. Among these, 98.2% were successfully reported by NGS, with an accuracy rate of 99.84% in an independent blind Quality Control audit performed by the NDMP. In this study, NGS-HLA typing identified 23 null alleles (0.023%), 92 rare alleles (0.091%) and 42 exon novelties (0.042%).ConclusionLong-range, unambiguous HLA genotyping is achievable on clinical buccal swab-extracted DNA. Importantly, full-length gene sequencing and the ability to curate full sequence data will permit future interrogation of the impact of introns, expanded exons, and other gene regulatory sequences on clinical outcomes in transplantation.

Published
2016

77. Platelet-Rich Plasma in Young and Elderly Humans Exhibits a Different Proteomic Profile

Author

Jiang, Zhitong, Huang, Can, Guo, Erliang, Zhu, Xiangbin, Li, Na, Huang, Yu, Wang, Peihe, Shan, Hui, Yin, Yuxin, Wang, Hong, Huang, Lei, Han, Zhen, Ouyang, Kunfu, Sun, Lu, Jiang, Zhitong, Huang, Can, Guo, Erliang, Zhu, Xiangbin, Li, Na, Huang, Yu, Wang, Peihe, Shan, Hui, Yin, Yuxin, Wang, Hong, Huang, Lei, Han, Zhen, Ouyang, Kunfu, and Sun, Lu

Abstract

As people age, their ability to resist injury and repair damage decreases significantly. Platelet-rich plasma (PRP) has demonstrated diverse therapeutic effects on tissue repair. However, the inconsistency of patient outcomes poses a challenge to the practical application of PRP in clinical practice. Furthermore, a comprehensive understanding of the specific impact of aging on PRP requires a systematic investigation. We derived PRP from 6 young volunteers and 6 elderly volunteers, respectively. Subsequently, 95% of high-abundance proteins were removed, followed by mass spectrometry analysis. Data are available via ProteomeXchange with the identifier PXD050061. We detected a total of 739 proteins and selected 311 proteins that showed significant differences, including 76 upregulated proteins in the young group and 235 upregulated proteins in the elderly group. Functional annotation and enrichment analysis unveiled upregulation of proteins associated with cell apoptosis, angiogenesis, and complement and coagulation cascades in the elderly. Conversely, IGF1 was found to be upregulated in the young group, potentially serving as the central source of enhanced cell proliferation ability. Our investigation not only provides insights into standardizing PRP preparation but also offers novel strategies for augmenting the functionality of aging cells or tissues. © 2024 American Chemical Society.

Published
2024

79. Impact of three Illumina library construction methods on GC bias and HLA genotype calling

Author

Lan, James H, Yin, Yuxin, Reed, Elaine F, Moua, Kevin, Thomas, Kimberly, and Zhang, Qiuheng

Subjects
Genetics, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Alleles, Cost-Benefit Analysis, Gene Library, Genotype, HLA Antigens, High-Throughput Nucleotide Sequencing, Histocompatibility Testing, Humans, Reproducibility of Results, Transposases, HLA genotyping, NGS, Transposase, Illumina Nextera, GC bias, Immunology
Abstract

Next-generation sequencing (NGS) is increasingly recognized for its ability to overcome allele ambiguity and deliver high-resolution typing in the HLA system. Using this technology, non-uniform read distribution can impede the reliability of variant detection, which renders high-confidence genotype calling particularly difficult to achieve in the polymorphic HLA complex. Recently, library construction has been implicated as the dominant factor in instigating coverage bias. To study the impact of this phenomenon on HLA genotyping, we performed long-range PCR on 12 samples to amplify HLA-A, -B, -C, -DRB1, and -DQB1, and compared the relative contribution of three Illumina library construction methods (TruSeq Nano, Nextera, Nextera XT) in generating downstream bias. Here, we show high GC% to be a good predictor of low sequencing depth. Compared to standard TruSeq Nano, GC bias was more prominent in transposase-based protocols, particularly Nextera XT, likely through a combination of transposase insertion bias being coupled with a high number of PCR enrichment cycles. Importantly, our findings demonstrate non-uniform read depth can have a direct and negative impact on the robustness of HLA genotyping, which has clinical implications for users when choosing a library construction strategy that aims to balance cost and throughput with data quality.

Published
2015

90. Dynamic Three Parameter Range Shifting Law of the Multi-range Hydro-Mechanical CVT

Author

Zhang, Mingzhu, Yin, Yuxin, Hao, Xiaoyang, Wang, Tingting, Cui, Mingming, Kacprzyk, Janusz, Series editor, Pal, Nikhil R., Advisory editor, Bello Perez, Rafael, Advisory editor, Corchado, Emilio S., Advisory editor, Hagras, Hani, Advisory editor, Kóczy, László T., Advisory editor, Kreinovich, Vladik, Advisory editor, Lin, Chin-Teng, Advisory editor, Lu, Jie, Advisory editor, Melin, Patricia, Advisory editor, Nedjah, Nadia, Advisory editor, Nguyen, Ngoc Thanh, Advisory editor, Wang, Jun, Advisory editor, Qiao, Feng, editor, Patnaik, Srikanta, editor, and Wang, John, editor

Published
2018
Full Text
View/download PDF

91. Integrated Optimal Speed Change Law of Hydro-Mechanical Continuously Variable Transmission Tractor

Author

Zhang, Mingzhu, Hao, Xiaoyang, Yin, Yuxin, Cui, Mingming, Wang, Tingting, Kacprzyk, Janusz, Series editor, Pal, Nikhil R., Advisory editor, Bello Perez, Rafael, Advisory editor, Corchado, Emilio S., Advisory editor, Hagras, Hani, Advisory editor, Kóczy, László T., Advisory editor, Kreinovich, Vladik, Advisory editor, Lin, Chin-Teng, Advisory editor, Lu, Jie, Advisory editor, Melin, Patricia, Advisory editor, Nedjah, Nadia, Advisory editor, Nguyen, Ngoc Thanh, Advisory editor, Wang, Jun, Advisory editor, Qiao, Feng, editor, Patnaik, Srikanta, editor, and Wang, John, editor

Published
2018
Full Text
View/download PDF

94. Fermentation of Robinia pseudoacacia flower for improving the antioxidation: optimized conditions, active composition, mechanism, and biotransformation process

Author

Yang, Yi, Zhang, Yunci, Gu, Dongyu, Liu, Chang, Wang, Yi, Tang, Shanshan, Yin, Yuxin, and Tian, Jing

Subjects
General Medicine, Biochemistry, Biotechnology
Abstract

Robinia pseudoacacia flower is a natural product with many biological activities, including antioxidation. To further develop its antioxidation, the extract was fermented by Aspergillus niger FFCC 3112 in the medium with carbon to nitrogen ratio of 1.4:1 and initial pH of 4.2 for 3.5 days to form the best antioxidant activity of the fermentation product by strain screening, single factor optimization, and response surface methodology. Further analysis, isolation and activity determination showed that a main chemical component, kaempferol-3-O-α-L-rhamnopyranosyl-(1→6)-β-D-galactopyranosyl-7-O-α-L-rhamnopyranoside, in the extract was completely hydrolyzed to kaempferol-7-O-α-L-rhamnopyranoside and kaempferol with better antioxidant activity through biotransformation, which was the basis for improving the antioxidant activity of fermentation products. Moreover, the mechanism of antioxidant and the contribution of phenolic hydroxyl groups were investigated by density functional theory. The result indicated that the antioxidant capacity of kaempferol-7-O-α-L-rhamnopyranoside and kaempferol increased with the increase of solvent polarity. In high-polarity solvents, they mainly scavenge free radicals through single electron transfer followed by proton transfer.

Published
2023
Full Text
View/download PDF

99. Tuning the Organ Tropism of Polymersome for Spleen‐Selective Nanovaccine Delivery to Boost Cancer Immunotherapy (Adv. Mater. 41/2023)

Author

Gu, Wenxing, primary, An, Jingnan, additional, Li, Yaxi, additional, Yang, Yajie, additional, Wang, Shumin, additional, Shan, Hui, additional, Li, Shenhua, additional, Li, Hui, additional, Liu, Guoyong, additional, Li, Kai, additional, Yin, Yuxin, additional, Mu, Jing, additional, and Chen, Xiaoyuan, additional

Published
2023
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results