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12. Additional file 1 of Hepatocellular carcinoma detection via targeted enzymatic methyl sequencing of plasma cell-free DNA

Author

Guo, Ping, Zheng, Hailing, Li, Yihan, Li, Yuntong, Xiao, Yue, Zheng, Jin, Zhu, Xingqiang, Xu, Huan, He, Zhi, Zhang, Qian, Chen, Jinchun, Qiu, Mingshan, Jiang, Min, Liu, Pingguo, and Chen, Hongliang

Abstract

Additional file 1: Figure S1. Comparison of conversion efficiency between EM-seq and BS-seq. a Dot plot compare individual methylation values in hypermethylated CpGs acquired by EM-Seq and BS-seq (r = 0.91, P < 0.0001). Percentages indicate the fraction of CpGs that differed between conditions. Hypermethylated CpGs are those with BS-seq detection values of > 80% on pUC19 DNA. b Genome plot for unmethylated control λ DNA(30,000–35,000)compares CH reads between EM-seq and BS-seq datasets. Boxes represent reads, and unmethylated (blue) and methylated (red) CHGs are indicated. c Pie charts compare the proportion of reads with 0, 1, 2 and ≥ 3 CH sites in EM-seq (SRR10532128) and BS-seq (SRR10532135) sequencing reads from public database. d Methylation values on hypermethylated CpGs acquired by EM-Seq and BS-seq, before and after ≥ 3CHs filtration. ns represents no significance. e Dot plot compare individual methylation values in hypomethylated CpGs acquired by EM-Seq and BS-seq after 3CH read filtering. Percentages indicate the fraction of CpGs that differed between conditions. Figure S2. Performance of targeted EM-seq. a Unique read depth (PCR duplication removed) observed in EM-seq and BS-seq with same input quantities (20 ng). b Heat maps compare individual CpG methylation values in the target panel acquired by targeted EM-Seq between technical replicates (r = 0.999). c Heat map shows coverage depth of CpGs between replicates of a 20 ng targeted EM-seq library (r = 0.982). d Fragment size distributions of plasma sample from a healthy donor. Figure S3. Comparison of HCC predictive model with AFP and PIVKA-II. a Proportions of positive calling by HCC screening model in HCC patients with different AFP levels in the test set. b Proportions of positive calling by HCC screening model in HCC patients with different PIVKA-II levels in the test set.

Published
2023
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22. An adaptive detection method for fetal chromosomal aneuploidy using cell-free DNA from 447 Korean women

Author

Kim, Sunshin, primary, Jung, HeeJung, additional, Han, Sung Hee, additional, Lee, SeungJae, additional, Kwon, JeongSub, additional, Kim, Min Gyun, additional, Chu, Hyungsik, additional, Han, Kyudong, additional, Kwak, Hwanjong, additional, Park, Sunghoon, additional, Joo, Hee Jae, additional, An, Minae, additional, Ha, Jungsu, additional, Lee, Kyusang, additional, Kim, Byung Chul, additional, Zheng, Hailing, additional, Zhu, Xinqiang, additional, Chen, Hongliang, additional, and Bhak, Jong, additional

Published
2016
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23. Species Identification of Silks from Bombyx mori, EriSilkworm and Chestnut Silkworm Using Western Blot and Proteomics Analyses

Author

Gu, Jincui, Xu, Chengfeng, Li, Menglu, Chen, Boyi, Shang, Yating, Zheng, Hailing, Zhou, Yang, Hu, Zhiwen, Peng, Zhiqin, and Wang, Bing

Abstract

Species identification is of key significance for exploring the origin and transmission of ancient silks. In this study, two novel methods, i.e.western blot (WB) and proteomics analyses, were proposed and established to identify the differences between silks from Bombyx mori(B. mori) and two other distinctive species (Eri silkworm and Chestnut silkworm). Three diagnostic antibodies, a polyclonal anti-silk fibroin (anti-SF) antibody (pAb), a polyclonal anti-SF-specific peptide antibody (pAsb), and a monoclonal anti-SF antibody (mAb) were designed and prepared to distinguish silk species using the antibody-based WB technique. Proteomics analysis by liquid chromatography–tandem mass spectrometry was performed to further identify silk species at the protein level. WB results indicated that the three antibodies showed high specificity and affinity and could discern B. morisilk from Eriand Chestnutsilks. Biomarkers for each SF were obtained using proteomics analysis, and they have the potential to serve as standards for identifying silk species. Thus, combining WB and proteomics analyses with conventional methods can provide more accurate silk information and may be suitable for identifying other proteinaceous materials in archaeological field.

Published
2019
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24. The Feasibility Study of Non-Invasive Fetal Trisomy 18 and 21 Detection with Semiconductor Sequencing Platform

Author

Jeon, Young Joo, primary, Zhou, Yulin, additional, Li, Yihan, additional, Guo, Qiwei, additional, Chen, Jinchun, additional, Quan, Shengmao, additional, Zhang, Ahong, additional, Zheng, Hailing, additional, Zhu, Xingqiang, additional, Lin, Jin, additional, Xu, Huan, additional, Wu, Ayang, additional, Park, Sin-Gi, additional, Kim, Byung Chul, additional, Joo, Hee Jae, additional, Chen, Hongliang, additional, and Bhak, Jong, additional

Published
2014
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25. Articles on Comparative Literature in China

Author

Yue, Daiyun, primary, Fang, Hanwen, additional, Zhang, Hong, additional, Cheng, Guangwei, additional, Li, Xiaojun, additional, Zheng, Hailing, additional, Song, BingHui, additional, Yang, Lixin, additional, Chen, Xiaolan, additional, Lei, Na, additional, and Yan, Jindong, additional

Published
2005
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