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| 1 | 染色体微阵列分析技术在产前诊断中的应用专家共识显示文摘目前,G显带染色体核型分析技术仍然是细胞遗传学产前诊断的“金标准”,但该技术具有细胞培养耗时长、分辨率低以及耗费人力的局限性.包括荧光原位杂交(fluorescence in situ hybridization,FISH)技术在内的快速产前诊断技术的引入虽然具有快速及特异性高的优点,但还不能做到对染色体组的全局分析.染色体微阵列分析(chromosomal microarray analysis,CMA)技术又被称为“分子核型分析”,能够在全基因组水平进行扫描,可检测染色体不平衡的拷贝数变异(copy number variant,CNV),尤其是对于检测染色体组微小缺失、重复等不平衡性重排具有突出优势. | | 2014 | 中华妇产科杂志2014，49，8： | 240 |
| 2 | 染色体基因组芯片在儿科遗传病的临床应用专家共识显示文摘自21世纪初发现并证实基因组拷贝数变异(copy number variations,CNV)可导致人类遗传病以来[1],基因组病作为遗传病中的一类重要疾病,受到越来越多关注.在欧美国家,染色体基因组芯片分析(chromosome microarray analysis,CMA)目前已成为一项常规的临床遗传学诊断工具.继美国医学遗传学会(American College of Medical Genetics and Genomics,ACMG)专家委员会CMA指南(2010年10月)发布后[2],加拿大、澳大利亚、法国和比利时等国相继发布各自的相关CMA临床应用指南或共识[3-4]. | | 2016 | 中华儿科杂志2016，54，6： | 56 |
| 3 | Analysis of long non-coding RNA expression profiles in gastric cancer显示文摘AIM: To investigate the expression patterns of long non-coding RNAs (lncRNAs) in gastric cancer. METHODS: Two publicly available human exon arrays for gastric cancer and data for the corresponding normal tissue were downloaded from the Gene Expression Omnibus (GEO). We re-annotated the probes of the human exon arrays and retained the probes uniquely mapping to lncRNAs at the gene level. LncRNA expression profiles were generated by using robust multi-array average method in affymetrix power tools. The normalized data were then analyzed with a Bioconductor package linear models for microarray data and genes with adjusted P -values below 0.01 were considered differentially expressed. An independent data set was used to validate the results. RESULTS: With the computational pipeline established to re-annotate over 6.5 million probes of the Affymetrix Human Exon 1.0 ST array, we identified 136053 probes uniquely mapping to lncRNAs at the gene level. These probes correspond to 9294 lncRNAs, covering nearly 76% of the GENCODE lncRNA data set. By analyzing GSE27342 consisting of 80 paired gastric cancer and normal adjacent tissue samples, we identified 88 lncRNAs that were differentially expressed in gastric cancer, some of which have been reported to play a role in cancer, such as LINC00152, taurine upregulated 1, urothelial cancer associated 1, Pvt1 oncogene, small nucleolar RNA host gene 1 and LINC00261. In the validation data set GSE33335, 59% of these differentially expressed lncRNAs showed significant expression changes (adjusted P -value < 0.01) with the same direction. CONCLUSION: We identified a set of lncRNAs differentially expressed in gastric cancer, providing useful information for discovery of new biomarkers and therapeutic targets in gastric cancer. | Wei-Jun Cao Hai-Lu Wu Bang-Shun He Yu-Shu Zhang Zhen-Yu Zhang | 2013 | World Journal of Gastroenterology2013，19，23： | 33 |
| 4 | miR-20b, miR-98, miR-125b-1*, and let-7e* as new potential diagnostic biomarkers in ulcerative colitis显示文摘AIM:To use microarray-based miRNA profiling of colonic mucosal biopsies from patients with ulcerative colitis (UC), Crohn's disease (CD), and controls in order to identify new potential miRNA biomarkers in inflammatory bowel disease. METHODS:Colonic mucosal pinch biopsies from the descending part were obtained endoscopically from patients with active UC or CD, quiescent UC or CD, as well as healthy controls. Total RNA was isolated and miRNA expression assessed using the miRNA microarray Geniom Biochip miRNA Homo sapiens (Febit GmbH, Heidelberg, Germany). Data analysis was carried out by principal component analysis and projection to latent structure-discriminant analysis using the SIMCA-P+12 software package (Umetrics, Umea, Sweden). The microarray data were subsequently validated by quantitative real-time polymerase chain reaction (qPCR) performed on colonic tissue samples from active UC patients (n = 20), patients with quiescent UC (n = 19), and healthy controls (n = 20). The qPCR results were analyzed with Mann-WhitneyU test.In silico prediction analysis were performed to identify potential miRNA target genes and the predicted miRNA targets were then compared with all UC associated susceptibility genes reported in the literature. RESULTS:The colonic mucosal miRNA transcriptome differs significantly between UC and controls, UC and CD, as well as between UC patients with mucosal inflammation and those without. However, no clear differences in the transcriptome of patients with CD and controls were found. The miRNAs with the strongest differential power were identified (miR-20b, miR-99a, miR-203, miR-26b, and miR-98) and found to be upregulated more than a 10-fold in active UC as compared to quiescent UC, CD, and controls. Two miRNAs, miR-125b-1* and let-7e*, were up-regulated more than 5-fold in quiescent UC compared to active UC, CD, and controls. Four of the seven miRNAs (miR-20b, miR-98, miR-125b-1*, and let-7e*) were validated by qPCR and found to be specifically upregulated in patients with UC. Usingin silico analysis we found several predicted pro-inflammatory target genes involved in various pathways, such as mitogen-activated protein kinase and cytokine signaling, which are both key signaling pathways in UC.CONCLUSION:The present study provides the first evidence that miR-20b, miR-98, miR-125b-1*, and let7e* are deregulated in patients with UC. The level of these miRNAs may serve as new potential biomarkers for this chronic disease. | Mehmet Coskun Jacob Tveiten Bjerrum Jakob Benedict Seidelin Jesper Thorvald Troelsen JΦrgen Olsen Ole Haagen Nielsen | 2013 | World Journal of Gastroenterology2013，19，27： | 19 |
| 5 | Perspectives of DNA microarray and next-generation DNA sequencing technologies显示文摘DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research,in revealing both the structural and functional characteristics of genomes.In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics,systems biology and pharmacogenomics.The next-generation DNA sequencing method was first introduced by the 454 Company in 2003,immediately followed by the establishment of the Solexa and Solid techniques by other biotech companies.Though it has not been long since the first emergence of this technology,with the fast and impressive improvement,the application of this technology has extended to almost all fields of genomics research,as a rival challenging the existing DNA microarray technology.This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research. | TENG XiaoKun1 & XIAO HuaSheng1,2 1 National Engineering Center for Biochip at Shanghai,Shanghai 201203,China 2 Shanghai-MOST Key Laboratory of Health and Disease Genomics,Chinese National Human Genome Center,Shanghai 201203,China | 2009 | Science China(Life Sciences)2009，52，1： | 15 |
| 6 | miR-374b-5p suppresses RECK expression and promotes gastric cancer cell invasion and metastasis显示文摘AIM:To profile expression of micro RNAs(mi RNAs)in gastric cancer cells and investigate the effect of mi R-374b-5p on gastric cancer cell invasion and metastasis.METHODS:An mi RNA microarray assay was performed to identify mi RNAs differentially expressed in gastric cancer cell lines(MGC-803 and SGC-7901)compared with a normal gastric epithelial cell line.Upregulation of mi R-374b-5p was newly identified and confirmed via quantitative real-time reverse transcriptionPCR(q RT-PCR).MGC-803 cells were transfected with a synthesized anti-mi R-374b-5p sequence or a control vector using Lipofectamine reagent,or treated with transfection reagent alone or phosphate-buffered saline as controls.Rate of transfection was verified after 48 h by q RT-PCR.Cells were then subjected to transwell migration,wound scratch and cell counting kit-8 assays.A bioinformatic analysis to identify mi R-374b-5p target genes was performed using mi Randa,Pic Tar and Target Scan software.A dual luciferase reporter assay was performed to evaluate the influence of mi R-374b-5p on target gene activation,and q RT-PCR and Western blot were used to evaluate the levels of target m RNA and protein following transfection with mi R-374b-5p antisense oligonucleotides.RESULTS:The microarray profiling revealed downregulation of 14(fold change<0.667;P<0.05)and upregulation of 12(fold change>1.50;P<0.05)mi RNAs in MGC-803 and SGC-7901 cells compared with GES-1 controls.The upregulation of mi R-374b-5p(fold change=1.75 and 1.64 in MGC-803 and SGC-7901,respectively;P<0.05)was confirmed by q RT-PCR.Compared with the control groups,the restoration of mi R-374b-5p expression with anti-mi R-374b-5p significantly suppressed the metastasis,invasion and proliferation of MGC-803 cells.The bioinformatic analysis predicted that the 3’untranslated region(UTR)of reversion-inducing cysteine-rich protein with Kazal motif(RECK)contains three mi R-374b-5p target sequences.RECK was verified as a target gene in a dual luciferase reporter assay showing that activation of RECK 3’UTR-pmir GLO was increased by co-transfection with mi R-374b-5p.Finally,transfection of mi R-374b-5p antisense oligonucleotides increased m RNA and protein levels of RECK in MGC-803cells(P<0.05).CONCLUSION:These findings indicate that upregulation of mi R-374b-5p contributes to gastric cancer cell metastasis and invasion through inhibition of RECK expression. | Juan Xie Zhi-Hui Tan Xia Tang Ming-Shu Mo Yan-Ping Liu Run-Liang Gan Yi Li Li Zhang Guo-Qing Li | 2014 | World Journal of Gastroenterology2014，20，46： | 15 |
| 7 | HER2 in gastric cancer: Comparative analysis of three different antibodies using whole-tissue sections and tissue microarrays显示文摘AIM:To compare the performance of three commercially available anti-human epidermalgrowth factor receptor 2(HER2)antibodies in whole-tissue sections and tissue microarrays(TMAs)of a series of gastric tumors.METHODS:We present a comparative analysis of three anti-HER2 antibodies(HercepTest,4B5 and SP3)using TMA and whole-tissue sections prepared from the same paraffin blocks of 199 gastric adenocarcinomas operated upon between January 2004 and December2008 at a Brazilian cancer hospital.The data on the patients’age,sex,the anatomical location of the tumor and the Lauren’s histological classification were collected from clinical and pathological records.The immunohistochemical(IHC)results were examined by two pathologists and the cases were classified as positive(3+),equivocal(2+)and negative(0 or 1+),according to the criteria of the IHC scoring system of gastric cancer.TMAs and whole-tissue sections were evaluated separately and independently.All cases yielding discordant IHC results and/or scored as 2+were subjected to dual-color in situ hybridization in order to determine the final HER2 status.Besides determining the sensitivity and predictive value for HER2-positive status,we measured the accuracy of each antibody by calculating the area under the receiver operating characteristic(ROC)curve.The agreement between the results obtained using the TMAs and those obtained using the whole-tissue sections was assessed by means of Kappa coefficient.RESULTS:Intratumoral heterogeneity of HER2 expression was observed with all antibodies.HER2-positive expression(3+)in the whole-tissue sections was observed in 23 cases(11.6%)using the 4B5 antibody,in 18 cases(9.1%)using the SP3 antibody and in 10 cases(5.1%)using the HercepTest antibody.In the TMAs,11 positive cases(5.6%)were identified using SP3 antibody,9(4.6%)using the 4B5 antibody and 6(3%)using the HercepTest antibody.The sensitivity using whole-tissue sections and TMA,respectively,was 95.2%and 42.9%with 4B5,90.5%and 66.7%with SP3 and 47.6%and42.9%with HercepTest.The accuracy,calculated from the area under the ROC curve,using whole-tissue sections and TMA,respectively,was 0.91 and 0.79 by 4B5,0.86 and 0.80 by SP3 and 0.73 and 0.71 by HercepTest.The concordance of the results obtained using wholetissue sections and TMA was 97.4%(Kappa 0.75)using HercepTest,85.6%(Kappa 0.56)using SP3 and 84.1%(Kappa 0.38)using 4B5.CONCLUSION:The use of the 4B5 antibody on wholetissue sections was the most accurate IHC method for evaluating HER2 expression in gastric adenocarcinoma. | Lucas Faria Abraho-Machado Alexandre Andrade dos Anjos Jácome Durval Renato Wohnrath José Sebastio dos Santos Estela Cristina Carneseca José Humberto Tavares Guerreiro Fregnani Cristovam Scapulatempo-Neto | 2013 | World Journal of Gastroenterology2013，19，38： | 12 |
| 8 | Use of blood-based biomarkers for early diagnosis and surveillance of colorectal cancer显示文摘Early screening for colorectal cancer(CRC) holds the key to combat and control the increasing global burden of CRC morbidity and mortality. However, the current available screening modalities are severely inadequate because of their high cost and cumbersome preparatory procedures that ultimately lead to a low participation rate. People simply do not like to have colonoscopies. It would be ideal, therefore, to develop an alternative modality based on blood biomarkers as the first line screening test. This will allow for the differentiation of the general population from high risk individuals. Colonoscopy would then become the secondary test, to further screen the high risk segment of the population. This will encourage participation and therefore help to reach the goal of early detection and thereby reduce the anticipated increasing global CRC incidence rate. A blood-based screening test is anappealing alternative as it is non-invasive and poses minimal risk to patients. It is easy to perform, can be repeated at shorter intervals, and therefore would likely lead to a much higher participation rate. This review surveys various blood-based test strategies currently under investigation, discusses the potency of what is available, and assesses how new technology may contribute to future test design. | Ganepola AP Ganepola Joel Nizin John R Rutledge David H Chang | 2014 | World Journal of Gastrointestinal Oncology2014，6，4： | 11 |
| 9 | Herb-partitioned moxibustion alleviates colon injuries in ulcerative colitis rats显示文摘AIM To observe the effect of herb-partitioned moxibustion(HPM) on expression of colonic cytokines in ulcerative colitis(UC) rats.METHODS A UC rat model was established by protein immunization in combination with topical chemical stimulation.Rats in the HPM group(n = 8) received HPM at bilateral Tianshu(ST25) points.The gross injury and pathological scores of the colon were recorded.The expression profile of colonic cytokines was assayed using the protein microarray technique.Specific differential cytokines were selected and verified by ELISA.The corresponding Uni Prot Accessions of the differentially expressed cytokines were retrieved in the Uni Prot database.The pathways involved were analyzed with the help of the KEGG PATHWAY database.The DAVID database was used for functional cluster and pathway analysis.RESULTS HPM improved colon injuries in UC rats,manifested by accelerated repair of ulcers and alleviation of inflammation,and the gross injury and pathological scores both significantly decreased(P < 0.01).Fold change > 1.3 or < 0.77 was taken as the screening standard.There were 77 down-regulated and 9 up-regulated differentially expressed colonic cytokines in the HPM group compared with the model group,and expression of 20 differed significantly(P < 0.05).Twelve of the 20 significantly differentially expressed cytokines [β-catenin,interleukin-1 receptor 6(IL-1 R6),IL-1β,B7-1,nerve growth factor receptor,AMP-activated protein kinase-α1,neuropilin-2,orexin A,adipocyte differentiation-related protein,IL-2,Fas and Fas L] were up-regulated in the model group(n = 3,compared with the normal group) but downregulated in the HPM group(n = 3,compared with the model group).Functional cluster analysis showed that the differentially expressed colonic cytokines in the HPM group regulated apoptosis and protein phosphorylation.KEGG pathway analysis showed that 52 down-regulated and 7 up-regulated differentially expressed colonic cytokines in the HPM group had pathways.The pathways that interacted between the cytokines and their receptors accounted for the largest proportion(28 of the downregulated and 5 of the up-regulated cytokines).CONCLUSION HPM promotes the repair of colon injuries in UC rats,which is related to the regulation of several abnormally expressed cytokines. | Dan Zhang Yan-Bo Ren Kai Wei Jue Hong Yan-Ting Yang Li-Jie Wu Ji Zhang Zheng Shi Huan-Gan Wu Xiao-Peng Ma | 2018 | World Journal of Gastroenterology2018，24，30： | 11 |
| 10 | Effect of Danshen on apoptosis and NF-кB protein expression of the intestinal mucosa of rats with severe acute pancreatitis or obstructive jaundice显示文摘BACKGROUND:Intestinal mucosa injury in cases of severe acute pancreatitis(SAP) or obstructive jaundice(OJ) is one of the main reasons for the accelerated aggravation of these diseases.Besides being an organ to digest and absorb nutrients,the intestine is also a unique immune organ.When SAP and OJ develop,the destruction of the intestinal mucosa barrier is an important contributing factor for the development of bacterial translocation,systemic inflammatory response syndrome,and multiple organ dysfunction syndrome.It is important to protect the intestinal mucosa in the therapy for SAP and OJ.In this study,we determined the effect of Radix Salviae Miltiorrhizae(Danshen) injection on apoptosis and NF-κB P65 protein expression in the intestinal mucosa of rats with SAP or OJ,and explored the protective mechanism of Danshen in their mucosa.METHODS:Sprague-Dawley rats were used in the SAP and OJ experiments.These rats were randomly divided into shamoperated,model control,and treated groups.At various times after operation,the mortality rates were calculated.Subsequently,the rats were killed to assess the pathological changes,the expression levels of Bax and NF-κB proteins,and the apoptosis indices in the intestinal mucosa.RESULTS:Compared to the corresponding model control group,the number of SAP or OJ rats that died in the treated group decreased but showed no statistically significant difference.At all time points after operation,there was no significant difference between the treated and model control groups in the staining intensity as well as the product of staining intensity and positive staining rate of Bax protein in the intestinal mucosa of SAP and OJ rats.At 3 hours after operation,the apoptosis index of the intestinal mucosa of SAP rats in the treated group was lower than that in the model control group(P<0.01).At 12 hours after operation in SAP rats and 28 days after operation in OJ rats,the staining intensity as well as the product of staining intensity and positive staining rate of NF-κB protein of the intestinal mucosa in the treated group were lower than those in the model control group(P<0.01).CONCLUSION:Danshen exerts protective effects on the intestinal mucosa of SAP and OJ rats perhaps by inhibiting apoptosis and down-regulating NF-κB protein. | | 2010 | Hepatobiliary & Pancreatic Diseases International2010，9，5： | 11 |
| 11 | AtMYB103 is a crucial regulator of several pathways affecting Arabidopsis anther development显示文摘Previous reports indicated that AtMYB103 has an important role in tapetum development,callose dissolution,and exine formation in A.thaliana anthers.Here,we further characterized its function in anther development by expression pattern analysis,transmission electron microscopy observation of the knockout mutant,and microarray analysis of downstream genes.A total of 818 genes differentially expressed between ms188 and the wild-type were identified by global expression profiling analysis.Functional classification showed that loss-of-function of AtMYB103 impairs cell wall modification,lipid metabolic pathways,and signal transduction throughout anther development.RNA in situ hybridization confirmed that transcription factors acting downstream of AtMYB103 (At1g06280 and At1g02040) were expressed in the tapetum and microspores at later stages,suggesting that they might have important roles in microsporogenesis.These results indicated that AtMYB103 is a crucial regulator of Arabidopsis anther development. | ZHU Jun1,ZHANG GuoQiang2,CHANG YuHua2,LI XiaoChuan2,YANG Jun2,HUANG XueYong2,YU QingBo2,CHEN Hui3,WU TianLong1* & YANG ZhongNan2* 1College of Agriculture and Biotechnology,Shanghai Jiao Tong University,Shanghai 200240,China 2College of Life and Environmental Sciences,Shanghai Normal University,Shanghai 200234,China 3Shanghai Institute of Plant Physiology and Ecology,Chinese Academy of Sciences,Shanghai 200032,China | 2010 | Science China(Life Sciences)2010，53，9： | 10 |
| 12 | Overexpression of miR-196b and HOXA10 characterize a poor-prognosis gastric cancer subtype显示文摘AIM:To identify molecular biologic differences between two gastric adenocarcinoma subgroups presenting different prognoses through the analysis of microRNA and protein expression.METHODS:Array technologies were used to generate1146 microRNAs and 124 proteins expression profiles of samples from 60 patients with gastric cancer.For the integrative analysis,we used established mRNA expression data published in our previous study.Whole mRNA expression levels were acquired from microarray data for 60 identical gastric cancer patients.Two gastric adenocarcinoma subgroups with distinct mRNA expression profiles presented distinctly different prognoses.MicroRNA and protein expression patterns were compared between gastric cancer tissue and normal gastric tissue and between two different prognostic groups.Aberrantly expressed microRNA,associated mRNA,and protein in patients with poor-prognosis gastric cancer were validated by quantitative reverse transcription polymerase chain reaction and immunochemistry in independent patients.RESULTS:We obtained the expression data of 1146microRNAs and 124 cancer-related proteins.Four microRNAs were aberrantly expressed in the two prognostic groups and in cancer vs non-cancer tissues(P<0.05).In the poor-prognosis group,miR-196b,miR-135b,and miR-93 were up-regulated and miR-29c*was down-regulated.miR-196b expression positively correlated with Homeobox A10(HOXA10)expression(r=0.726,P<0.001),which was significantly increased in poor-prognosis patients(P<0.001).Comparing gastric cancer with non-cancer tissues,46/124 proteins showed differential expression(P<0.05);COX2(P<0.001)and cyclin B1(P=0.017)were clearly overexpressed in the poor-prognosis group.CONCLUSION:Co-activation of miR-196b and HOXA10characterized a poor-prognosis subgroup of patients with gastric cancer.Elucidation of the biologic function of miR-196b and HOXA10 is warranted. | Jae Yun Lim Sun Och Yoon So-Young Seol Soon Won Hong Jong Won Kim Seung Ho Choi Ju-Seog Lee Jae Yong Cho | 2013 | World Journal of Gastroenterology2013，19，41： | 10 |
| 13 | Identification of Annexin A1 protein expression in human gastric adenocarcinoma using proteomics and tissue microarray显示文摘AIM:To study the differential expression of Annexin A1(ANXA1)protein in human gastric adenocarcinoma.This study was also designed to analyze the relationship between ANXA1 expression and the clinicopathological parameters of gastric carcinoma.METHODS:Purified gastric adenocarcinoma cells(GAC)and normal gastric epithelial cells(NGEC)were obtained from 15 patients with gastric cancer by laser capture microdissection.All of the peptide specimens were labeled as18O/16O after trypsin digestion.Differential protein expressions were quantitatively identified between GAC and NGEC by nanoliter-reverse-phase liquid chromatography-mass/mass spectrometry(nanoRPLC-MS/MS).The expressions of ANXA1 in GAC and NGEC were verified by western blot analysis.The tissue microarray containing the expressed ANXA1 in 75 pairs of gastric carcinoma and paracarcinoma specimens was detected by immunohistochemistry(IHC).The relationship between ANXA1 expression and clinicopathological parametes of gastric carcinoma was analyzed.RESULTS:A total of 78 differential proteins were identified.Western blotting revealed that ANXA1 expression was significantly upregulated in GAC(2.17/1,P<0.01).IHC results showed the correlations between ANXA1protein expression and the clinicopathological parameters,including invasive depth(T stage),lymph node metastasis(N stage),distant metastasis(M stage)and tumour-lymph node metastasis stage(P<0.01).However,the correlations between ANXA1 protein expression and the remaining clinicopathological parameters,including sex,age,histological differentiation and the size of tumour were not found(P>0.05).CONCLUSION:The upregulated ANXA1 expression may be associated with carcinogenesis,progression,invasion and metastasis of GAC.This protein could be considered as a biomarker of clinical prognostic prediction and targeted therapy of GAC. | Zhi-Qiang Zhang Xiu-Juan Li Gui-Tao Liu Xiang-Yang Zhang Yu Xia Hao Wen | 2013 | World Journal of Gastroenterology2013，19，43： | 9 |
| 14 | 染色体微阵列分析实验室技术要求专家共识显示文摘染色体微阵列分析(chromosomal microarray analysis,CMA),是以微阵列为技术基础的基因组拷贝数变异(copy number variations,CNVs)分析技术,主要包括基于比较基因组杂交的微阵列(array-based comparative genomic hybridization,aCGH)和基于单核苷酸多态性的微阵列(single nucleotide polymorphism array,SNP array)。CMA是一种高分辨率的全基因组染色体变异检测技术,近年来其在临床的应用逐步深入和广泛,国内外已出台相关指南与专家共识以推动其在临床的规范应用。为进一步规范染色体微阵列分析技术的临床应用,保证医疗质量与医疗安全,国家卫生健康委员会临床检验中心产前筛查与诊断室间质量评价专家委员会组织专家进行了充分讨论,拟在CMA实验室技术等方面作出规范和建议,以规范CMA技术在遗传病诊断领域中的应用。随着技术的更新与成熟,本共识将持续更新以满足临床需求。 | 无 王治国 徐两蒲 黄海龙 | 2019 | 中华检验医学杂志2019，42，9： | 9 |
| 15 | Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis显示文摘AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma. | Kai Shi Zhi-Tong Bing Gui-Qun Cao Ling Guo Ya-Na Cao Hai-Ou Jiang Mei-Xia Zhang | 2015 | International Journal of Ophthalmology(English edition)2015，8，2： | 9 |
| 16 | Clinical Application of Chromosome Microarray Analysis in Han Chinese Children with Neurodevelopmental Disorders显示文摘Chromosome microarray analysis(CMA) is a cost-effective molecular cytogenetic technique that has been used as a first-line diagnostic test in neurodevelopmental disorders in the USA since 2011. The impact of CMA results on clinical practice in China is not yet well studied, so we aimed to better evaluate this phenomenon.We analyzed the CMA results from 434 patients in our clinic, and characterized their molecular diagnoses, clinical features, and follow-up clinical actions based on these results. The overall diagnostic yield for our patients was 13.6%(59 out of 434). This gave a detection rate of 14.7%for developmental delay/intellectual disability(DD/ID,38/259) and 12% for autism spectrum disorders(ASDs,21/175). Thirty-three recurrent(n≥2) variants were found, distributed at six chromosomal loci involving known chromosome syndromes(such as DiGeorge, Williams Beuren, and Angelman/Prader-Willi syndromes).The spectrum of positive copy number variants in our study was comparable to that reported in Caucasian populations, but with specific characteristics. Parental origin tests indicated an effect involving a significant maternal transmission bias to sons. The majority of patients with positive results(94.9%) had benefits, allowing earlier diagnosis(36/59), prioritized full clinical management(28/59), medication changes(7/59), a changed prognosis(30/59), and prenatal genetic counseling(15/59). Our results provide information on de novo mutations in Chinese children with DD/ID and/or ASDs. Our data showed that microarray testing provides immediate clinical utility for patients. It is expected that the personalized medical care of children with developmental disabilities will lead to improved outcomes in long-term developmental potential.We advocate using the diagnostic yield of clinically actionable results to evaluate CMA as it provides information of both clinical validity and clinical utility. | Mingyu Xu Yiting Ji Ting Zhang Xiaodong Jiang Yun Fan Juan Geng Fei Li | 2018 | Neuroscience Bulletin2018，34，6： | 8 |
| 17 | Label-free detection of hybridization of oligonucleotides by oblique-incidence reflectivity difference method显示文摘The microarrays of 20-base oligonucleotide with different concentrations are detected before and after hybridization by the oblique-incidence reflectivity difference (OI-RD) method. The experimental results prove that OI-RD is a label-free method which can not only distinguish the concentration difference of oligonucleotides before and after the hybridization but also detect the hybridization of short oligonucleotides. At present the OI-RD method can detect 0.39 μmol/L 20-base oligonucleotide or less. These results suggest that the OI-RD method is a promising and potential technique for label-free detection of biological microarrays. | YUAN Kun1, WANG Xu1, LU Heng1, WEN Juan1, LU HuiBin1*, ZHOU YueLiang1, JIN Kui-Juan1, YANG GuoZhen1, LI Wei2 & RUAN KangCheng2* 1 Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China 2 Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China | 2010 | Science China(Physics,Mechanics & Astronomy)2010，53，8： | 8 |
| 18 | Analysis of gene expression profiles in pancreatic carcinoma by using cDNA microarray显示文摘OBJECTIVES: To survey the gene expression profiles in pancreatic carcinoma by using cDNA microarrayand detect target genes for further study.METHODS: Three mixed samples from 2 cases of normal pancreatic tissue and 4 cases ofmoderate-differentiated pancreatic carcinoma were studied by means of cDNA microarray consisting of18 000 genes.RESULTS: 1484 and 1353 different expressed genes were observed in two cancer samples respectively.We identified 455 genes altered with the same tendency in both samples, including 102 up-regulated and353 down-regulated genes. There were 274 known genes and 181 unknown genes; 27.8% and 52.0%genes respectively had an expression level in cancer that was 2-fold higher or lower than that in normalsamples. Tumor suppressor genes, growth factors and receptor genes, signal conduction genes,transcription factor genes were identified.CONCLUSIONS: cDNA microarray is an efficient and high-throughout method to investigate geneexpression profiles in pancreatic carcinoma. MBD1, EDG1 and gene hypermethylation mechanism wouldplay an important role in the pathogenesis of pancreatic carcinoma. | Xian-Jun Yu Jiang Long De-Liang Fu Qun-Hua Zhang Quan-Xin Ni the Center for Pancreatic Cancer, Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China | 2003 | Hepatobiliary & Pancreatic Diseases International2003，2，3： | 8 |
| 19 | Expression signatures of long non-coding RNA and mRNA in human traumatic brain injury显示文摘Long non-coding RNAs(lncRNAs) play a key role in craniocerebral disease, although their expression profiles in human traumatic brain injury are still unclear. In this regard, in this study, we examined brain injury tissue from three patients of the 101 st Hospital of the People's Liberation Army, China(specifically, a 36-year-old male, a 52-year-old female, and a 49-year-old female), who were diagnosed with traumatic brain injury and underwent brain contusion removal surgery. Tissue surrounding the brain contusion in the three patients was used as control tissue to observe expression characteristics of lncRNAs and mRNAs in human traumatic brain injury tissue. Volcano plot filtering identified 99 lncRNAs and 63 mRNAs differentially expressed in frontotemporal tissue of the two groups(P < 0.05, fold change > 1.2). Microarray analysis showed that 43 lncRNAs were up-regulated and 56 lncRNAs were down-regulated. Meanwhile, 59 mRNAs were up-regulated and 4 mRNAs were down-regulated. Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) analyses revealed 27 signaling pathways associated with target genes and, in particular, legionellosis and influenza A signaling pathways. Subsequently, a lncRNA-gene network was generated, which showed an absolute correlation coefficient value > 0.99 for 12 lncRNA-mRNA pairs. Finally, quantitative real-time polymerase chain reaction confirmed different expression of the five most up-regulated mRNAs within the two groups, which was consistent with the microarray results. In summary, our results show that expression profiles of mRNAs and lncRNAs are significantly different between human traumatic brain injury tissue and surrounding tissue, providing novel insight regarding lncRNAs' involvement in human traumatic brain injury. All participants provided informed consent. This research was registered in the Chinese Clinical Trial Registry(registration number: ChiCTR-TCC-13004002) and the protocol version number is 1.0. | Li-Xiang Yang Li-Kun Yang Jie Zhu Jun-Hui Chen Yu-Hai Wang Kun Xiong | 2019 | Neural Regeneration Research2019，14，4： | 8 |
| 20 | MicroRNA regulatory pattern in spinal cord ischemia-reperfusion injury显示文摘After spinal cord injury, dysregulated miRNAs appear and can participate in inflammatory responses, as well as the inhibition of apoptosis and axon regeneration through multiple pathways. However, the functions of miRNAs in spinal cord ischemia-reperfusion injury progression remain unclear. miRCURY LNATM Arrays were used to analyze miRNA expression profiles of rats after 90 minutes of ischemia followed by reperfusion for 24 and 48 hours. Furthermore, subsequent construction of aberrantly expressed miRNA regulatory patterns involved cell survival, proliferation, and apoptosis. Remarkably, the mitogen-activated protein kinase(MAPK) signaling pathway was the most significantly enriched pathway among 24-and 48-hour groups. Bioinformatics analysis and quantitative reverse transcription polymerase chain reaction confirmed the persistent overexpression of miR-22-3 p in both groups. These results suggest that the aberrant miRNA regulatory network is possibly regulated MAPK signaling and continuously affects the physiological and biochemical status of cells, thus participating in the regulation of spinal cord ischemia-reperfusion injury. As such, miR-22-3 p may play sustained regulatory roles in spinal cord ischemia-reperfusion injury. All experimental procedures were approved by the Animal Ethics Committee of Jilin University, China [approval No. 2020(Research) 01]. | Zhi-Gang Liu Yin Li Jian-Hang Jiao Hao Long Zhuo-Yuan Xin Xiao-Yu Yang | 2020 | Neural Regeneration Research2020，15，11： | 8 |
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