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comparative genomic hybridization analysis of genetic aberrations associated with development of esophageal squamous cell carcinoma in Henan, China

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World Journal of Gastroenterology 2008年第12期14卷 1828-1835页

作者： Yan-Ru Qin Li-Dong Wang Zong-Min Fan Dora Kwong Xin-Yuan Guan Department of Clinical Oncology The FirstAffiliated Hospital of Zhengzhou University Zhengzhou 450052Henan Province China Laboratory for Cancer Research Experimental Medical Center College of Medicine ZhengzhouUniversity Zhengzhou 450052 Henan Province China Department of Clinical Oncology Queen Mary Hosptital The University of Hong Kong Room 129Professorial Block Pokfulam Road Hong Kong China

AIM: To characterize cytogenetic alterations in esophageal squamous cell carcinoma (ESCC) and its metastasis. METHODS: A total of 37 cases of primary ESCC and 15 pairs of primary ESCC tumors and their matched metastatic lymph nodes cases were enrolled from Linzhou, the high incidence area for ESCC in Henan, northern China. The comparative genomic hybridization (CGH) was applied to determine the chromosomal aberrations on the DNA extracted from the frozen ESCC and metastatic lymph node samples from these patients. RESULTS: CGH showed chromosomal aberrations in all the cases. In 37 cases of primary ESCC, chromosomal profile of DNA copy number was characterized by frequently detected gains at 8q (29/37, 78%), 3q (24/37, 65%), 5p (19/37, 51%); and frequently detected losses at 3p (21/37, 57%), 8p and 9q (14/37, 38%). In 15 pairs of primary ESCC tumors and their matched metastatic lymph node cases, the majority of the chromosomal aberrations in both primary tumor and metastatic lymph node lesions were consistent with the primary ESCC cases, but new candidate regions of interest were also detected. The most significant finding is the gains of chromosome 6p with a minimum high-level amplification region at 6p12-6q12 in 7 metastatic lymph nodes butonly in 2 corresponding primary tumors (P = 0.05) and 20p with a minimum high-level amplification region at 20p12 in 11 metastatic lymph nodes but only in 5 corresponding primary tumors (P < 0.05). Another interesting finding is the loss of chromosome 10p and 10q in 8 and 7 metastatic lymph nodes but only in 2 corresponding primary tumors (P < 0.05). CONCLUSION: Using the CGH technique to detect chromosomal aberrations in both the primary tumor and its metastatic lymph nodes of ESCC, gains of 8q, 3q and 5p and loss of 3p, 8p, 9q and 13q were specifically implicated in ESCC in Linzhou population. Gains of 6p and 20p and loss of 10pq may contribute to the lymph node metastasis of ESCC. These findings suggest that the gains and losse

关键词： comparative genomic hybridization Geneticalterations Esophageal squamous cell carcinoma Metastatic lymph nodes

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Association between chromosomal aberration of COX8C and tethered spinal cord syndrome:array-based comparative genomic hybridization analysis

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Neural Regeneration Research 2016年第8期11卷 1333-1338页

作者： Qiu-jiong Zhao Shao-cong Bai Cheng Cheng Ben-zhang Tao Le-kai Wang Shuang Liang Ling Yin Xing-yi Hang Ai-jia Shang Department of Neurosurgery Chinese PLA General Hospital Beijing China iGeneTech Biotechnology Co. Ltd. Beijing China Department of Neurology Chinese PLA General Hospital Beijing China

Copy number variations have been found in patients with neural tube *** this study,we performed genome-wide screening using high-resolution array-based comparative genomic hybridization in three children with tethered spinal cord syndrome and two healthy *** eight copy number variations,four were *** non-polymorphic copy number variations were associated with Angelman and Prader-Willi syndromes,and *** function enrichment analysis revealed that COX8 C,a gene associated with metabolic disorders of the nervous system,was located in the copy number variation region of Patient *** results indicate that array-based comparative genomic hybridization can be used to diagnose tethered spinal cord *** results may help determine the pathogenesis of tethered spinal cord syndrome and prevent occurrence of this disease.

关键词： nerve regeneration neural tube defects tethered spinal cord syndrome comparative genomic hybridization COX8C gene function enrichment analysis database of genomic variants database of DECIPHER copy number variations neural regeneration

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SINGLE CELL DEGENERATE OLIGONUCLEOTIDE PRIMER-PCR AND comparative genomic hybridization WITH MODIFIED CONTROL REFERENCE

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Journal of Zhejiang University-Science A(Applied Physics & Engineering) 2001年第3期2卷 79-82页

作者：金帆 Women’s Hospital College of Medicine Zhejiang University Hangzhou China Department of Obstetrics and Gynecology University of Adelaide Australia

For investigating the possibility of applying degenerate oligonucleotide primer PCR (DOP\|PCR) and comparative genomic hybridization (CGH) technique to analyses of genomic genetics in a single cell, the whole genomic DNA of a single cell with XX, XY, XO, XXY, +13 or +21 was amplified by DOP\|PCR. Single cell DOP\|PCR CGHs with conventional and modified control references, the genomic DNA and a single cell DOP\|PCR product from normal male, were carried out respectively. The results showed that the average profile of the fluorescence intensity ratio in CGH with the genomic DNA as reference fluctuates much and that the standard deviation in about 30% haploid is beyond the normal limits. False positive hyper\|representation was found to exist in X chromosome while trisomy 13 and 21 were not detected. However, the distributions of the mean and the standard deviation of the ratio in the CGH with DOP\|PCR product as reference were quite acceptable. The copy number changes of chromosome X,Y,13 and 21 were revealed. Those results suggested that there is unrandom unequal amplification in a single cell DOP\|PCR. Using a single DOP\|PCR product as reference can decrease its influence on CGH. Single cell DOP\|PCR\|CGH and its application in the genetic analyses of preimplantation embryo or fetal cell in maternal blood may be possible.

关键词： degenerate oligonucleotide primer PCR comparative genomic hybridization single cell

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Chromosomal imbalances revealed in primary rhabdomyosarcomas by comparative genomic hybridization

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Chinese Medical Journal 2009年第11期122卷 1277-1282页

作者： LI Qiao-xin LIU Chun-xia CHUN Cai-pu QI Yan CHANG Bin LI Xin-xia CHEN Yun-zhao NONG Wei-xia LI Hong-an LI Feng Department of Pathology Key Laboratory of Xinjiang Endemic & Ethnic Disease of Ministry of Education Shihezi University School of Medicine Shihezi Xinjiang 832002 China

Background Previous cytogenetic studies revealed rhabdomyosarcoma. We profiled chromosomal imbalances aberrations varied among the three subtypes of n the different subtypes and investigated the relationships between clinical parameters and genomic aberrations. Methods comparative genomic hybridization was used to investigate genomic imbalances in 25 cases of primary rhabdomyosarcomas and two rhabdomyosarcoma cell lines. Specimens were reviewed to determine histological type, pathological grading and clinical staging. Results Changes involving one or more regions of the genome were seen in all rhabdomyosarcomal patients. For rhabdomyosarcoma, DNA sequence gains were most frequently （〉30%） seen in chromosomes 2p, 12q, 6p, 9q, 10q, lp, 2q, 6q, 8q, 15q and 18q; losses from 3p, 11p and 6p. In aggressive alveolar rhabdomyosarcoma, frequent gains were seen on chromosomes 12q, 2p, 6p, 2q, 4q, 10q and 15q; losses from 3p, 6p, lq and 5q. For embryonic rhabdomyosarcoma, frequent gains were on 7p, 9q, 2p, 18q, lp and 8q; losses only from 11p. Frequently gained chromosome arms of translocation associated with rhabdomyosarcoma were 12q, 2, 6, 10q, 4q and 15q; losses from 3p, 6p and 5q. The frequently gained chromosome arms of nontranslocation associated with rhabdomyosarcoma were 2p, 9q and 18q, while 11p and 14q were the frequently lost chromosome arms. Gains on chromosome 12q were significantly correlated with translocation type. Gains on chromosome 9q were significantly correlated with clinical staging. Conclusions Gains on chromosomes 2p, 12q, 6p, 9q, 10q, lp, 2q, 6q, 8q, 15q and 18q and losses on chromosomes 3p, 11p and 6p may be related to rhabdomyosarcomal carcinogenesis. Furthermore, gains on chromosome 12q may be correlated with translocation and gains on chromosome 9q with the early stages of rhabdomyosarcoma.

关键词： rhabdomyosarcoma fusion gene comparative genomic hybridization

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A Microarray Based genomic hybridization Method for Identification of New Genes in Plants：Case Analyses of Arabidopsis and Oryza

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Journal of Integrative Plant Biology 2007年第6期49卷 915-926页

作者： Chuanzhu Fan Maria D. Vibranovski Ying Chen Manyuan Long Department of Ecology and Evolution The University of Chicago Chicago IL 60637 USA

To systematically estimate the gene duplication events In closely related species, we have to use comparative genomlc approaches, either through genomlc sequence comparison or comparative genomlc hybridization （CGH）. Given the scarcity of complete genomlc sequences of plant species, in the present study we adopted an array based CGH to Investigate gene duplications In the genus Arabldopsls. Fragment genomlc DNA from four species, namely Arabidopsls thallana, A. lyrata subsp, lyrata, A. lyrata subsp, petraea, and A. halleri, was hybridized to Affymetrlx （Santa Clara, CA, USA） tiling arrays that are designed from the genomlc sequences of A. thallana. Pairwlse comparisons of signal intensity were made to infer the potential duplicated candidates along each phylogenetic branch. Ninety-four potential candidates of gene duplication along the genus were Identified. Among them, the majority （69 of 94） were A. thallana lineage specific. This result indicates that the array based CGH approach may be used to Identify candidates of duplication In other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. satlva and A. thallana and found a strikingly higher number of chimera retroposed genes In rice. The higher rate of gene duplication through retroposltlon and other mechanisms may Indicate that the grass species Is able to adapt to more diverse environments.

关键词： Arabidopsis comparative genomic hybridization microarray new genes Oryza retroposition.

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Genetic Analysis of ele Mutants and comparative Mapping of ele1 Locus in the Control of Organ Internal Asymmetry in Garden Pea

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Journal of Integrative Plant Biology 2010年第6期52卷 528-535页

作者： Xin Li Li-Li Zhuang Mike Ambrose M. Phil. Catherine Rameau Xiao-He Hu Jun Yana Da Luo School of Life Science and Biotechnology Shanghai JiaoTong University Shanghai 200030 China Department of Crop Genetics John Innes Centre Colney Norwich NR4 7UH United Kingdom Station de Genetique et d'Amelioration des Plantes Institut J.P. Bourgin UR 254 INRA Versailles France National Key Laboratory of Plant Molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biologica Sciences the Chinese Academy of Sciences Shanghai 200032 China

Previous study has shown that during zygomorphic development in garden pea （Pisum sativum L.）, the organ internal （IN） asymmetry of lateral and ventral petals was regulated by a genetic locus, SYMMETRIC PETAL 1 （SYP1）, while the dorsoventral （DV） asymmetry was determined by two CYC-like TCP genes or the PsCYC genes, KEELED WINGS （K） and LOBED STANDARD 1 （LST1）. In this study, two novel loci, ELEPHANT EAR-LIKE LEAF 1 （ELE1） and ELE2 were characterized. These mutants exhibit a similar defect of IN asymmetry as syp1 in lateral and ventral petals, but also display pleiotropic effects of enlarged organ size. Genetic analysis showed that ELE1 and ELE2 were involved in same genetic pathway and the enlarged size of petals but not compound leaves in e/e2 was suppressed by introducing k and Ist1, indicating that the enlargement of dorsal petal in e/e2 requires the activities of K and LST1. An experimental framework of comparative genomic mapping approach was set up to map and clone LjELE1 locus in Lotus japonicus. Cloning the ELE1 gene will shed light on the underlying molecular mechanism during zygomorphic development and further provide the molecular basis for genetic improvement on legume crops.

关键词： GENETIC research PEAS GENETICS FOLIAR diagnosis LOCUS (Genetics) comparative genomic hybridization LEGUMES

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Copy number changes of target genes in chromosome 3q25.3-qter of esophageal squamous cell carcinoma: TP63is amplified in early carcinogenesis but down-regulated as disease progressed

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World Journal of Gastroenterology 2005年第9期11卷 1267-1272页

作者： Chueh-ChuanYen Yann-JangChen Chin-ChenPan Kai-HsiLu PaulChih-HsuehChen Jiun-YiHsia Jung-TaChen Yu-ChungWu Wen-HuHsu Liang-ShunWang Min-HsiungHuang Biing-ShiungHuang Cheng-PoHu Po-MinChen Chi-HungLin DivisionofMedicalOncology DepartmentofMedicineTaipeiVeteransGeneralHospitalandNationalYang-MingUniversitySchoolofMedicineTaipeiTaiwanChina FacultyofLifeScience NationalYang-MingUniversityTaipeiTaiwanChina DepartmentofPathology NationalYang-MingUniversityandTaipeiVeteransGeneralHospitalTaiwanChina InstituteofMicrobiologyandImmunology NationalYang-MingUniversityTaipeiTaiwanChina DivisionofThoracicSurgery DepartmentofSurgeryTaichungVeteransGeneralHospitalTaichungTaiwanChina DepartmentofPathology.TaichungVeteransGeneralHospital andDepartmentofPathologyChung-ShanMedicalUniversityTaichungTaiwanChina DivisionofThoracicSurgery DepartmentofSurgeryTaipeiVeteransGeneralHospitalandNationalYang-MingUniversityTaipeiTaiwanChina InstituteofMicrobiologyandImmunology NationalYang-MingUniversityandDepartmentofMedicalResearchandEducationTaipeiVeteransGeneralHospitalTaipeiTaiwanChina InstituteofMicrobiologyandImmunology andInstituteofBiophotonicsNationalYang-MingUniversityTaipeiTaiwanChina

AIM: By using comparative genomic hybridization, gain of 3q was found in 45-86% cases of esophageal squamous cell carcinoma (EC-SCC). Chromosome 3q25.3-qter is the minimal common region with several oncogenes found within this region. However, amplification patterns of these genes in EC-SCC have never been reported. The possible association of copy number changes of these genes with pathologic characteristics is still not clear. METHODS: Real-time quantitative PCR (Q-PCR) was performed to analyze the copy number changes of 13 candidate genes within this region in 60 primary tumors of EC-SCC, and possible association of copy number changes with pathologic characteristics was analyzed by statistics. Immunohistochemistry (IHC) study was also performed on another set of 111 primary tumors of EC-SCC to verify the association between TP63 expression change and lymph node metastasis status. RESULTS: The average copy numbers (±SE) per haploid genome of individual genes in 60 samples were (from centromere to telomere): SSR3: 4.19 (±0.69); CCNL1: 5.24 (±0.67); SMC4L1: 2.01 (±0.16); EVI1: 2.02 (±0.12); hTERC. 5.28 (±0.54); SKIL 2.71 (±0.14); EIF5A2. 1.95 (±0.12); ECT2: 9.18 (±1.68); PIK3CA: 8.13 (±1.17); EIF4G1: 1.07 (±0.05); 557: 3.07 (±0.25); TP63: 2.51 (±0.22); TFRC. 2.42 (±0.19). Four clusters of amplification were found: SSR3 and CCLN1 at 3q25.31; hTERC and SKIL at 3q26.2; ECT2 and PIK3CA at 3q26.31-q26.32; and 55T, TP63 and TFRC at 3q27.3-q29. Patients with lymph node metastasis had significantly lower copy number of TP63 in the primary tumor than those without lymph node metastasis. IHC study on tissue arrays also showed that patients with lymph node metastasis have significantly lower TP63 staining score in the primary tumor than those without lymph node metastasis. CONCLUSION: This study showed that different amplification patterns were seen among different genes within 3q25.3-qter in EC-SCC, and several novel candidate oncogenes (SSR3, SMC4L1, ECT2, and SST) were ide

关键词： Chromosomal aberration comparative genomic hybridization Esophageal neoplasm Immunohistochemistry Quantitative real-time PCR Tissue array Tumor protein 63

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Copy number variants of ABCF1, IL17REL, and FCGR3A are associated with the risk of gout

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Protein & Cell 2017年第6期8卷 467-470页

作者： Dong, Zheng Li, Yuan Zhou, Jingru Jiang, Shuai Wang, Yi Chen, Yulin Zhao, Dongbao Yang, Chengde Qian, Qiaoxia Ma, Yanyun He, Hongjun Ji, Hengdong Yang, Yajun Wang, Xiaofeng Xu, Xia Pang, Yafei Zou, Hejian Jin, Li Zhang, Feng Wang, Jiucun Fudan Univ Sch Life Sci Collaborat Innovat Ctr Genet & Dev State Key Lab Genet Engn Shanghai 200433 Peoples R China Changhai Hosp Div Rheumatol & Immunol Shanghai 200433 Peoples R China Shanghai Jiao Tong Univ Sch Med Ruijin Hosp Div Rheumatol Shanghai 200025 Peoples R China Taixing Peoples Hosp Div Rheumatol Taixing 225499 Peoples R China Taizhou Peoples Hosp Div Rheumatol Taizhou 225300 Peoples R China Fudan Taizhou Inst Hlth Sci Taizhou 225316 Peoples R China Fudan Univ Huashan Hosp Div Rheumatol Shanghai 200040 Peoples R China Fudan Univ Inst Rheumatol Immunol & Allergy Shanghai 200040 Peoples R China

Dear Editor Gout is usually characterized by recurrent flares of acute inflammatory arthritis and the crystallization of urate in tissues and joints （Dong et al., 2017）. The formation of monosodium urate crystals （MSU） is due to the elevated uric acid levels in the blood （Yang et al., 2016）. But only 10% of individuals with hyperuricemia develop gout, suggesting that certain people are at a higher risk of developing MSU crystals （Mer- riman and Dalbeth, 2011） or initiating of the acute inflamma- tory response than others.

关键词： Systemic Lupus Erythematosus Gout Copy Number Variant comparative genomic hybridization High Copy Number

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DNA COPY PROFILE IN NASOPHARYNGEAL CARCINOMA AND ITS CORRELATION WITH CLINICAL STAGING

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Chinese Journal of Cancer Research 2001年第4期13卷 276-279页

作者：鄢践方嬿梁启万曾益新 Department of Aetiology Cancer InstituteCancer CenterSun Yat-sen University of Medical SciencesGuangzhou 510060

Objective: To detect genetic alterations in nasopharyngeal carcinoma (NPC) in Cantonese, the population with the highest incidence of NPC, and to correlate the findings with clinical staging. Methods: comparative genomic hybridization (CGH) was performed on 35 primary nasopharyngeal carcinomas and a nonparametric x2 test was used to analyze relationship between chromosome changes and clinical staging. Results: The identified common chromosomal alterations in NPC included gain of chromosomes 12q (21 cases, 60%), 4q (19cases, 43%), 3q (18 cases, 51%), 1q (15 cases, 43%),8q (14 cases, 40%), and 2q (12 cases, 30%). The most frequently detected loss of chromosomal materials involved chromosome 1p (24 cases, 69%), chromosome 3p (21 cases, 60%), 11q (20 cases, 57%), 14q (18 cases, 51%), 16q (14 cases, 40%), 13(12 cases, 34%), and 9p(11 cases, 31%). The high frequency (>50%) 4q gain and 1p loss were novel findings. Compared by nonparametric x2 test, gains on 12q and 8q were found mainly in stages III/IV and there were significant differences between two clinical stage groups (stages I/II vs stages III/IV). Conclusions: Current analysis has revealed a comprehensive profile of the chromosomal regions showing DNA copy number changes, which may harbor oncogenes or tumor suppressor genes involved in the development of primary NPC.

关键词： Nasopharyngeal carcinoma comparative genomic hybridization Chromosomal alteration

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