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Array Comparative Genomic Hybridization as a Diagnostic Tool in Cancer
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作者 Panagiotis Apostolou Ioannis Papasotiriou 《Journal of Cancer Therapy》 2019年第7期518-524,共7页
The knowledge of the primary origin of tumor is essential in designing an efficient cancer treatment algorithm. Useful diagnostic tools enable determination of primary origin of the tumor;however the majority of them ... The knowledge of the primary origin of tumor is essential in designing an efficient cancer treatment algorithm. Useful diagnostic tools enable determination of primary origin of the tumor;however the majority of them require tissue examination. Recent years, exploration of circulating tumor cells enabled scientists to study different parameters using the painless liquid biopsy. The present study aimed to identify whether aCGH might be used as a diagnostic tool in cancer detecting the primary origin of the tumor. Blood was extracted from healthy individuals and cancer samples and CTCs isolated. DNA extracted from the above samples and aCGH experiments followed. The samples were blinded analyzed and then unmasked to calculate specificity and sensitivity of the method. The sensitivity was 94%, the specificity 88%, while the positive prediction rate of the primary tumor was 72%. aCGH is a powerful tool in cancer diagnosis and treatment plan with high sensitivity and specificity rates. It can be performed from blood sample, which makes it an appropriate method for every patient, mainly for patients with unknown origin of the primary tumor. 展开更多
关键词 CANCER of UNKNOWN Primary Origin array comparative genomic hybridization CYTOGENETIC CANCER
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Analysis of Chinese women with primary ovarian insufficiency by high resolution array-comparative genomic hybridization 被引量:8
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作者 LIAO Can FU Fang +2 位作者 YANG Xin SUN Yi-min LI Dong-zhi 《Chinese Medical Journal》 SCIE CAS CSCD 2011年第11期1739-1742,共4页
Background Primary ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 years. T... Background Primary ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 years. The etiology of primary ovarian insufficiency in human female patients is still unclear. The purpose of this study is to investigate the potential genetic causes in primary amenorrhea patients by high resolution array based comparative genomic hybridization (array-CGH) analysis. Methods Following the standard karyotyping analysis, genomic DNA from whole blood of 15 primary amenorrhea patients and 15 normal control women was hybridized with Affymetrix cytogenetic 2.7M arrays following the standard protocol. Copy number variations identified by array-CGH were confirmed by real time polymerase chain reaction. 展开更多
关键词 primary ovarian insufficiency array based comparative genomic hybridization technology NSF gene deletion
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Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples 被引量:4
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作者 Qinghua Zhou Shen-Yin Wu +2 位作者 Katherine Amato Autumn DiAdamo Peining Li 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2016年第3期121-131,共11页
Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants (CNVs) in products ... Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants (CNVs) in products of conception (POC) and the underlying gene- dosage-sensitive mechanisms causing spontaneous abortions remain largely unknown. In this study, array comparative genornic hybridiza- tion (aCGH) analysis was performed as a salvage procedure for 128 POC culture failure (POC-CF) samples and as a supplemental procedure for 106 POC normal karyotype (POC-NK) samples. Chromosomal abnormalities were detected in 10% of POC-CF and pathogenic CNVs were detected in 3.9% of POC-CF and 5.7% of POC-NK samples. Compiled results from this study and relevant case series through a literature review demonstrated an abnormality detection rate (ADR) of 35% for chromosomal abnormalities in POC-CF samples, 3.7% for pathogenic CNVs in POC-CF samples, and 4.6% for pathogenic CNVs in POC-NK samples. Ingenuity Pathway Analysis (IPA) was performed on the genes from pathogenic CNVs found in POC samples. The denoted primary gene networks suggested that apoptosis and cell proliferation pathways are involved in miscarriage. In summary, a similar spectrum of cytogenomic abnormalities was observed in POC culture success and POC-CF samples. A threshold effect correlating the number of dosage-sensitive genes in a chromosome with the observed frequency of autosomai trisomy is proposed. A rationalized approach using firstly fluorescence in situ hybridization (FISH) testing with probes of chromosomes X/Y/ 18, 13/21, and 15/16/22 for common aneuploidies and polyploidies and secondly aCGH for other cytogenomic abnormalities is recommended for POC-CF samples. 展开更多
关键词 Products of conception (POC) Culture failure Normal karyotype array comparative genomic hybridization (aCGH) Chromosomal andgenomic abnormalities Apoptosis
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Analyses of Genotypes and Phenotypes of Ten Chinese Patients with Wolf-Hirschhorn Syndrome by Multiplex Ligation-dependent Probe Amplification and Array Comparative Genomic Hybridization 被引量:3
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作者 Wen-Xu yang Hong Pan +5 位作者 Lin Li Hai-Rong Wu Song-Tao Wang Xin-Hua Bao Yu-Wu Jiang Yu Qi 《Chinese Medical Journal》 SCIE CAS CSCD 2016年第6期672-678,共7页
Background: Wolf-Hirschhorn syndrome (WHS) is a contiguous gene syndrome that is typically caused by a deletion of the distal portion of the short arm of chromosome 4. However, there are few reports about the featu... Background: Wolf-Hirschhorn syndrome (WHS) is a contiguous gene syndrome that is typically caused by a deletion of the distal portion of the short arm of chromosome 4. However, there are few reports about the features of Chinese WHS patients. This study aimed to characterize the clinical and molecular cytogenetic features of Chinese WHS patients using the combination of multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (array CGH). Methods: Clinical information was collected from ten patients with WHS. Genomic DNA was extracted from the peripheral blood of the patients. The deletions were analyzed by MLPA and array CGH. Results: All patients exhibited the core clinical symptoms of WHS, including severe growth delay, a Greek warrior helmet facial appearance, differing degrees of intellectual disability, and epilepsy or electroencephalogram anomalies. The 4p deletions ranged from 2.62 Mb to 17.25 Mb in size and included LETM1, WHSC1, and FGFR3. Conclusions: The combined use of MLPA and array CGH is an effective and specific means to diagnose WHS and allows for the precise identification of the breakpoints and sizes of deletions. The deletion of genes in the WHS candidate region is closely correlated with the core WHS phenotype. 展开更多
关键词 array comparative genomic hybridization Multiplex Ligation-dependent Probe Amplification Wolf-HirschhornSyndrome
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Genomic landscape of pancreatic neuroendocrine tumors
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作者 Niklas Gebauer Christian Schmidt-Werthern +7 位作者 Veronica Bernard Alfred C Feller Tobias Keck Nehara Begum Dirk Rades Hendrik Lehnert Georg Brabant Christoph Thorns 《World Journal of Gastroenterology》 SCIE CAS 2014年第46期17498-17506,共9页
AIM: To investigate the prognostic role of genomic stability and copy number alterations (CNAs) pancreatic neuroendocrine tumors (PanNETs).
关键词 array comparative genomic hybridization Copy number alterations Chromosomal aberrations Pancreatic neuroendocrine tumors PROGNOSIS
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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 被引量:5
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作者 Chueh-ChuanYen Yann-JangChen +12 位作者 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 《World Journal of Gastroenterology》 SCIE CAS CSCD 2005年第9期1267-1272,共6页
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 wi... 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 identified. TP63 is amplified in early stage of EC-SCC carcinogenesis but down-regulated in advanced stage of disease. 展开更多
关键词 Chromosomal aberration comparative genomic hybridization Esophageal neoplasm IMMUNOHISTOCHEMISTRY Quantitative real-time PCR Tissue array Tumor protein 63
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Loss of fragile histidine triad and amplification of 1p36.22 and 11p15.5 in primary gastric adenocarcinomas 被引量:1
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作者 Ji-Yun Lee 《World Journal of Gastroenterology》 SCIE CAS CSCD 2012年第33期4522-4532,共11页
AIM: To investigate the genomic copy number alterations that may harbor key driver genes in gastric tumorigenesis. METHODS: Using high-resolution array comparative genomic hybridization (CGH), we investigated the geno... AIM: To investigate the genomic copy number alterations that may harbor key driver genes in gastric tumorigenesis. METHODS: Using high-resolution array comparative genomic hybridization (CGH), we investigated the genomic alterations of 20 advanced primary gastric adenocarcinomas (seventeen tubular and three mucinous) of Chinese patients from the Jilin province. Ten matching adjacent normal regions from the same patients were also studied. RESULTS: The most frequent imbalances detected in these cancer samples were gains of 3q26.31-q27.2, 5p, 8q, 11p, 18p, 19q and 20q and losses of 3p, 4p,18q and 21q. The use of high-resolution array CGH increased the resolution and sensitivity of the observed genomic changes and identified focal genetic imbalances, which included 54 gains and 16 losses that were smaller than 1 Mb in size. The most interesting focal imbalances were the intergenic loss/homozygous deletion of the fragile histidine triad gene and the amplicons 11q13, 18q11.2 and 19q12, as well as the novel amplicons 1p36.22 and 11p15.5. CONCLUSION: These regions, especially the focal amplicons, may harbor key driver genes that will serve as biomarkers for either the diagnosis or the prognosis of gastric cancer, and therefore, a large-scale investigation is recommended. 展开更多
关键词 array comparative genomic hybridization Amplicon Gastric adenocarcinoma Oncogene Fragile histidine triad
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Methyl-CpG-Binding protein 2 duplication syndrome in a Chinese patient:A case report and review of the literature
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作者 Xu-Hang Xing Russel Takam +2 位作者 Xiu-Ying Bao Nour Abdallah Ba-alwi Hong Ji 《World Journal of Clinical Cases》 SCIE 2023年第27期6505-6514,共10页
BACKGROUND Chromosomal Xq28 region duplication encompassing methyl-CpG-binding protein 2(MECP2)results in an identifiable phenotype and global developmental delay known as MECP2 duplication syndrome(MDS).This syndrome... BACKGROUND Chromosomal Xq28 region duplication encompassing methyl-CpG-binding protein 2(MECP2)results in an identifiable phenotype and global developmental delay known as MECP2 duplication syndrome(MDS).This syndrome has a wide range of clinical manifestations,including abnormalities in appearance,neurodevelopment,and gastrointestinal motility;recurrent infections;and spasticity.Here,we report a case of confirmed MDS at our institution.CASE SUMMARY A 12-year-old Chinese boy presented with intellectual disability(poor intellectual[reasoning,judgment,abstract thinking,and learning]and adaptive[lack of communication and absent social skills,apraxia,and ataxia]functioning)and dysmorphism.He had no history of recurrent infections,seizures,or bowel dysfunction,which is different from that in reported cases.Microarray comparative genomic hybridization confirmed MECP2 duplication in the patient and his mother who is a carrier.The duplication size was the same in the patient and his mother.No prophylactic antibiotic or anti-seizure therapy was offered to the patient or his mother before or after the consultation.CONCLUSION MDS is rare and has various clinical presentations.Clinical suspicion is critical in patients presenting with developmental delays. 展开更多
关键词 Methyl-CpG-binding protein 2 Neurodevelopmental Delay Xq28 duplication array comparative genomic hybridization Case report
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Advances in preimplantation genetic diagnosis/screening 被引量:3
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作者 YAN LiYing WEI Yuan +9 位作者 HUANG Jin ZHU XiaoHui SHI XiaoDan XIA Xi YAN Jie LU CuiLing LIAN Ying LI Rong LIU Ping QIAO Jie 《Science China(Life Sciences)》 SCIE CAS 2014年第7期665-671,共7页
Preimplantation genetic diagnosis(PGD)gives couples who have a high risk of transmitting genetic disorders to their baby the chance to have a healthy offspring through embryo genetic analysis and selection.Preimplanta... Preimplantation genetic diagnosis(PGD)gives couples who have a high risk of transmitting genetic disorders to their baby the chance to have a healthy offspring through embryo genetic analysis and selection.Preimplantation genetic screening(PGS)is an effective method to select euploid embryos that may prevent repeated implantation failure or miscarriage.However,how and to whom PGS should be provided is a controversial topic.The first successful case of PGD of a human being was reported in 1990,and there have been tremendous improvements in this technology since then.Both embryo biopsy and genetic technologies have been improved dramatically,which increase the accuracy and expand the indications of PGD/PGS. 展开更多
关键词 preimplantation genetic diagnosis preimplantation genetic screening INDICATIONS biopsy methods array comparative genomic hybridization next-generation sequencing
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Identification of Tumor Evolution Patterns by Means of Inductive Logic Programming
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作者 Vitoantonio Bevilacqua Patrizia Chiarappa +3 位作者 Giuseppe Mastronardi Filippo Menolascina Angelo Paradiso Stefania Tommasi 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2008年第2期91-97,共7页
In considering key events of genomic disorders in the development and progression of cancer, the correlation between genomic instability and carcinogenesis is currently under investigation. In this work, we propose an... In considering key events of genomic disorders in the development and progression of cancer, the correlation between genomic instability and carcinogenesis is currently under investigation. In this work, we propose an inductive logic programming approach to the problem of modeling evolution patterns for breast cancer. Using this approach, it is possible to extract fingerprints of stages of the disease that can be used in order to develop and deliver the most adequate therapies to patients. Furthermore, such a model can help physicians and biologists in the elucidation of molecular dynamics underlying the aberrations-waterfall model behind carcinogenesis. By showing results obtained some hints about further approach to the hypotheses. on a real-world dataset, we try to give knowledge-driven validations of such 展开更多
关键词 array comparative genomic hybridization breast cancer cancer evolution model gene selection inductive logic programming
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Cryptic NUP214-ABL1 fusion with complex karyotype, episomes and intra-tumor genetic heterogeneity in a T-cell lymphoblastic lymphoma
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作者 Moneeb A.K Othman Beate Grygalewicz +3 位作者 Agnieszka Kołkowska-Lesniak Joana B.Melo Isabel M.Carreira Thomas Liehr 《Journal of Cancer Metastasis and Treatment》 CAS 2018年第1期597-605,共9页
T-lymphoblastic lymphoma(T-LBL)is a rare and aggressive form of non-Hodgkin’s lymphoma and little is known about their molecular background.However,complex karyotypes were already related to this group of malignancy ... T-lymphoblastic lymphoma(T-LBL)is a rare and aggressive form of non-Hodgkin’s lymphoma and little is known about their molecular background.However,complex karyotypes were already related to this group of malignancy and associated with poor outcome.Here,we describe a 17-year-old female being diagnosed with T-LBL and a normal karyotype after standard G-banding with trypsin-Giemsa(GTG)-banding.However,further analyses including high-resolution molecular approaches,array-comparative genomic hybridization(aCGH),multiplex ligation-dependent probe amplification,fluorescence in situ hybridization and multicolor chromosome banding revealed a cryptic complex karyotype,NUP214-ABL1 gene fusion,episomes and intra-tumor genetic heterogeneity.In addition,homozygous loss of CDKN2A,as well as amplification of oncogene TLX1(HOX11)were detected.Actually,NUP214-ABL1 fusion gene replicated autonomously in this case as episomes.Overall,highly amplification of NUP214-ABL1 fusion gene defines possibly a new subgroup of T-LBL patients which accordingly could benefit from treatment with tyrosine kinase inhibitors.As episomes are missed in standard karyotyping aCGH should be performed routinely in T-LBL to possibly detect more of such cases. 展开更多
关键词 T-cell lymphoblastic lymphoma NUP214-ABL1 fusion complex karyotype episomes intra-tumor genetic heterogeneity molecular cytogenetics array comparative genomic hybridization
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Prenatal Testing or Screening?
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作者 Evans Mark I. Evans Shara M. 《Maternal-Fetal Medicine》 2020年第4期217-222,共6页
Over the past 50 years,the scope and extent of prenatal diagnosis and screening for genetic disorders have improved geometrically.There has been a pendulum like swing from testing to screening back and forth as new te... Over the past 50 years,the scope and extent of prenatal diagnosis and screening for genetic disorders have improved geometrically.There has been a pendulum like swing from testing to screening back and forth as new technologies emerge.The concurrent developments of cell free fetal DNA analysis of maternal blood has dramatically changed patient’s choices towards screening.However,with the use of array comparative genomic hybridization of fetal DNA that requires diagnostic procedures(Chorionic villus sampling and amniocentesis),much more extensive diagnosis can be obtained.Until noninvasive methods can replicate what can be done with diagnostic procedures there still will be a"price to be paid"for opting for the non-invasive methods. 展开更多
关键词 Genetic counseling Prenatal diagnosis Chorionic villus sampling AMNIOCENTESIS array comparative genomic hybridization Noninvasive prenatal testing
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