鼻咽癌转移相关基因的比较基因组杂交和cDNA微阵列研究

为筛选在鼻咽癌转移中起重要作用的基因 ,应用比较基因组杂交 (CGH)和cDNA微阵列方法研究成瘤和转移能力不同的鼻咽癌细胞株 6 10B和 5 8F .CGH结果显示 ,2种细胞株在 5p、7q、8p、9q、11p、12q和 17p的一定区域存在差异性扩增 ,在 2q存在差异性缺失 ;cDNA微阵列显示 ,相对于非转移性 6 10B细胞株 ,高转移性 5 8F细胞表现一些基因表达的上调及下调 ,CGH和cDNA微阵列的结合是筛选转移相关基因较好方法     

喉癌的比较基因组杂交研究

寻找与喉癌发生进展的相关基因,应用比较基因组杂交技术分析了18例喉癌患者。结果显示,每例喉癌细胞染色体均有不同程度的变化,包括染色体全部或部分的扩增或丢失。平均每例有12．9处异常区域,丢失多于扩增,分别为每例7．2处和5．7处。主要为3q(78％,)、5p(61％)、11q(56％)、1q(50％,)、8p(44％)、8q(39％)和15q(39％)的扩增;3p(70％)、5q(78％)、90(67%)、13q(50％)、1p(44％)和14q(39％)的丢失。有多条染色体区带上出现特异的扩增或丢失,特别是1p13-21(8／18)、3p21-23(14／18)、5p21-22(14／18)、9p12-pter(10／18)和13q21-31(8／18)的拷贝数增加明显,而1q11-2l(11／18)、3q15-21(12／18)、8p22-24(6／18)、11q12-13(8／18)、15q21-23(7／18)和18p11(8／18)区域的丢失为喉癌的特征性变化,说明这些区域中存在与喉癌发生发展密切相关的癌基因、抑癌基因或其他相关基因。     

三种寡核苷酸芯片片基的比较

将荧光标记的寡核苷酸打印在Corning、多聚赖氨酸包被的DAKO玻片和多聚赖氨酸处理的一种显微镜载玻片上,并按常规方法进行洗脱,通过GenePix4100A扫描并以Genepix6．0软件分析点的大小、荧光强度和背景荧光强度来衡量3种片基的均一性和固定效率,并通过不同浓度梯度的60bp寡核苷酸探针的杂交实验来衡量片基对杂交效率的影响．结果显示,3种片基的均一性都较好,而多聚赖氨酸包被的DAKO和Cornning芯片的固定效率和杂交效率优于国产芯片．     

遗传变异的又一来源：拷贝数变异

人们很早就发现DNA拷贝数变异与特定染色体重组和基因组异常相关这一现象,但最近才知道它与疾病的相关联系。我们对拷贝数变异的原理、最新研究方法,及其与复杂疾病的相关性研究等进展进行了综述;总结了拷贝数变异研究所存在的问题;对拷贝数变异未来的研究重点和需要解决的问题进行了展望。     

一种基于寡核苷酸微阵列芯片的多重可扩增探针杂交技术

多重可扩增探针杂交技术(multiplex amplifiable probe hybridization,MAPH)是近年来发展起来的一种用于基因组中DNA拷贝数检测的新技术。并发展了一种基于寡核苷酸微阵列芯片的MAPH技术。该方法根据所检测的DNA序列,制备若干具有通用引物的FCR产物作为可扩增探针组,与固定在尼龙膜上待测的基因组DNA杂交。用磁珠回收特异性杂交的探针,经生物素标记的通用引物扩增后,与相应的寡核苷酸微阵列芯片杂交。该特异性的寡核苷酸微阵列芯片包括10个抗肌营养不良基因的外显子探针和阴性、阳性探针。杂交清冼后,链霉亲和素-Cy3染色用芯片扫描仪得到杂交的荧光图像。分析荧光信号的强度差异给出特定基因片段拷贝数的变化。该方法用微阵列技术代替MAPH中的电泳检测技术,可大幅度增加检测的通量。选择了一个正常男性、一个正常女性和一个肌营养不良症患者的基因组DNA来进行验证。结果表明,该方法能够同时给出抗肌营养不良基因多个外显子中的基因片段拷贝数差异信息。     

微阵列（microarrays）技术及其应用

微阵列分为cDNA微阵列和寡聚核苷酸微阵列,微阵列上“印”有大量已知部分序列的DNA探针,微阵列技术就是利用分子杂交原理,使同时被比较的标本（用同位素或荧光素标记）与微阵列杂交,通过检测杂交信号强度及数据处理,把他们转化成不同标本中特异基因的丰度,从而全国比较不同标本的基因表达水平的差异,微阵列技术是一种探索基因组功能的有力手段。     

通过比较基因组杂交研究肝癌中非随机染色体畸变

本研究通过使用比较基因组杂交的方法,研究肝癌中的非随机染色体畸变,旨在为肝癌的临床诊断和治疗提供参考资料。本研究收集了我院在2016年9月至2017年9月收治的10例肝癌患者,采集其肝癌标本。使用比较基因组杂交法(CGH)对所有肝癌标本的非随机染色体畸变进行分析。结果表明,所有肝癌标本均出现了非随机染色体畸变,即4q区域、16q区域、8p区域和17p区域的缺失变化。同时在1q区域、8q区域、17q区域以及6p区域出现了扩增变化。本研究初步得出结论,在肝癌出现后,其非随机区域会出现染色体畸变,这些情况的出现可对肝癌进行较好诊断,同时也可指导对肝癌的治疗。     

比较基因组学及其应用

比较基因组学是利用某些基因组图谱和测序获得的信息推测其他生物基因组的基因数目、位置、功能、表达机制和物种进化的学科。比较基因组学的发展与序列数据的积累密切相关,目前该学科已经成为研究生物基因组的最主要手段之一。利用FASTA、BLAST和CLUSTAL W等序列比对工具,种间的比较基因组学能够让人们了解物种间在基因组结构上的差异,发现基因的功能、物种的进化关系,以及进行功能基因的克隆。种内的比较基因组学研究主要涉及个体或群体基因组内诸如SNP、CNP等变异和多态现象。比较基因组学的研究结果不但有助于深入了解生命体的遗传机制,也有助于阐明人类复杂疾病的致病机制,揭示生命的本质规律。     

人类基因组DNA单核苷酸多态性的检测方法

单核苷酸多态性（SNP）作为新的遗传标记对基因定位及相关疾病的研究意义重大。本文对近年来9种SNP检测方法的原理、应用及优缺点,包括基于FRET原理的Taqman法和分子灯塔法;基于分子杂交技术的寡核苷酸连接分析、等位基因特异性寡核苷酸探针杂交法、动态等位基因特异性杂交法及DNA芯片法;及质谱法、变性－高压液相色谱法和单个碱基延伸标记法进行综述。     

西瓜与近缘种亲缘关系的比较基因组原位杂交分析

物种间亲缘关系的研究是杂交育种的理论基础,野生西瓜在西瓜育种中具有重要作用,然而目前对西瓜属物种间亲缘关系的研究十分有限,而且对西瓜属物种的分类问题还存在分歧.比较基因组原位杂交是分析物种间亲缘关系的有效手段,本研究以西瓜基因组DNA作探针,分别对缺须西瓜、热迷西瓜、药西瓜和诺丹西瓜有丝分裂中期染色体进行了比较基因组原位杂交分析,揭示了西瓜属物种间的亲缘关系,同时对分类地位尚存在争议的诺丹西瓜的归属问题进行了分析,发现诺丹西瓜和甜瓜之间具有非常近的亲缘关系,本研究结果为西瓜与近缘种间的远缘杂交提供了重要的理论依据.     

Diversity Suppression-Subtractive Hybridization Array for Profiling Genomic DNA Polymorphisms

Genomlc DNA polymorphlsms are very useful for tracing genetic traits end studying biological diversity among species. Here, we present a method we call the ＂diversity suppresslon-subtractlve hybridization array＂ for effectively profiling genomlc DNA polymorphisms. The method first obtains the subtracted gDNA fragments between any two species by suppression subtraction hybridization （SSH） to establish e subtracted gDNA library, from which diversity SSH arrays are created with the selected subtracted clones. The diversity SSH array hybridizes with the DIG-labeled genomlc DNA of the organism to be assayed. Six closely related Dendrobium species were studied as model samples. Four Dendrobium species as testers were used to perform SSH. A total of 617 subtracted positive clones were obtained from four Dendrobium species, and the average ratio of positive clones was 80.3%. We demonstrated that the average percentage of polymorphlc fragments of palrwlse comparisons of four Dendrobium species was up to 42.4%. A dendrogram of the relatedness of six Dendrobium species was produced according to their polymorphic profiles. The results revealed that the diversity SSH array Is a highly effective platform for profiling genomlc DNA polymorphlsms and dendrograms.     

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Array CGH for the detection of genomic copy number variants has replaced G-banded karyotype analysis. This paper describes the technology and its application in a clinical diagnostic service laboratory. DNA extracted from a patient’s sample (blood, saliva or other tissue types) is labeled with a fluorochrome (either cyanine 5 or cyanine 3). A reference DNA sample is labeled with the opposite fluorochrome. There follows a cleanup step to remove unincorporated nucleotides before the labeled DNAs are mixed and resuspended in a hybridization buffer and applied to an array comprising ~60,000 oligonucleotide probes from loci across the genome, with high probe density in clinically important areas. Following hybridization, the arrays are washed, then scanned and the resulting images are analyzed to measure the red and green fluorescence for each probe. Software is used to assess the quality of each probe measurement, calculate the ratio of red to green fluorescence and detect potential copy number variants.     

DNA Copy Number Aberrations in Breast Cancer by Array Comparative Genomic Hybridization

Array comparative genomic hybridization (CGH) has been popularly used for an-alyzing DNA copy number variations in diseases like cancer. In this study, we investigated 82 sporadic samples from 49 breast cancer patients using 1-Mb reso-lution bacterial artificial chromosome CGH arrays. A number of highly frequent genomic aberrations were discovered, which may act as "drivers" of tumor pro-gression. Meanwhile, the genomic profiles of four "normal" breast tissue samples taken at least 2 cm away from the primary tumor sites were also found to have some genomic aberrations that recurred with high frequency in the primary tu-mors, which may have important implications for clinical therapy. Additionally, we performed class comparison and class prediction for various clinicopathological pa-rameters, and a list of characteristic genomic aberrations associated with different clinicopathological phenotypes was compiled. Our study provides clues for further investigations of the underlying mechanisms of breast carcinogenesis.     

Comparison of Established Cell Lines at Different Passages by Karyotype and Comparative Genomic Hybridization

Two established cancer cell lines, MCF-7 and Ishikawa, were both obtained directly from a cell repository and through another laboratory. The karyotypes from the two MCF-7 cell lines had up to 83 chromosomes and similarities for chromosomal gain and structural abnormalities. The two Ishikawa cell lines had up to 60 chromosomes with only a missing X as the common chromosome abnormality. CGH studies were performed by co-hybridizing the two Ishikawa or MCF-7 cell lines to normal metaphases. The differences seen between the two MCF-7 cell cultures reflect changes due to passage number and culture conditions. For Ishikawa, DNA polymorphic data and mutation studies suggest that the two cell lines are not derived from the same established tumor cell line. Our study shows the utilization of CGH in comparing cell lines originating from the same specimen. Our study also demonstrates the necessity for periodically evaluating cell lines to confirm their origin.     

Comparison of Comparative Genomic Hybridization Technologies Across Microarray Platforms

In the 2007 Association of Biomolecular Resource Facilities Microarray Research Group project, we analyzed HL-60 DNA with five platforms: Agilent, Affymetrix 500K, Affymetrix U133 Plus 2.0, Illumina, and RPCI 19K BAC arrays. Copy number variation was analyzed using circular binary segmentation (CBS) analysis of log ratio scores from four independently assessed hybridizations of each platform. Data obtained from these platforms were assessed for reproducibility and the ability to detect formerly reported copy number variations in HL-60. In HL-60, all of the tested platforms detected genomic DNA amplification of the 8q24 locus, trisomy 18, and monosomy X; and deletions at loci 5q11.2~q31, 9p21.3~p22, 10p12~p15, 14q22~q31, and 17p12~p13.3. In the HL-60 genome, at least two of the five platforms detected five novel losses and five novel gains. This report provides guidance in the selection of platforms based on this wide-ranging evaluation of available CGH platforms.     

Mutation Screening and Array Comparative Genomic Hybridization Using a 180K Oligonucleotide Array in VACTERL Association

In order to identify genetic causes of VACTERL association (V vertebral defects, A anorectal malformations, C cardiac defects, T tracheoesofageal fistula, E esophageal atresia, R renal anomalies, L limb deformities), we have collected DNA samples from 20 patients diagnosed with VACTERL or with a VACTERL-like phenotype as well as samples from 19 aborted fetal cases with VACTERL. To investigate the importance of gene dose alterations in the genetic etiology of VACTERL association we have performed a systematic analysis of this cohort using a 180K array comparative genomic hybridization (array-CGH) platform. In addition, to further clarify the significance of PCSK5, HOXD13 and CHD7 genes in the VACTERL phenotype, mutation screening has been performed. We identified pathogenic gene dose imbalances in two fetal cases; a hemizygous deletion of the FANCB gene and a (9;18)(p24;q12) unbalanced translocation. In addition, one pathogenic mutation in CHD7 was detected, while no apparent disease-causing mutations were found in HOXD13 or PCSK5. Our study shows that although large gene dose alterations do not seem to be a common cause in VACTERL association, array-CGH is still important in clinical diagnostics to identify disease cause in individual cases.