Genomic characterization of prenatally detected chromosomal structural abnormalities using oligonucleotide array comparative genomic hybridization

Detection of chromosomal structural abnormalities using conventional cytogenetic methods poses a challenge for prenatal genetic counseling due to unpredictable clinical outcomes and risk of recurrence. Of the 1,726 prenatal cases in a 3-year period, we performed oligonucleotide array comparative genomic hybridization (aCGH) analysis on 11 cases detected with various structural chromosomal abnormalities. In nine cases, genomic aberrations and gene contents involving a 3p distal deletion, a marker chromosome from chromosome 4, a derivative chromosome 5 from a 5p/7q translocation, a de novo distal 6q deletion, a recombinant chromosome 8 comprised of an 8p duplication and an 8q deletion, an extra derivative chromosome 9 from an 8p/9q translocation, mosaicism for chromosome 12q with added material of initially unknown origin, an unbalanced 13q/15q rearrangement, and a distal 18q duplication and deletion were delineated. An absence of pathogenic copy number changes was noted in one case with a de novo 11q/14q translocation and in another with a familial insertion of 21q into a 19q. Genomic characterization of the structural abnormalities aided in the prediction of clinical outcomes. These results demonstrated the value of aCGH analysis in prenatal cases with subtle or complex chromosomal rearrangements. Furthermore, a retrospective analysis of clinical indications of our prenatal cases showed that approximately 20% of them had abnormal ultrasound findings and should be considered as high risk pregnancies for a combined chromosome and aCGH analysis.     

Analysis of ovarian cancer cell lines using array-based comparative genomic hybridization

In this study, 23 ovarian cancer cell lines were screened using array-comparative genomic hybridization (aCGH) based on large-insert clones at about 1 Mb density from throughout the genome. The most frequent recurrent changes at the level of the chromosome arm were loss of chromosome 4 or 4q, loss of 18q and gain of 20 or 20q; other recurrent changes included losses of 6q, 8p, 9p, 11p, 15q, 16q, 17p, and 22q, and gain of 7q. Losses of 4q and 18q occurred together more often than expected. Evidence was found for two types of ovarian cancer, one typically near-triploid and characterized by a generally higher frequency of chromosomal changes (especially losses of 4p, 4q, 13q, 15q, 16p, 16q, 18p and 18q), and the other typically near-diploid/tetraploid and with fewer changes overall, but with relatively high frequencies of 9p loss, 9q gain, and 20p gain. Multiple novel changes (amplifications, homozygous deletions, discrete regions of gain or loss, small overlapping regions of change and frequently changed clones) were also detected, each of which might indicate the locations of oncogenes or tumour suppressor loci. For example, at least two regions of amplification on chromosome 11q13, one including cyclin D1 and the other the candidate oncogene PAK1, were found. Amplification on 11q22 near the progesterone receptor gene and a cluster of matrix metalloproteinase loci was also detected. Other potential oncogenes, which mapped to regions found by this study, included cyclin E and PIK3C2G. Candidate tumour suppressor genes in regions of loss included CDKN2C, SMAD4-interacting protein and RASSF2.     

Chromosomal imbalances revealed in primary renal cell carcinomas by comparative genomic hybridization

Renal cell carcinoma (RCC) accounts for approximately 3% of all new cancer cases. Although the classification of RCC is based mainly on histology, this method is not always accurate. We applied comparative genomic hybridization (CGH) to determine genomic alterations in 46 cases of different RCC histological subtypes [10 cases of clear cell RCC (CCRCC), 13 cases of papillary RCC (PRCC), 12 cases of chromophobe RCC (CRCC), 9 cases of Xp11.2 translocation RCC (Xp11.2RCC), 2 cases of undifferentiated RCC (unRCC)], and investigated the relationships between clinical parameters and genomic aberrations. Changes involving one or more regions of the genome were seen in all RCC patients; DNA sequence gains were most frequently (>30%) seen in chromosomes 7q, 16p, and 20q; losses from 1p, 3p, 13q, 14q, and 8p. We conclude CGH is a useful complementary method for differential diagnosis of RCC. Loss of 3p21-25, 15q, and gain of 16p11-13 are relatively particular to CCRCC vs. other types of RCC. Gain of 7p13-22, 8q21-24, and loss of 18q12-ter, 14q13-24, and Xp11-q13/Y are more apparent in PRCC, and gain of 8q21-24 is characteristic of type 2 PRCC vs. type 1 PRCC. Loss of 2q12-32, 10p12-15, and 11p11-15, 13p are characteristic of CRCC, and gain of 3p and loss of 11p11-15 and 13p are significant differentiators between common CRCC and CRCC accompanied by sarcomatous change groups. Gain of Xp11-12 is characteristic of the Xp11.2RCC group. Based on Multivariate Cox regression analysis, aberration in 5 chromosome regions were poor prognostic markers of RCC, and include the gain of chromosome 12p12-ter (P = 0.034, RR = 3.502, 95% CI 1.097-11.182), 12q14-ter (P = 0.002, RR = 5.115, 95% CI 1.847-14.170), 16q21-24 (P = 0.044, RR = 2.629, 95% CI 1.027-6.731), 17p12-ter (P = 0.017, RR = 3.643, 95% CI 1.262-10.512) and the loss of 18q12-23 (P = 0.049, RR = 2.911, 95% CI 1.006-8.425), which may provide clues of new genes involved in RCC tumorigenesis.     

Chromosomal and genetic imbalances in Chinese patients with rhabdomyosarcoma detected by high-resolution array comparative genomic hybridization

Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma in children. Although associations between ARMS tumorigenesis and PAX3, PAX7, and FKHR are well recognized, the complete genetic etiology underlying RMS pathogenesis and progression remains unclear. Chromosomal copy number variations (CNVs) and the involved genes may play important roles in the pathogenesis and progression of human malignancies. Using high-resolution array comparative genomic hybridization (aCGH), we examined 20 formalin-fixed, paraffin-embedded (FFPE) RMS tumors to explore the involvement of the relevant chromosomal regions with resident genes in RMS tumorigenesis. In RMS, frequent gains were identified on chromosome regions 12q13.3-q14.1, 12q24.31, 17q25.1, 1q21.1, and 7q11.23, whereas frequent losses were observed on chromosome regions 5q13.2, 14q32.33, and 15q11.2. Amplifications were observed on chromosome regions 9p13.3, 12q13.3-q14.1, 12q15, and 16p13.11, whereas deletions were detected on chromosome regions 1p36.33, 1p13.1, 2q11.1, 5q13.2, 8p23.1, 9p24.3, and 16p11.2. Frequent gains were detected in GLI1, GEFT, OS9, and CDK4 (12q13.3-q14.1), being 60% in embryonal rhabdomyosarcoma (ERMS) and 66.67% in alveolar rhabdomyosarcoma (ARMS), respectively. However, frequent losses were detected in IGHG1, IGHM, IGHG3, and IGHG4 (14q32.33), being 70% in ERMS and 55.56% in and ARMS, respectively. Frequent gains were detected in TYROBP, HCST, LRFN3, and ALKBH6 (19q13.12) in ERMS but not in ARMS. The frequency of TYROBP, HCST, LRFN3, and ALKBH6 gains is significantly different in ERMS versus ARMS (P=0.011). The results suggest that novel TYROBP, HCST, LRFN3, and ALKBH6 genes may play important roles in ERMS. The technique used is a feasible approach for array comparative genomic hybridization analysis in archival tumor samples.     

采用微阵列-比较基因组杂交进行产前诊断的局限性和困难

应用微阵列-比较基因组杂交(microarray comparative genomic hybridization,aCGH)技术检测基因拷贝数变异(copy Bumber variation,CNV)可对染色体亚微结构异常进行定位,在研究领域和临床实验室中迅速成为一个了解基因和患者遗传病因的有力的工具.由于它在产前诊断上的应用时间较短,目前对aCGH是否可以作为产前诊断工具及其潜在的不确定性存在比较大的争议.此外,对于大多数CNV的表型效应还知之甚少,因此,临床医生向患者进行解释的难度很大,导致许多临床医生拒绝以临床诊断为目的使用aCGH.根据已知的与临床疾病密切相关的一些区域定制的寡核苷酸芯片应运而生,可以降低这种不确定性,在过量信息和信息量不足之间寻求到了一个平衡.本综述的目的是从临床医生的角度探讨aCGH技术用于产前诊断所面临的问题和应用前景.

Abstract：

Subchromosomal abnormalities can be positioned by the detection of copy number variation (CNV) using microarray comparative genomic hybridization (aCGH). aCGH has become a powerful tool in understanding the association between gene and genetic etiology in both research and clinical laboratories.Meanwhile as a new technique, controversies inevitably arose in its clinical application. As for the phenotype of CNV, little has been disclosed. For the clinicians, the difficulty in explanation of the CNV to the patients is obvious, which makes many doctors refuse to use aCGH for clinical diagnosis. Customized arrays have been exploited to decrease the uncertainty and efforts to search for a balance between overloaded information and insufficient information have been made. The purpose of this review is to discuss the current limitations and difficulties on application of aCGH in prenatal diagnosis and its application prospect from the point of a clinician.     

Determination of amplicon boundaries at 20q13.2 in tissue samples of human gastric adenocarcinomas by high-resolution microarray comparative genomic hybridization

Comparative genomic hybridization (CGH) of gastric adenocarcinomas frequently shows gains and amplifications of chromosome 20. However, the underlying genetic lesion is unknown and conventional CGH results do not allow specification of the target region. In order to investigate this chromosomal aberration with a higher resolution and sensitivity, microarray-based CGH was performed with both scanning and high-resolution arrays of chromosome 20 in a series of 27 gastric adenocarcinomas. Locus-specific fragments of genomic DNA from bacterial artificial chromosome (BAC) clones were spotted as microarrays. A scanning array contained a set of 27 BAC clones covering chromosome 20q. A high-resolution array contained 27 overlapping BAC clones at 20q13.2. This high-resolution array was used to narrow down the amplicon at 20q13.2 in tumours showing amplification of this chromosomal region with the scanning array. Positive copy number changes on chromosome 20q were detected in 12 of 27 cases (44%). These changes included gain of the whole arm of chromosome 20q in 8 of 27 (30%) cases, amplification restricted to 20q12.1 in one case, and amplifications restricted to 20q13 in three cases (11%). The three tumours showing amplification restricted to 20q13 were analysed further using the high-resolution array. In one tumour, the whole contig was amplified at a constant level. One of the other two tumours had a clear proximal breakpoint, while the other tumour had a clear distal breakpoint within the 20q13.2 region. The proximal and the distal breakpoint were approximately 800 kb apart. In the present study, an amplicon at 20q13.2 has been narrowed down to 800 kb which is likely to harbour one or more putative oncogenes relevant to gastric carcinogenesis, for which ZNF217 and CYP24 are good candidates.     

Comparative genomic hybridization analysis of human oocytes and polar bodies

BACKGROUND: Classical cytogenetic methods and fluorescent in situ hybridization (FISH) have been employed for the analysis of chromosomal abnormalities in human oocytes. However, these methods are limited by the need to spread the sample on a microscope slide, a process that risks artefactual chromosome loss. Comparative genomic hybridization (CGH) is a DNA-based method that enables the investigation of the entire chromosome complement. We optimized and evaluated a CGH protocol for the chromosomal analysis of first polar bodies (PBs) and oocytes. The protocol was then employed to obtain a detailed picture of meiosis I errors in human oogenesis. METHODS: 107 MII oocyte-PB complexes were examined using whole genome amplification (WGA) and CGH. RESULTS: Data was obtained for 100 complexes, donated from 46 patients of average age 32.5 (range 18-42). 22 complexes from 15 patients were abnormal, giving an aneuploidy rate of 22%. CONCLUSIONS: The results presented in this study more than double the quantity of CGH data from female gametes currently available. Abnormalities caused by whole chromosome non-disjunction, unbalanced chromatid predivision and chromosome breakage were reliably identified using the CGH protocol. Analysis of the data revealed a preferential participation of chromosome X and the smaller autosomes in aneuploidy and provided further evidence for the existence of age-independent factors in female aneuploidy.     

Genetic aberrations in oligodendroglial tumours: an analysis using comparative genomic hybridization (CGH)

Four low-grade oligodendrogliomas, nine anaplastic oligodendrogliomas and two mixed oligoastrocytomas were investigated for chromosomal aberrations by comparative genomic hybridization on formalin-fixed, paraffin-embedded tissue samples. The most frequent losses observed involved 1p, 9p, 10pq, 14q, 16p, 19q, while the most frequent gains were seen on 7pq, 11pq, 17p, 19pq, and Xp. In one oligodendroglioma, a highly specific amplification of 1q32.1 was seen. The frequent losses of 14q have not been reported previously. In the two cases of mixed oligoastrocytomas multiple gains and losses were found that did not show a clear overlap with the alterations found in the pure oligodendrogliomas. Copyright © 1999 John Wiley & Sons, Ltd.     

软组织肿瘤的比较基因组杂交研究进展

比较基因组杂交(comparative genomic hybridization,CGH) 是1992年建立起来的重大分子细胞遗传学分析技术,它在对整个基因组DNA拷贝数变异的检测方面是一种有效的方法。通过CGH检测,可找出染色体DNA拷贝数的变异特点,即基因拷贝数的扩增或丢失,从而确定相关的癌基因和抑癌基因所在的区域,为探讨肿瘤的发病机制提供依据。在过去的十几年中,用CGH对各种软组织肿瘤进行研究,已探测到了各种各样的有不同程度特异性的基因组的不平衡性,不仅开辟了探测各种癌症相关基因的新途径,并且找到了一些与临床相关的基因改变,可用于肿瘤的发生、发展、鉴别诊断、预后以及治疗等研究。     

G-显带技术、荧光原位杂交和比较基因组杂交技术在产前诊断中的应用

目的 探讨G显带、荧光原位杂交(fluorescencein situ hybridization,FISH)和比较基因组杂交(comparative genomic hybridization,CGH)技术在产前诊断中应用的程序及意义.方法 采集102例妊娠16周～24周胎儿的羊水,采用G显带、G显带/FISH和G显带/FISH/CGH三阶梯的核型诊断程序,并分析其在产前诊断中的意义.结果 102例胎儿中,经第1阶梯诊断核型98例,诊断困难2例,失败2例;第2阶梯诊断核型2例,诊断困难1例,失败1例;第3阶梯诊断核型2例.经3阶梯诊断程序核型的诊断率达100%(102/102例),异常核型7例(7/102例,6.68 0A),其中第1、第2和第3阶梯分别诊断异常核型4例(4/7例,57.1 oA)、1例(1/7例,14.3%)和2例(2/7例,28.5%).结论 在产前诊断中实施3阶梯诊断程序有助于提高核型的确诊率,规范染色体诊断流程.     

Fluorescence in situ hybridization, comparative genomic hybridization, and other molecular biology techniques in the analysis of effusions

Over the last 20 yr, the introduction of immunocytochemistry as a diagnostic tool has dramatically revolutionized diagnostic pathology. With the introduction of molecular methods as part of the diagnostic armamentarium, the practicing pathologist is facing the new challenge of grasping novel concepts of the molecular cytogenetics era. Herein, we review the diagnostic contribution of ancillary molecular techniques, including fluorescent and chromogenic in situ hybridization, telomerase assays, loss of heterozygosity, comparative genomic hybridization (CGH), and microarray-based CGH, for the practicing cytopathologists and discuss how these techniques will help pathologists in decision-making.     

人食管鳞癌细胞系EC9706的建立及其比较基因组杂交分析

目的 以中国男性食管鳞癌为来源，建立一个可良好传代的细胞系，从而提价七个有用的体外模式用于食管癌的研究。方法 采用组织块培养法，以新鲜的食管癌组织细胞系EC9706，做了初步的生物学特性观察，并采用比较基因组杂交的方法进行细胞遗传学的检测。结果 食管癌细胞系EC9706生长曲线显示其生长良好，易于培养。传代时间为26h，平皿集落形成率为91．9％，且能够在软琼脂中形成集落。经异种接种到裸鼠中均形成移植性肿瘤，肿瘤的病理诊断为中－低分化鳞状细胞癌。比较基因组杂交结果得出染色体1p1,q2-4,2p1,5p,7p14,7q21,11q1,11q2,20q扩增，其中5p表现出高水平的扩增。而染色体2p2,2q2,3p,4,9p,14,18,Xq缺失。结论 建立的细胞系EC9706可用于研究食管癌的癌变过程。     

微阵列比较基因组杂交技术诊断9p部分三体患儿一例

目的 确定1例生长发育迟缓、语言发育障碍患儿的核型,分析其染色体畸变与表型的相关性,探讨微阵列比较基因组杂交(array-based comparative genomic hybridization,array-CGH)在临床分子遗传学诊断中的应用及其优越性.方法 应用G显带对患儿及其父母进行核型分析,进一步采用array-CGH技术对患儿进行全基因组高分辨率扫描分析,确定其衍生染色体片段的来源.结果 G显带染色体分析显示患儿及其母亲均为inv(9)(p13q13)携带者,患儿13号染色体存在一衍生片段.array-CGH结果证实患儿衍生片段源自9号染色体短臂,确定为9p13.1-p24.3三体.患儿母亲array-CGH结果未见异常.结论 inv(9)(p13q13)与患儿异常表型无关,患儿的异常表型可归因于9p13.1-p24.3三体.同传统细胞遗传分析方法相比,array-CGH具有高分辨率和高精确性的优点.     

髓母细胞瘤比较基因组杂交分析及ERBB-2异常表达的意义

目的研究髓母细胞瘤全基因组的遗传学异常,探讨癌基因的异常表达在髓母细胞瘤发病机制中的作用以及与预后的关系。方法应用比较基因组杂交（comparative genomic hybridization,CGH）技术检测14例髓母细胞瘤全基因组的遗传学改变;同时,在扩大系列的29例髓母细胞瘤中,应用荧光原位杂交（fluorescence in situ hybridization,FISH）和免疫组化染色分别检测ERBB-2在基因水平和蛋白水平的表达。结果（1）CGH结果显示,在所有14例髓母细胞瘤标本中,每一条染色体臂上都检测到了染色体的失衡（获得或丢失）,最常见的染色体异常为17q（85．7％）和7q（35．7％）的获得,以及8p（50％）、16q（28．6％）和17p（35．7％）的丢失;（2）FISH检测中,44．5％（13／29例）的肿瘤细胞有ERBB-2基因的异常表达;（3）免疫组化结果显示,37．9％（11／29例）的病例有抗体c-erbB-2的阳性表达;（4）在预后较差的16例患者中,56％（9／16例）的病例有ERBB-2的过度表达。结论CGH研究发现了髓母细胞瘤全基因组的染色体失衡。在染色体17q特异性位点上ERBB-2基因的异常改变很可能在髓母细胞瘤的发病机制中起着重要的作用,其过度表达与患者的预后密切相关。     

微阵列比较基因组杂交分析一例足月小样儿的染色体畸变

目的 分析一例足月小样儿的染色体畸变,探讨患儿低出生体重的原因.方法 采集临床已确诊的足月小样儿外周血并抽提基因组DNA,进行微阵列比较基因组杂交,分析患儿基因组拷贝数的改变.培养患儿及其父母外周血淋巴细胞,进行染色体核型分析并确定患儿染色体畸变的来源.结果 微阵列比较基因组杂交显示患儿在10q125.2→qter区域存在长22 Mb片段的重复,同时在15q26.2→qter区域存在长5 Mb片段的缺失.核型分析显示患儿核型为46,XY,-15,+der(15)t(10;15)(q25;q26)pat.结论 患儿在10q25.2→qter区域存在部分三体,而在15q26.2→qter区域存在部分单体,这两种染色体畸变可能均是导致患儿表现为足月小样儿的病因之一.     

A cytogeneticist's perspective on genomic microarrays

The identification of cytogenetic imbalance is an important component of clinical genetics. About 1 in 154 newborns has a chromosome abnormality. Conventional cytogenetic analysis has enabled the identification of microscopic alterations of the chromosomes. The development of fluorescence in situ hybridization (FISH) and other molecular methodologies has made possible the identification of submicroscopic aberrations. An additional development was comparative genomic hybridization (CGH), a method that directly compares two genomes for DNA copy differences. As first developed, the substrate for CGH analysis is normal metaphase chromosomes. Recently, CGH has been applied to microarrays (array CGH) constructed from large insert clones to identify chromosome imbalance. Array CGH has many advantages over conventional cytogenetic and molecular cytogenetic techniques. Array CGH can be comprehensive (genome-wide), high resolution, amenable to automation, rapid, and sensitive. We anticipate that array CGH will be employed in the clinical cytogenetics laboratory in the near future and will lead to the identification of the chromosomal basis of new syndromes and existing genetic conditions.     

用高分辨率微阵列比较基因组杂交分析一个孤独症家系的新生拷贝数变异

目的 对1个孤独症家系进行新发拷贝数变异(copy number variations,CNV)分析.方法 应用高分辨率全基因组芯片(Affymetrix Cytogenetics Whole-Genome 2.7M Array)检测该家系4名成员的基因组拷贝数,用Affymetrix Chromosome Analysis Suite软件分析结果.以基因组变异数据库亚洲正常人群及先证者父母、同胞为对照,分析先证者的新发CNV.结果 先证者存在89个新发拷贝数变异,其中5号、11号和14号染色体新发CNV总长占染色体全长超过1‰.3p26.1、4q22.2、5p15.2等区域也存在新发CNV,涉及GRM7、GRID2、CTNND2等10个与神经系统发育相关基因.结论 先证者多个与神经系统发育相关的基因存在新发拷贝数变异,这为探索孤独症的发病机理提供了新的线索.高分辨率基因组CNV芯片能够快速、准确地检测基因组的微小失衡,在遗传病诊断方面具有广阔的应用前景.     

Reliability of comparative genomic hybridization to detect chromosome abnormalities in first polar bodies and metaphase II oocytes

BACKGROUND: Preimplantation Genetic Diagnosis (PGD) using FISH to analyze up to nine chromosomes to discard chromosomally abnormal embryos has resulted in an increase of pregnancy rates in certain groups of patients. However, the number of chromosomes that can be analyzed is a clear limitation. We evaluate the reliability of using comparative genomic hybridization (CGH) to detect the whole set of chromosomes, as an alternative to PGD using FISH. METHODS AND RESULTS: We have analysed by CGH both, first polar bodies (1PBs) and metaphase II (MII) oocytes from 30 oocytes donated by 24 women. The aneuploidy rate was 48%. Considering two maternal age groups, a higher number of chromosome abnormalities were detected in the older group of oocytes (23% versus 75%, P < 0.02). About 33% of the 1PB-MII oocyte doublets diagnosed as aneuploid by CGH would have been misdiagnosed as normal if FISH with nine chromosome probes had been used. CONCLUSION: We demonstrate the reliability of 1PB analysis by CGH, to detect almost any chromosome abnormality in oocytes as well as unbalanced segregations of maternal translocations in a time frame compatible with regular in vitro fertilization (IVF). The selection of euploid oocytes could help to increase implantation and pregnancy rates of patients undergoing IVF treatment.