Comparative genomic hybridization analysis of genetic aberrations associated with development of esophageal squamous cell carcinoma in Henan, 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 losses of chromosomal regions may contain ESCC-related oncogenes and tumor suppressor genes and provide important theoretic information for identifying and cloning novel ESCC-related oncogenes and tumor suppressor genes.

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

Copy number variations have been found in patients with neural tube abnormalities.In 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 parents.Of eight copy number variations,four were non-polymorphic.These non-polymorphic copy number variations were associated with Angelman and Prader-Willi syndromes,and microcephaly.Gene 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 1.Our results indicate that array-based comparative genomic hybridization can be used to diagnose tethered spinal cord syndrome.Our results may help determine the pathogenesis of tethered spinal cord syndrome and prevent occurrence of this disease.

Array Comparative Genomic Hybridization as a Diagnostic Tool in Cancer

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.

Detection of chromosomal imbalance in oligodendroglial tumors by comparative genomic hybridization

Objective To investigate the relationship between genomic DNA imbalance in oligodendroglial tumors and its different classification. Methods 16 oligodendrogliomas and 17 anaplastic oligodendrogliomas were investigated by comparative genomic hybridization on Paraffin-Embedded tissue samples,and the chromosomal genomic DNA imbalances were analyzed. Results Chromosome DNA imbalance rates in oligodendrogliomas

aCGH应用于产前诊断意外发现DMD基因缺失或重复病例分析

目的 探讨微阵列比较基因组杂交(aCGH)技术应用在产前诊断中发现抗肌萎缩蛋白基因(又称DMD基因)缺失或重复的重要价值。方法 收集2019年9月至2020年7月在西北妇女儿童医院因高危因素(高龄、血清学筛查高风险、无创筛查高风险或超声软指标异常等)选择aCGH技术进行产前诊断的851例孕妇的羊水样本进行检测,并进一步采用多重连接探针扩增(MLPA)方法对DMD基因变异样本进行验证。结果 在851例孕妇的羊水样本中,经aCGH产前诊断时意外发现4例羊水样本存在DMD基因缺失或重复,同时MLPA检测验证了上述变异。胎儿1:男胎,arr[GRCh37]Xp21.1(31691172-31766673)×0,DMD基因E52-53缺失;胎儿2:男胎,arr[GRCh37]Xp21.2(31016983-31351900)×2,DMD基因E61-79重复;胎儿3:女胎,arr[GRCh37]Xp21.2(31182699-31474949)×3,DMD基因E58-74重复;胎儿4:男胎,arr[GRCh37]Xp21.1(31777925-32152126)×2,DMD基因E45-51重复。4例变异均遗传自母亲。结论 产前诊断是防止DMD患者出生的重要手段,aCGH技术用于产前诊断不仅可以检测染色体微缺失和微重复综合征,还有助于检测由基因缺失或重复引起的单基因疾病,从而为临床诊断及遗传咨询提供了理论依据。

Identification of metastasis-associated genes in colorectal cancer through an integrated genomic and transcriptomic analysis

Objective： Identification of colorectal cancer （CRC） metastasis genes is one of the most important issues in CRC research. For the purpose of mining CRC metastasis-associated genes, an integrated analysis of mJcroarray data was presented, by combined with evidence acquired from comparative genornic hybridization （CGH） data. Methods： Gene expression profile data of CRC samples were obtained at Gene Expression Omnibus （GEO） website. The 15 important chromosomal aberration sites detected by using CGH technology were used for integrated genomic and transcriptomic analysis. Significant Analysis of Microarray （SAM） was used to detect significantly differentially expressed genes across the whole genome. The overlapping genes were selected in their corresponding chromosomal aberration regions, and analyzed by using the Database for Annotation, Visualization and Integrated Discovery （DAVID）. Finally, SVM-T-RFE gene selection algorithm was applied to identify ted genes in CRC. Results： A minimum gene set was obtained with the minimum number [14] of genes, and the highest classification accuracy （100%） in both PRI and META datasets. A fraction of selected genes are associated with CRC or its metastasis. Conclusions- Our results demonstrated that integration analysis is an effective strategy for mining cancer- associated genes.

Novel chromosomal alterations detected in primary nasopharyngeal carcinoma by comparative genomic hybridization

Objective To gain a better understanding of genetic changes in Cantonese nasopharyngeal carcinoma (NPC) Methods Comparative genomic hybridization (CGH) was performed on 17 primary nasopharyngeal carcinomas Results A novel copy number gain an chromosome 4q and loss of chromosome 1p were found at a high frequency (>50%) Conclusions Current analysis revealed a comprehensive profile of the chromosomal regions showing gain of chromosomes 4q, 12q, and 1q as well as loss of chromosomes 1p, 3p, 11q, 14q, 15q, 13q, Xq, 9q, 10p, 10q, and 16q Frequently altered loci may encode oncogenes or tumor suppressor genes involved in the development of primary NPC

Comparative genome research between maize and rice using genomic in situ hybridization

Using the genomic DNAs of maize and rice as probes respectively, the homology of maize and rice genomes was assessed by genomic in situ hybridization. When rice genomic DNAs were hybridized to maize, all chromosomes displayed many multiple discrete regions, while each rice chromosome delineated a single consecutive chromosomal region after they were hybridized with maize genomic DNAs. The results indicate that the genomes of maize and rice share high homology, and confirm the proposal that maize and rice are diverged from a common ancestor.

Analysis of Chinese women with primary ovarian insufficiency by high resolution array-comparative genomic hybridization

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.

Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples

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.

Chromosomal imbalances revealed in primary rhabdomyosarcomas by comparative genomic hybridization

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.

Characterization of serogroup C meningococci isolated from 14 provinces of China during 1966—2005 using comparative genomic hybridization

Neisseria meningitidis is a major cause of bacterial meningitis and septicemia worldwide. In China, serogroup A strains were responsible for over 95% of the cases, while serogroup B strains were mainly the cause of localized outbreaks and sporadic cases. Before 2003, serogroup C strains were only re-covered from a few sporadic cases. However, a sudden increase in the number of cases due to sero-group C strains occurred during 2003—2005 in Anhui Province, China. Many cases were found in other provinces at the same time. Multilocus sequence typing (MLST) results indicated that the unique se-quence type 4821 clone meningococci, a new hyper-virulent lineage, was responsible for the serogroup C meningitis outbreaks. We have completed the project of sequencing the whole genome of the Chi-nese N. meningitidis serogroup C representative isolate 053442. We fabricated a whole-genome mi-croarray of N. meningitidis isolate 053442 and analyzed the genome composition differences among 81 serogroup C isolates which were isolated from 14 provinces of China during 1966—2005. The com-parative genomic hybridization (CGH) result shows that the genome compositions of nearly all sero-group C isolates are similar to that of 053442. The products of many absent open reading frames (ORFs) are conserved hypothetical proteins. The results will provide a valuable resource from which one can analyze the genome composition and genetic background of serogroup C meningococci in China.

Analyses of Genotypes and Phenotypes of Ten Chinese Patients with Wolf-Hirschhorn Syndrome by Multiplex Ligation-dependent Probe Amplification and Array Comparative Genomic Hybridization

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.

Analysis of comparative genomic hybridization and loss of heterozygosity in 43 primary gastric carcinomas

To investigate common chromosomal changes and the LOH frequency of microsatellite loci in primary gastric cancer samples in order to locate the deleted regions in which human gastric cancer related genes might exist Methods Comparative genomic hybridization (CGH) was used to define global chromosomal aberrations in 43 primary gastric tumors Based on the results of CGH, analysis of loss of heterozygosity (LOH) was performed in chromosome 19 in which the loss was first discovered in the gastric cancers The PCR-based approach was used to investigate 22 loci, which are spaced at 1 1-10 9 cM intervals throughout chromosome 19 The amplified PCR fragments were subjected to electrophoresis in PAGE gel and analyzed with Genescan TM and Genotyper TM Results CGH analysis revealed gains in chromosome 3p(8/43), 8q(8/43), 20 [20 (9/43), 20p(7/43), 20q(4/43)], 12q(16/43), 13q(12/43) and losses in 19 [19 (15/43)], 7 [17 (8/43), 17p (10/43)], 16 (10/43) and 1p (11/43) Among the 43 evaluated samples, the most frequent LOH was detected at locus D19S571 (27 81%) Conclusions The tumorigenesis of gastric cancer includes several chromosomal changes The aberration of chromosome 19 was the first common change founded in gastric cancer The region near the D19S571 might harbor potential genes related to the tumorigenesis of gastric cancer

Genomic landscape of pancreatic neuroendocrine tumors

AIM: To investigate the prognostic role of genomic stability and copy number alterations (CNAs) pancreatic neuroendocrine tumors (PanNETs).

Preimplantation testing:Transition from genetic to genomic diagnosis

Preimplantation genetic testing refers to the procedure to determine the genetic status of embryos formed by in vitro fertilization(IVF) prior to initiating a pregnancy.Traditional genetic methods for preimplantation genetic diagnosis(PGD) examine distinct parts of an individua genome, require the development of a custom assay for every patient family, and are time consuming and inefficient. In the last decade technologies for wholegenome amplification(WGA) from single cells have led to innovative strategies for preimplantation testing.Applications of WGA technology can lead to a universa approach that uses single-nucleotide polymorphisms(SNPs) and mutations across the entire genome for the analysis. Single-cell WGA by multiple displacement amplification has enabled a linkage approach to PGD known as "preimplantation genetic haplotyping", as well as microarray-based techniques for preimplantation diagnosis. The use of microarrays in preimplantation diagnosis has provided genome-wide testing for gains or losses of single chromosomes(aneuploidies)or chromosomal segments. Properly designed randomized controlled trials are, however, needed to determine whether these new technologies improve IVF outcomes by increasing implantation rates and decreasing mis-carriage rates. In genotype analysis of single cells, allele dropout occurs frequently at heterozygous loci. Preimplantation testing of multiple cells biopsied from blastocysts, however, can reduce allele dropout rates and increase the accuracy of genotyping, but it allows less time for PGD. Future development of fast SNP microarrays will enable a universal preimplantation testing for aneuploidies, single-gene disorders and unbalanced translocations within the time frame of an IVF cycle.

应用DNA分子标记鉴定瓦氏黄颡鱼、长吻鮠及其杂交种

瓦氏黄颡鱼与长吻鮠的杂交后代与其父母本形态学特征相似,在生产中容易产生混淆,而DNA分子标记可以快速准确地区分物种,常被用于物种鉴定。基于目前已有的瓦氏黄颡鱼、长吻鮠的基因组数据,实验通过比较基因组学分析,发现瓦氏黄颡鱼与长吻鮠在演化关系上较为接近,估算出二者分化时间为370万年前。同时,通过染色体序列共线性分析,发现二者均具有26对染色体,且染色体一一对应,并未发现染色体间的融合重组现象,仅存在染色体内部的重排。基于以上结果,实验发现2种鱼在patj基因序列上存在一段391 bp的INDEL。根据该差异片段,设计出了引物PVLL。该引物在瓦氏黄颡鱼中仅扩增出339 bp的条带,在长吻鮠中仅扩增出730 bp的条带,而在其杂交种中可以同时扩增出339与730 bp这2种大小的条带。根据扩增条带的差别可以准确区分三者,此研究结果不受性别影响,并且在不同群体中也验证了引物的有效性。研究表明,比较基因组学可用于准确鉴别瓦氏黄颡鱼、长吻鮠及其杂交种,从而提高杂交育种生产的效率。

G显带和aCGH技术联合检测92例早期自然流产妊娠物核型分析

目的:探讨影响早期自然流产妊娠物染色体异常的因素以及微阵列比较基因组杂交技术(aCGH)在流产妊娠物核型检测中的应用价值。方法:收集在我院妇产科门诊确诊为"胚胎停育"的病例共92例,对清宫后获得的妊娠物进行绒毛染色体G显带核型分析,绒毛体外培养或G显带分析失败的进行aCGH检测。结果:本实验对92例自然流产妊娠物的绒毛组织进行体外培养,85例(92.4%)G显带染色体核型分析成功,失败的7例进行aCGH检测,两种方法联合分析的成功率100%。其中异常核型50例(异常率54.3%),非整倍体40例(非整倍体率43.5%)。复发性流产和偶发性流产患者的异常率分别是50.0%和58.3%,差异无统计学意义(P>0.05)。年龄≥35岁患者妊娠物核型为非整倍体的概率(61.5%)大于年龄<35岁的患者(36.4%),差异有统计学意义(P<0.05)。流产儿男女性别比约为1∶1.2,男性胚胎核型异常率(42.9%)小于女性(64.0%),差异有统计学意义(P<0.05)。超声检查示妊娠囊内无胎芽和有胎芽患者的核型异常率分别为53.3%和54.8%(P>0.05);曾见胎心和从未见胎心患者的异常率分别为58.7%和50.0%,差异均无统计学意义(P>0.05)。结论:自然流产妊娠物核型异常的风险与流产次数以及有无胎芽或胎心无关,非整倍体妊娠的风险随母体年龄增大,女性胚胎在早孕期更易发生染色体异常。aCGH技术在检测流产妊娠物核型中有优越性。

先天性疾病研究及产前诊断中Array CGH的应用

染色体微缺失、重复、扩增和非整倍体等基因组DNA失衡是导致胎儿发育迟缓、畸形、死胎、流产和其他先天性疾病的内在原因。微阵列-比较基因组杂交技术(Array CGH)利用基因芯片取代了传统比较基因组杂交技术的正常中期染色体作为杂交靶标,与分别采用不同荧光标记的待测DNA和参照DNA杂交,通过比较两种荧光强度的比率,检测出染色体基因拷贝数变化。Array CGH已成为一个重要的细胞遗传学研究工具,用于产前诊断和先天性疾病诊断染色体亚显微结构异常。

应用aCGH技术建立胚胎植入前遗传学筛查

目的应用微阵列比较基因组杂交技术(aCGH)对移植前胚胎进行染色体遗传学筛查,建立胚胎染色体非整倍体检测方法。方法对冷冻囊胚、对照质控品先进行全基因组扩增,然后再继续aCGH检测。结果 4个冷冻囊胚中1个染色体正常,另外3个染色体异常,对照质控全部检测出。结论应用全基因组扩增以及aCGH技术,对囊胚成功进行了植入前遗传学筛查,能够全面评估胚胎染色体的非整倍体情况,为复发流产患者提高生殖成功率提供重要依据。