Array Comparative Genomic Hybridization in Sarcomas

Over the past years, much research on sarcomas based on low-resolution cytogenetic and molecular cytogenetic methods has been published, leading to the identification of genetic abnormalities partially underlying the tumourigenesis. Continued progress in the identification of genetic events such as copy number aberrations relies upon adapting the rapidly evolving high-resolution microarray technology, which will eventually provide novel insights into sarcoma biology, and targets for both diagnostics and drug development. The aim of this Thesis was to characterize DNA copy number changes that are involved in the pathogenesis of soft tissue leiomyosarcoma (LMS), dermatofibrosarcoma protuberans (DFSP), osteosarcoma (OS), malignant fibrous histiocytoma (MFH), and uterine leiomyosarcoma (ULMS) by applying fine resolution array comparative genomic hybridization (aCGH) technology. Both low- and high-grade LMS tumours showed distinct copy number patterns, in addition to sharing two minimal common regions of gains and losses. Small aberrations were detected by aCGH, which were beyond the resolution of chromosomal comparative genomic hybridization (cCGH). DFSP tumours analysed by aCGH showed gains in 17q, 22q, and 21 additional gained regions, but only one region (22q) with copy number loss. Recurrent amplicons identified in OS by aCGH were 12q11-q15, 8q, 6p12-p21, and 17p. Amplicons 12q and 17p were further characterized in detail. The amplicon at 17p was characterized by aCGH in low- and high-grade LMS, OS, and MFH. In all but one case this amplicon, with minimal common regions of gains at 17p11-p12, started with the distal loss of 17p13-pter. OS and high-grade LMS were grouped together as they showed a complex pattern of copy number gains and amplifications at 17p, whereas MFH and low-grade LMS showed a continuous pattern of copy number gains and amplification at 17p. In addition to the commonly gained and lost regions identified in ULMS by aCGH, various biological processes affected by these copy number changes were also indicated by pathway analysis. The three novel findings obtained in this work were: characterization of amplicon 17p in low- and high-grade LMS and MFH, profiles of DNA copy number changes in LMS, and detection of various pathways affected by copy number changes in ULMS. These studies have not been undertaken previously by aCGH technology, thus this Thesis adds new information regarding DNA copy number changes in sarcomas. In conclusion, the aCGH technique used in this Thesis has provided new insights into the genetics of sarcomas by detecting the precise regions affected by copy number changes and some potential candidate target genes within those regions, which had not been uncovered by previously applied low resolution techniques.no abstract avaliable

Comparative Genomic Hybridization Array Analysis

At the present time, there is increasing evidence that cancer may be regulated by the number of copies of genes in tumor cells. Through microarray technology it is now possible to measure the number of copies of thousands of genes and gene segments in samples of chromosomal DNA. Microarray comparative genomic hybridization (array CGH) provides the opportunity to both measure DNA sequence copy number gains and losses and map these aberrations to the genomic sequence. Gains can signify the over-expression of oncogenes, genes which stimulate cell growth and have become hyperactive, while losses can signify under-expression of tumor suppressor genes, genes whose activity stops the formation of tumors. In order to better understand the progression of cancer and the differences between cancer and non-cancer tissue it is of great importance to fully understand what is happening at the chromosomal level. In the hopes of finding a genetic signature for subtypes of cancer, it is our intention to explore statistical approaches to array CGH data. The Waldman Lab at UCSF-CCC graciously allowed us to access data from their renal cancer study. This project was designed to determine whether microarray information on copy number of genes could be used to discriminate among four subtypes of renal cancer

Chromosome-breakage genomic instability and chromothripsis in breast cancer

Background: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. Results: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. Conclusions: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes

Array Comparative Genomic Hybridization (aCGH): A Diagnostic Test for the Prenatal Diagnosis of Chromosomal Abnormalities with Emphasis on Patients with Abnormal Ultrasounds

Background: When abnormalities are found during the anatomy scan most patients are offered amniocentesis and conventional karyotyping, using Giemsa (G)-banding of metaphase chromosomes to detect aneuploidies and large structural changes in the prenatal diagnosis. The use of fluorescent in situ hybridization (FISH) reduces the time to obtain a result because culture is not necessary, but can only detect a limited number of prespecified targets. Small studies have shown that array comparative genomic hybridization (aCGH) can detect all unbalanced chromosomal abnormalities as well as smaller deletions and duplications that cannot be detected with routine cytogenetic analysis. Should aCGH screening be used instead of karyotyping to diagnose prenatal chromosomal abnormalities in pregnant patients with abnormal ultrasound? Methods: An exhaustive search of available medical literature from the past 5 years was conducted using Medline-OVID, CINAHL, Web of Science. Key words included: comparative genomic hybridization, pregnancy, abnormal ultrasound, prenatal ultrasound and ultrasound. Relevant articles were assessed for quality using GRADE. Results: Two studies met inclusion criteria and were used in this review. The first is a large prospective, comparison to gold standard (karyotyping). This study compared prenatal diagnostic samples, and found microarray (aCGH) was equivalent to standard karyotype analysis for common aneuploidies and found additional clinically relevant information when patients had abnormal ultrasounds. The second study was a prospective study of over 5000 pregnancies and again additional clinical significant findings were found using aCGH. Conclusion: Array comparative genomic hybridization should be considered for all patients who wish to undergo invasive prenatal screening and should be offered to all patients with abnormal prenatal ultrasounds. Adequate genetic counseling should be provided by a trained professional in all cases. A cost analysis should be done comparing tests. Keywords: Array comparative genomic hybridization, pregnancy, abnormal ultrasound, prenatal diagnosi

The group fused Lasso for multiple change-point detection

We present the group fused Lasso for detection of multiple change-points shared by a set of co-occurring one-dimensional signals. Change-points are detected by approximating the original signals with a constraint on the multidimensional total variation, leading to piecewise-constant approximations. Fast algorithms are proposed to solve the resulting optimization problems, either exactly or approximately. Conditions are given for consistency of both algorithms as the number of signals increases, and empirical evidence is provided to support the results on simulated and array comparative genomic hybridization data

Familial cases of a submicroscopic Xp22.2 deletion : genotype-phenotype correlation in microphthalmia with linear skin defects syndrome

Purpose: Microphthalmia with linear skin defects syndrome (MLS or MIDAS, OMIM #309801) is a rare X-linked male-lethal disorder characterized by microphthalmia or other ocular anomalies and skin lesions limited to the face and neck. However, inter-and intrafamilial variability is high. Here we report a familial case of MLS. Methods: A mother and daughter with MLS underwent a complete ophthalmological examination, and extensive imaging, including anterior segment pictures, corneal topography and keratometry, autofluorescence, infrared reflectance and red free images, as well as spectral-domain optical coherence tomography. The mother also underwent full-field flash electroretinography. In addition, high-resolution array comparative genomic hybridization analysis was performed in both as well as in the maternal grandparents of the proband. Results: Microphthalmia and retinal abnormalities were noted in the proband and the mother, whereas only the mother presented with scars of the typical neonatal linear skin defects. Array comparative genomic hybridization analysis revealed a 185-220 kb deletion on chromosome band Xp22.2 including the entire HCCS gene. Conclusions: The identification of a deletion including HCCS led to the diagnosis of MLS in these patients. Retinal abnormalities can be part of the ocular manifestations of MLS

Microarray-based ultra-high resolution discovery of genomic deletion mutations

BACKGROUND: Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. RESULTS: Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. CONCLUSIONS: Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence

Joint segmentation of many aCGH profiles using fast group LARS

Array-Based Comparative Genomic Hybridization (aCGH) is a method used to search for genomic regions with copy numbers variations. For a given aCGH profile, one challenge is to accurately segment it into regions of constant copy number. Subjects sharing the same disease status, for example a type of cancer, often have aCGH profiles with similar copy number variations, due to duplications and deletions relevant to that particular disease. We introduce a constrained optimization algorithm that jointly segments aCGH profiles of many subjects. It simultaneously penalizes the amount of freedom the set of profiles have to jump from one level of constant copy number to another, at genomic locations known as breakpoints. We show that breakpoints shared by many different profiles tend to be found first by the algorithm, even in the presence of significant amounts of noise. The algorithm can be formulated as a group LARS problem. We propose an extremely fast way to find the solution path, i.e., a sequence of shared breakpoints in order of importance. For no extra cost the algorithm smoothes all of the aCGH profiles into piecewise-constant regions of equal copy number, giving low-dimensional versions of the original data. These can be shown for all profiles on a single graph, allowing for intuitive visual interpretation. Simulations and an implementation of the algorithm on bladder cancer aCGH profiles are provided

Genomic alterations in primary gastric adenocarcinomas correlate with clinicopathological characteristics and survival.

Background & aimsPathogenesis of gastric cancer is driven by an accumulation of genetic changes that to a large extent occur at the chromosomal level. In order to investigate the patterns of chromosomal aberrations in gastric carcinomas, we performed genome-wide microarray based comparative genomic hybridisation (microarray CGH). With this recently developed technique chromosomal aberrations can be studied with high resolution and sensitivity.MethodsArray CGH was applied to a series of 35 gastric adenocarcinomas using a genome-wide scanning array with 2275 BAC and P1 clones spotted in triplicate. Each clone contains at least one STS for linkage to the sequence of the human genome. These arrays provide an average resolution of 1.4 Mb across the genome. DNA copy number changes were correlated with clinicopathological tumour characteristics as well as survival.ResultsAll thirty-five cancers showed chromosomal aberrations and 16 of the 35 tumours showed one or more amplifications. The most frequent aberrations are gains of 8q24.2, 8q24.1, 20q13.12, 20q13.2, 7p11.2, 1q32.3, 8p23.1-p23.3, losses of 5q14.1, 18q22.1, 19p13.12-p13.3, 9p21.3-p24.3, 17p13.1-p13.3, 13q31.1, 16q22.1, 21q21.3, and amplifications of 7q21-q22, and 12q14.1-q21.1. These aberrations were correlated to clinicopathological characteristics and survival. Gain of 1q32.3 was significantly correlated with lymph node status (p=0.007). Tumours with loss of 18q22.1, as well as tumours with amplifications were associated with poor survival (p=0.02, both).ConclusionsMicroarray CGH has revealed several chromosomal regions that have not been described before in gastric cancer at this frequency and resolution, such as amplification of at 7q21-q22 and 12q14.1-q21.1, as well gains at 1q32.3, 7p11.2, and losses at 13q13.1. Interestingly, gain of 1q32.3 and loss of 18q22.1 are associated with a bad prognosis indicating that these regions could harbour gene(s) that may determine aggressive tumour behaviour and poor clinical outcome