Looking for online definition of comparative genomic hybridization in the Medical Dictionary? comparative genomic hybridization explanation free. What is comparative genomic hybridization? Meaning of comparative genomic hybridization medical term. What does comparative genomic hybridization mean?

Nasopharyngeal carcinoma (NPC) is a distinct geographical disease with high incidence in Southeast Asia. Previous CGH studies have located multiple regions of chromosomal gains and losses in NPC. To elucidate the regions of gain and amplification, a high-resolution array comparative genomic hybridization (array CGH) was applied to characterize the common amplicons in NPC cell lines and xenografts. Consistent with our previous CGH findings, frequent gains at chromosomes 1q, 3q, 7, 8, 9q, 12q and 20q were detected. High incidence of gains were identified on chromosome 3q and 12q. The findings were further confirmed by FISH analysis. Using 16 BAC clones on 3q26-28 and 6 BAC clones on 12q13, the smallest regions of gain at 3q and 12q were defined on five NPC cell lines. Chromosome 3q26.33 (RP11-510K16) and 12q13.2-q13.3 (RP11-183H16) showed the highest amplification frequency in FISH analysis with 100 and 66.7%, respectively. PIK3CA, a candidate oncogene located at 3q26.32 adjacent to this 3q ...

OBJECTIVE: During IVF, non-transferred embryos are usually selected for cryopreservation on the basis of morphological criteria. This investigation evaluated an application for array comparative genomic hybridization (aCGH) in assessment of surplus embryos prior to cryopreservation. METHODS: First-time IVF patients undergoing elective single embryo transfer and having at least one extra non-transferred embryo suitable for cryopreservation were offered enrollment in the study. Patients were randomized into two groups: Patients in group A (n=55) had embryos assessed first by morphology and then by aCGH, performed on cells obtained from trophectoderm biopsy on post-fertilization day 5. Only euploid embryos were designated for cryopreservation. Patients in group B (n=48) had embryos assessed by morphology alone, with only good morphology embryos considered suitable for cryopreservation. RESULTS: Among biopsied embryos in group A (n=425), euploidy was confirmed in 226 (53.1%). After fresh single embryo

The incidence of and mortality from colorectal cancers (CRC) can be reduced by early detection. Currently there is a lack of established markers to detect early neoplastic changes. We aimed to identify the copy number variations (CNVs) and the associated genes which could be potential markers for the detection of neoplasia in both ulcerative colitis-associated neoplasia (UC-CRN) and sporadic colorectal neoplasia (S-CRN). We employed array comparative genome hybridization (aCGH) to identify CNVs in tissue samples of UC nonprogressor, progressor and sporadic CRC. Select genes within these CNV regions as a panel of markers were validated using quantitative real time PCR (qRT-PCR) method along with the microsatellite instability (MSI) in an independent cohort of samples. Immunohistochemistry (IHC) analysis was also performed. Integrated analysis showed 10 overlapping CNV regions between UC-Progressor and S-CRN, with the 8q and 12p regions showing greater overlap. The qRT-PCR based panel of MYC, MYCN, CCND1,

TY - JOUR. T1 - Olfactory copy number association with age at onset of Alzheimer disease. AU - Shaw, C. A.. AU - Li, Y.. AU - Wiszniewska, J.. AU - Chasse, S.. AU - Zaidi, S. N.Y.. AU - Jin, W.. AU - Dawson, B.. AU - Wilhelmsen, K.. AU - Lupski, J. R.. AU - Belmont, J. W.. AU - Doody, R. S.. AU - Szigeti, K.. PY - 2011/4/12. Y1 - 2011/4/12. N2 - Objectives: Copy number variants (CNVs) have been recognized as a source of genetic variation that contributes to disease phenotypes. Alzheimer disease (AD) has high heritability for occurrence and age at onset (AAO). We performed a cases-only genome-wide CNV association study for age at onset of AD. Methods: The discovery case series (n = 40 subjects with AD) was evaluated using array comparative genome hybridization (aCGH). A replication case series (n = 507 subjects with AD) was evaluated using Affymetrix array (n = 243) and multiplex ligation-dependent probe amplification (n = 264). Hazard models related onset age to CNV. Results: The discovery ...

Introduction: Hereditary non-polyposis colorectal cancer (HNPCC), is an autosomal dominant disorder characterized by the development of multiple cancer types. Molecular diagnosis of HNPCC requires the precise identification of pathogenic germline variants in DNA mismatch repair (MMR) genes. Next Generation Sequencing (NGS) is now the gold standard test in practice, to identify these variants. However, large genomic rearrangements (LGR) in cancer predisposing genes (CPGs) are missed by NGS. This may lead to underestimation of the frequency of the variants, misleading the genetic diagnosis and delaying intervention in high risk individuals. Hence this study was aimed at identifying the presence of large genomic alterations that could explain the missing heritable risk of colon cancer in affected patients with family history strongly suggestive of hereditary colorectal cancer in Sri Lanka. Methods: A cohort of six patients affected with hereditary colorectal cancer who tested negative for pathogenic

TY - JOUR. T1 - High burden of copy number alterations and c-MYC amplification in prostate cancer from BRCA2 germline mutation carriers. AU - Castro, E.. AU - Jugurnauth-Little, S.. AU - Karlsson, Q.. AU - Al-Shahrour, F.. AU - Pineiro-Yanez, E.. AU - Van de Poll, F.. AU - Leongamornlert, D.. AU - Dadaev, T.. AU - Govindasami, K.. AU - Guy, M.. AU - Eeles, R.. AU - Kote-Jarai, Z.. AU - UKGPCS Study. AU - EMBRACE Study. AU - IMPACT Study. AU - Oosterwijk, J. C. PY - 2015/11. Y1 - 2015/11. N2 - Background: Germline BRCA2 mutations are associated with poorer outcome prostate cancer ( PCa) compared with sporadic tumours but this association remains to be characterised. In this study, we aim to assess if there is a signature set of copy number alterations ( CNA) that could aid to the identification of BRCA2- mutated tumours and would assist us to understand their aggressive clinical behaviour. Methods: High- resolution array comparative genomic hybridisation profiling of DNA from PCa and matched ...

TY - JOUR. T1 - aCGH Analysis of Predictive Biomarkers for Response to Bevacizumab plus Oxaliplatin- or Irinotecan-Based Chemotherapy in Patients with Metastatic Colorectal Cancer. AU - Fujita, Yoshihiko. AU - Taguri, Masataka. AU - Yamazaki, Kentaro. AU - Tsurutani, Junji. AU - Sakai, Kazuko. AU - Tsushima, Takahiro. AU - Nagase, Michitaka. AU - Tamagawa, Hiroshi. AU - Ueda, Shinya. AU - Tamura, Takao. AU - Tsuji, Yasushi. AU - Murata, Kohei. AU - Taira, Koichi. AU - Denda, Tadamichi. AU - Moriwaki, Toshikazu. AU - Funai, Sadao. AU - Nakajima, Takako Eguchi. AU - Muro, Kei. AU - Tsuji, Akihito. AU - Yoshida, Motoki. AU - Suyama, Koichi. AU - Kurimoto, Takuya. AU - Sugimoto, Naotoshi. AU - Baba, Eishi. AU - Seki, Nobuhiko. AU - Sato, Mikio. AU - Shimura, Takaya. AU - Boku, Narikazu. AU - Hyodo, Ichinosuke. AU - Yamanaka, Takeharu. AU - Nishio, Kazuto. N1 - Funding Information: We thank Okumoto K. and Kitayama T. for technical support and Marco A. De Velasco for critically reading the manuscript. ...

Torenbeek, R., Hermsen, M.A., Meijer, G.A., Baak, J.P. and Meijer, C.J. (1999) Analysis by Comparative Genomic Hybridization of Epithelial and Spindle Cell Components in Sarcomatoid Carcinoma and Carcinosarcoma Histogenetic Aspects. Journal of Pathology, 189, 338-343.

Background: Previous data implicating genetic and epigenetic events on chromosome 9, including the CDKN2A/2B locus, as molecular predictors of Wilms tumour relapse, have been conflicting. Aims: To clarify this using genome-wide and focused molecular genetic analysis. Methods: Microarray-based comparative genomic hybridisation (aCGH) using genome-wide coverage was applied to 76 favourable histology Wilms tumours. Additional investigation of the 9p21 locus was carried out using loss of heterozygosity (LOH) and fluorescence in situ hybridisation (FISH), as well as immunohistochemistry for CDKN2A/p16INK4a on a paediatric renal tumour tissue microarray. Results: Approximately half of the tumours were found to show chromosome 9 copy number changes. Those cases which harboured alterations comprised at least four distinct patterns: gain of the entire chromosome, loss of 9p, gain of 9q34, or a more complex combination of gains/losses. None of these tumour groups showed any statistically significant ...

This example shows how to use a Bayesian hidden Markov model (HMM) technique to identify copy number alteration in array-based comparative genomic hybridization (CGH) data.

Early gastric carcinoma (GC) is considered to be a curable cancer, as it progresses to the advanced stage following varying durations. Understanding the early stage of GC may provide an insight into its pathogenesis and contribute to reducing the mortality rate of this disease. To investigate the genomic aberrations associated with 22 cases of early GC, high-density microarray comparative genomic hybridization was performed in the present study. The most notable finding was copy number gains (log2 ratio >0.25) on the long arm of chromosome 8, which occurred in 77.3% (17/22) of GC cases, and the delineated minimal common region was 8q22.1-q24.3. More specifically, two amplified (log2 ratio >1) loci in the 8q22.1-q24.3 region were detected in 18.2% (4/22) of GC cases. The first loci covered a region of 102.4-107.9 kb, mapping on 8q22.3-q23.1, and comprised the transcription factor CP2-like 3 gene. The second loci, spanning 128.7-145.7 kb on 8q24.21-q24.3, comprised the representative oncogene of ...

TY - JOUR. T1 - Genome-wide aberrations in pancreatic adenocarcinoma. AU - Nowak, Norma J.. AU - Gaile, Daniel. AU - Conroy, Jeffrey M.. AU - McQuaid, Devin. AU - Cowell, John Kenneth. AU - Carter, Randy. AU - Goggins, Michael G.. AU - Hruban, Ralph H.. AU - Maitra, Anirban. PY - 2005/8/1. Y1 - 2005/8/1. N2 - Chromosomal instability, manifesting as copy number alterations (CNAs), is characteristic of pancreatic adenocarcinoma. We used bacterial artificial chromosome (BAC) array-based comparative genomic hybridization (aCGH) to examine the pancreatic adenocarcinoma genome for submicroscopic amplifications and deletions. Profiles of 33 samples (17 first-passage xenografts and 16 cell lines) identified numerous chromosomal regions with CNAs, including losses at 1p36.33∼p34.3, 1p13.3∼p13.2, 3p26, 3p25.2∼p22.3, 3p22.1∼p14.1, 4q28.3, 4q31, 4q35.1, 5q14.3, 6p, 6q, 8p23.3∼p12, 9p, 9q22.32∼q31.1, 13q33.2, 15q11.2, 16p13.3, 17p, 18q11.21∼q23 , 19p13.3∼p13.12, 19q13.2, 21p, 21q, and 22p, ...

CGH stands for comparative genome hybridisation, which aims to compare the presence / absence / number of similar genes in 2 genomes (i.e. its a survey of genetic differences between 2 organisms). So, a CGH experiment might compare gemomic DNA from 2 closely related bacterial species or strains. The difference between CGH array experiments and gene expression array experiments is just the target which is hybridised to the array: labelled genomic DNA for CGH; labelled cDNA (or cRNA - derived from mRNA in either case) for gene expression. You can use exactly the same arrays for both types of experiment, although the objective of CGH is normally genome-wide comparison of 2 genomes, so CGH normally uses whole-genome microarrays (for prokaryotes, at least). In general, you can use any genomic array for either gene expression or CGH ...

Formalin-fixed paraffin-embedded (FFPE) archival clinical specimens are invaluable in discovery of prognostic and therapeutic targets for diseases such as cancer. However, the suitability of FFPE-derived genetic material for array-based comparative genomic hybridization (array-CGH) studies is underexplored. In this study, genetic profiles of matched FFPE and fresh-frozen specimens were examined to investigate DNA integrity differences between these sample types and determine the impact this may have on genetic profiles. Genomic DNA was extracted from three patient-matched FFPE and fresh-frozen clinical tissue samples. T47D breast cancer control cells were also grown in culture and processed to yield a fresh T47D sample, a fresh-frozen T47D sample and a FFPE T47D sample. DNA was extracted from all the samples; array-CGH conducted and genetic profiles of matched samples were then compared. A loss of high molecular weight DNA was observed in the FFPE clinical tissues and FFPE T47D samples. A dramatic

Leukemic non-nodal mantle cell lymphoma (lMCL) is a particular subtype of mantle cell lymphoma (MCL), characterized by leukemic non-nodal disease and slow progression. Recognition of this entity is relevant to avoid overtreatment. Despite indolent clinical behaviour, lMCL might transform to a more aggressive disease. The purpose of this study was to compare lMCL with classical MCL (cMCL) and aggressive MCL (aMCL) using immunohistochemistry, interphase fluorescence in situ hybridization (FISH), and array-based comparative genomic hybridization, in order to identify biomarkers for lMCL diagnosis and prognosis. Seven lMCL patients were included. All had bone marrow involvement without lymphadenopathy. An lMCL phenotype was distinct from that of cMCL and aMCL: SOX11-, ATM+, PARP1+/-, and low KI67 (average 2 %). Beyond the t(11;14) translocation, fewer secondary cytogenetic alterations were found in lMCL compared to cMCL and aMCL, including deletion of PARP1 and 13q14. At last follow-up, one patient with

1. Raish M, Khurshid M, Ansari MA. et al. Analysis of molecular cytogenetic alterations in uterine leiomyosarcoma by array-based comparative genomic hybridization. J Cancer Res Clin Oncol. 2012;138:1173-1186 2. Dash DP, Silvestri G, Hughes AE. Fine mapping of the keratoconus with cataract locus on chromosome 15q and candidate gene analysis. Mol Vis. 2006;12:499-505 3. Birkenkamp-Demtroder K, Maghnouj A, Mansilla F. et al. Repression of KIAA1199 attenuates wnt-signalling and decreases the proliferation of colon cancer cells. Br J Cancer. 2011;105:552-561 4. He QY, Liu XH, Li Q. et al. G8: A novel domain associated with polycystic kidney disease and non-syndromic hearing loss. Bioinformatics. 2006;22:2189-2191 5. Yoshida H, Nagaoka A, Nakamura S. et al. N-terminal signal sequence is required for cellular trafficking and hyaluronan-depolymerization of KIAA1199. FEBS Lett. 2014;588:111-116 6. Abe S, Usami S, Nakamura Y. Mutations in the gene encoding KIAA1199 protein, an inner-ear protein expressed ...

To find similarities that may possibly indicate novel mutations, we performed comparative genomic hybridization (CGH) analysis following degenerate oligonucleotide primed polymerase chain reaction (PCR) for DNA obtained from unique material of breast cancer that developed in monozygotic twin-pairs. …

To validate segments selected as rare CNVs according to our density score we automate the process of a manual validation of segments based on UCSC [29], i.e. the protocol by which geneticians usually act. Lastly, we compare resulting sets of segments with the set produced manually by geneticists from IMC.. Manual validation by geneticists involves inspecting reported CNVs segments, overlaying them on UCSC tracks. This purposes to filter out known polymorphisms and, by interrogation of all known syndrome regions, to try to narrow down the segment set to only those clinically relevant. This step is followed by FISH or PCR confirmation of the CNVs existence in patients DNA [30, 31].. For the automated process we decided to focus on three main databases storing the information related to genomic variations and diseases resulting from it: ISCA, DGV and GAD.. ISCA is a group of clinical cytogenetics laboratories committed to improve the quality of patients care related to clinical genetic testing ...

Purpose: As genome-scale technologies begin to unravel the complexity of the equivalent tumors in adults, we can attempt detailed characterization of high-grade gliomas in children, that have until recently been lacking. Toward this end, we sought to validate and extend investigations of the differences between pediatric and adult tumors.. Experimental Design: We carried out copy number profiling by array comparative genomic hybridization using a 32K bacterial artificial chromosome platform on 63 formalin-fixed paraffin-embedded cases of high-grade glioma arising in children and young people (,23 years).. Results: The genomic profiles of these tumors could be subclassified into four categories: those with stable genomes, which were associated with a better prognosis; those with aneuploid and those with highly rearranged genomes; and those with an amplifier genotype, which had a significantly worse clinical outcome. Independent of this was a clear segregation of cases with 1q gain (more common in ...

Introduction: Lung carcinoids comprise a group of smoking-unrelated neuroendocrine tumors, which can be classified in typical (TC) and atypical (AC) carcinoids. Classification is complex and its accuracy to predict disease outcome is variable. In a previous array comparative genomic hybridization (arrayCGH) study, we showed that the average number of chromosomal alterations (≥ 1Mb) was significantly higher in ACs than in TCs (512 v. 226 per tumor) and that the most common region of chromosome loss was 11q21-q25 (Neuroendocrinology 2009;90:136-137 ...

237 total publications from NE-1334 Project participants 2013-2017. *= 33 cooperative publications among 2 or more project participants. *Abernathy, J., X. Li, X. Jia, W. Chou, S. J. Lamont, R. Crooijmans, and H. Zhou, H. 2014. Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization. Anim. Genet. 45:400-411.. *Banat, G. R., S. Tkalcic, J. A. Dzielawa, M. W. Jackwood, M. D. Saggese, L. Yates, R. Kopulos, W. Briles, and E. W. Collisson. 2013. Association of the chicken MHC B haplotypes with resistance to avian coronavirus. Dev. Comp. Immunol. 39:430-437.. *Bauer, M. M., M. M. Miller, W. E. Briles, and K. M. Reed. 2013. Genetic variation at the MHC in a population of introduced wild turkeys. Animal biotechnology 24:210-228.. *Coble, D. J., E. E. Sandford, T. Ji, J. Abernathy, D. Fleming, H. Zhou, and S. J. Lamont. 2013. Impacts of Salmonella enteritidis infection on liver transcriptome in broilers. Genesis 51:357-364. *Da Silva A. P., Hauck R., ...

A number of results of array-CGH analysis of breast tumours and breast cancer cell lines have been published [19, 21, 22, 25, 27, 80-88] (Table 1). Some of these results, together with large amounts of conventional CGH, FISH and SKY data of breast cancer, are freely available through the Progenetix repository [89, 90]; NCI and NCBIs SKY/M-FISH and CGH Database (2001) [91]; Charité, Berlin University [92]; and in the supplementary data of many individual publications. Cytogenetic data has been described [53, 54] and is available for more then 1000 cases at NCBI. The following discussion illustrates the use and usefulness of array-CGH for various breast cancer genomes.. A detailed study of 31 advanced archival breast tumours conducted by Nessling and coworkers [47] elegantly demonstrates how specificity, sensitivity and resolution are increased in (matrix) array-CGH compared with conventional CGH by using the same samples on both platforms. They identified 44 genes by array-CGH and verified all ...

In Vitro Fertilization (IVF) $7,950. Anesthesia $350. *Intra-Cytoplasmic Sperm Injection (ICSI) $1,500. *Assisted Hatching (AH) $450. *First year freezing & Cryopreservation $650. Array Comparative Genomic Hybridization (aCGH) including Preimplantation Genetic Diagnosis (PGD) and family balancing - $3750. *Fees apply if deemed medically necessary. All fees in effect as of July 2016.. ...

Introduction: Based on high-throughput transcriptional profiling and array comparative genomic hybridization, a three-gene predictor encompassing c-MYC, EGFR and FGFR2 has been identified to predict survival in cisplatin and fluorouracil (FU) - treated metastatic gastric cancer (GC) patients by others (1).. The aim of our study was to determine the value of the expression of these three genes to predict response and/or survival for GC patients treated by a platin/5FU based chemotherapy in the neoadjuvant setting.. Material and methods: Expression was analyzed in pretherapeutic tumor biopsies of 69 patients treated by platinum/5FU based neoadjuvant chemotherapy. Histopathological response was divided into three grades, tumor regression grade 1 (TRG1) corresponding to complete/major response, TRG2 corresponding to partial and TRG3 corresponding to minimal or no response. mRNA was isolated from manually microdissected formalin fixed and paraffin embedded tumor biopsies. Relative quantification of ...

Systematic forward genetics using somatic cell mutants is a powerful tool in elucidating biochemical pathways [1]. However, it is often difficult to identify the genetic loci responsible for a particular somatic cell mutant phenotype. Map-based positional cloning strategies can be used in somatic cell hybrids to analyze mutants with recessive phenotypes. By tracking DNA sequence variants that co-segregate with heritable traits, the genes accounting for these traits can be localized to specific chromosomal locations [2]. Recent advances in genome sequencing have facilitated the assembly of physical maps of candidate regions, but fine mapping and narrowing of candidate regions is still often tedious and remains a major obstacle in somatic cell genetics. Consequently, there is a need to efficiently map the positions of genes in somatic cell mutants.. We previously established a method to enrich for human genes that complement rodent somatic cell mutants [3]. The mutant rodent cells are fused with ...

Vulvar squamous cell carcinoma (VSCC) is a rare disease that has a high mortality rate (∼40%). However, little is known about its molecular signature. Therefore, an integrated genomics approach, based on comparative genome hybridization (aCGH) and genome-wide expression (GWE) array, was performed to identify driver genes in VSCC. To achieve that, DNA and RNA were extracted from frozen VSCC clinical specimens and examined by aCGH and GWE array, respectively. On the basis of the integration of data using the CONEXIC algorithm, PLXDC2 and GNB3 were validated by RT-qPCR. The expression of these genes was then analyzed by IHC in a large set of formalin-fixed paraffin-embedded specimens. These analyses identified 47 putative drivers, 46 of which were characterized by copy number gains that were concomitant with overexpression and one with a copy number loss and downregulation. Two of these genes, PLXDC2 and GNB3, were selected for further validation: PLXDC2 was downregulated and GNB3 was ...

ABSTRACT = { BACKGROUND: Copy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays. Gene CNVs were assessed in three full-sib families from species with 20 Gb genomes, i.e., white and black spruce, and interior spruce - a natural hybrid. RESULTS: We discovered hundreds of gene CNVs in each species, 3612 in total, which were enriched in functions related to stress and defense responses and narrow expression profiles, indicating a potential role in adaptation. The number of shared CNVs was in accordance with the degree of relatedness between individuals and species. The ...

Microcephaly can present in the newborn period, either at birth or postnatally. In large cohorts, genetic factors and perinatal brain damage secondary to maternal exposures and prenatally acquired infections are the leading causative factors. However, in up to ∼40% of children with microcephaly, no etiology is identified. Although many classifications exist, it is important to remember that both congenital microcephaly and postnatal-onset microcephaly can be due to genetic or acquired causes. Careful history and physical examination is the initial step in evaluating a neonate with microcephaly. Diagnostic evaluation should be tailored based on these findings. In all-comers with microcephaly, neuroimaging proves to have the highest diagnostic yield, with magnetic resonance imaging providing the highest sensitivity. Genetic testing has the next highest diagnostic yield, and if presentation does not suggest a specific genetic disorder, comparative genomic hybridization would be the recommended ...

Comparative genomic hybridizations have been used to examine genetic relationships between bacteria. The microarrays used in these experiments may have open reading frames from one or more reference strains, or they may be composed of random DNA fragments from a large number of strains (mixed-genome microarrays; MGM). Herein both experimental and virtual arrays are analyzed to assess the validity of genetic inferences from these experiments with a focus on MGMs. Empirical data is analyzed from an Enterococcus MGM while a virtual MGM is constructedin silico using sequenced genomes (Streptococcus). On average a small MGM is capable of correctly deriving phylogenetic relationships between seven species of Enterococcus with 100% (n=100 probes) and 95% (n=46 probes) accuracy; more probes are required for intra-specific differentiation. Compared to multilocus sequence methods and whole-genome microarrays, MGM provides additional discrimination between closely related strains and offers the possibility ...

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Oxford Gene Technology this week launched a new microarray that can be used to screen embryos for chromosomal abnormalities prior to implantation during an in vitro fertilization cycle.

6.1 × 10-20). In an additional 12 CKiD cases, we identified 12 likely pathogenic genomic imbalances that would be considered reportable in a clinical setting. These genomic imbalances were evenly distributed among patients diagnosed with congenital and noncongenital forms of CKD. In the vast majority of these cases, the genomic lesion was unsuspected based on the clinical assessment and either reclassified the disease or provided information that might have triggered additional clinical care, such as evaluation for metabolic or neuropsychiatric disease.. ...

6.1 × 10-20). In an additional 12 CKiD cases, we identified 12 likely pathogenic genomic imbalances that would be considered reportable in a clinical setting. These genomic imbalances were evenly distributed among patients diagnosed with congenital and noncongenital forms of CKD. In the vast majority of these cases, the genomic lesion was unsuspected based on the clinical assessment and either reclassified the disease or provided information that might have triggered additional clinical care, such as evaluation for metabolic or neuropsychiatric disease.. ...

GenomePlex® Single Cell WGA Kit CGH Data. The GenomePlex Single Cell WGA (WGA-4) provides accurate and unbiased amplification that preserves the original genome representation.

Aims The clinical significance of TOP2A as a prognostic marker has not been clarified. The aims of this study were to investigate the frequency of TOP2A copy number change; to correlate TOP2A with HER2 status, hormone ...

We have some time ahead of us to finish developing the product to the point where it can be put in someone elses lab, he said. We are still working on the instrument format, but we are aiming at something that will be very available and accessible to users - not requiring something too sophisticated or exotic ...

TY - JOUR. T1 - Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma. AU - Snijders, Antoine M.. AU - Schmidt, Brian. AU - Fridlyand, Jane. AU - Dekker, Nusi. AU - Pinkel, Daniel. AU - Jordan, Richard C K. AU - Albertson, Donna. PY - 2005/6/16. Y1 - 2005/6/16. N2 - Genomes of solid tumors are characterized by gains and losses of regions, which may contribute to tumorigenesis by altering gene expression. Often the aberrations are extensive, encompassing whole chromosome arms, which makes identification of candidate genes in these regions difficult. Here, we focused on narrow regions of gene amplification to facilitate identification of genetic pathways important in oral squamous cell carcinoma (SCC) development. We used array comparative genomic hybridization (array CGH) to define minimum common amplified regions and then used expression analysis to identify candidate driver genes in amplicons that spanned ,3Mb. We found genes involved ...

TY - JOUR. T1 - Molecular cytogenetic definition of a translocation t(X;15) associated with premature ovarian failure. AU - Bertini, Veronica. AU - Ghirri, Paolo. AU - Bicocchi, Maria Patrizia. AU - Simi, Paolo. AU - Valetto, Angelo. PY - 2010/8. Y1 - 2010/8. N2 - Objective: To characterize the breakpoints of a t(X;15) found in a woman with premature ovarian failure (POF). Design: Case report. Setting: Molecular and cytogenetics unit in a university-affiliated hospital. Patient(s): A 19-year-old infertile woman presenting with a normal female phenotype but primary amenorrhea. Intervention(s): Molecular cytogenetic analyses and genetic counseling. Main Outcome Measure(s): Translocation t(X;15) defined by fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (array CGH). Result(s): Chromosome and FISH analysis revealed 46,XX, t(X;15)(Xq22.1;p11); the active X was translocated and had been inherited from her mother. Detailed molecular characterization by FISH showed ...

Copy number analysis usually refers to the process of analyzing data produced by a test for DNA copy number variation in patients sample. Such analysis helps detect chromosomal copy number variation that may cause or may increase risks of various critical disorders. Copy number variation can be detected with various types of tests such as fluorescent in situ hybridization, comparative genomic hybridization and with high-resolution array-based tests based on array comparative genomic hybridization (or aCGH), SNP array technologies and high resolution microarrays that include copy number probes as well an SNPs. Array-based methods have been accepted as the most efficient in terms of their resolution and high-throughput nature and the highest coverage (choose an array with over 2 million probes) and they are also referred to as Virtual Karyotype. Data analysis for an array-based DNA copy number test can be very challenging though due to very high volume of data that come out of an array platform. ...

To detect novel genetic alterations, many astrocytomas have been investigated by comparative genomic hybridization (CGH). To identify aberration profiles characteristic of World Health Organization (WHO) grade I, II, III, and IV astrocytoma, we performed a meta-analysis of detailed genome wide CGH data of all 467 cases published so far. After expansion of all given aberrations to the maximum of 850 GTG-band resolution, the frequencies of genetic imbalances were calculated for each chromosomal band, separately for all four WHO grades. Low-grade astrocytoma has already demonstrated one characteristic of glioblastoma multiforme, gain of chromosome 7 with a hot spot at 7q32, but without loss of chromosome 10. In anaplastic astrocytoma, a more complex aberration pattern emerges from diffuse genetic imbalances. Gains of 7q32-q36 and 7p12 become the most frequent aberrations at chromosome 7. In glioblastoma multiforme, coarse aberrations like +7, -9p, -10, and -13 represent the most frequent ...

In this chapter submicroscopic structural variation is described with a particular focus on copy number variation. There is a growing body of evidence to show that copy number variation is a common and important class of genetic variation. Recent technological advances for mapping the extent of copy number variation including microarray based comparative genomic hybridisation are described, together with the results of large scale surveys of copy number variation among healthy individuals. The consequences of such genetic diversity for gene expression are discussed. The important role of copy number variation in susceptibility to a variety of common multifactorial traits is described including infectious and autoimmune disease. Copy number variation is also discussed in relation to evidence for selection in relation to copy number of the gene encoding salivary amylase and a high starch diet, and in relation to drug metabolism with important consequences for pharmacogenomics.

Deregulation of the EGFR signaling pathway is one of the most frequently observed genetic abnormalities that drives cancer development. Although mutations in the downstream components of the EGFR signaling pathway, including KRAS, BRAF and PIK3CA, have been reported in numerous cancers, extensive mutation and copy number analysis of these genes in clinical samples has not been performed for head and neck squamous cell carcinoma (HNSCC). We examined the mutations and copy number alterations of KRAS, BRAF and PIK3CA in 115 clinical specimens of HNSCC obtained from surgically treated patients. We used DNA sequencing to detect mutations and the copy number changes were evaluated by qPCR and array comparative genomic hybridization (CGH) analysis. We examined the mutations and copy number alterations of KRAS, BRAF and PIK3CA in 115 clinical specimens of HNSCC obtained from surgically treated patients. We identified 3 mutations (2.6%) in K-RAS and 3 mutations (2.6%) in PIK3CA. Copy number amplification was

Oncogenic point mutations in KIT or PDGFRA are recognized as the primary events responsible for the pathogenesis of most gastrointestinal stromal tumors (GIST), but additional genomic alterations are frequent and presumably required for tumor progression. The relative contribution of such alterations for the biology and clinical behavior of GIST, however, remains elusive. In the present study, somatic mutations in KIT and PDGFRA were evaluated by direct sequencing analysis in a consecutive series of 80 GIST patients. For a subset of 29 tumors, comparative genomic hybridization was additionally used to screen for chromosome copy number aberrations. Genotype and genomic findings were cross-tabulated and compared with available clinical and follow-up data. We report an overall mutation frequency of 87.5%, with 76.25% of the tumors showing alterations in KIT and 11.25% in PDGFRA. Secondary KIT mutations were additionally found in two of four samples obtained after imatinib treatment. Chromosomal imbalances

3q29 microdeletion syndrome is a rare genetic disorder resulting from the deletion of a segment of chromosome 3. This syndrome was first described in 2005. The clinical phenotype of 3q29 microdeletion syndrome is variable. Clinical features can include mild/moderate mental retardation with mildly dysmorphic facial features (long and narrow face, short philtrum and a high nasal bridge). Of the 6 reported patients, additional features including autism, ataxia, chest-wall deformity and long, tapering fingers were found in at least two patients. A review of 14 children with insterstitial deletions of 3q29, found 11 who had the common recurrent 1.6Mb deletion and displayed mental retardation and microcephaly. The variability of phenotype is underscored by the report on a 6 and 9/12 year-old male patient with a de novo chromosome 3q29 microdeletion identified by BAC array comparative genomic hybridization assay (aCGH), with accompanying normal 46,XY high-resolution chromosome analysis. The patient has ...

Translocations affecting chromosome subband 6p25.3 containing the IRF4 gene have been recently described as characteristic alterations in a molecularly distinct subset of germinal center B-cell-derived lymphomas. Secondary changes have yet only been described in few of these lymphomas. Here, we performed array-comparative genomic hybridization and molecular inversion probe microarray analyses on DNA from 12 formalin-fixed paraffin-embedded and two fresh-frozen IRF4 translocation-positive lymphomas, which together with the previously published data on nine cases allowed the extension of copy number analyses to a total of 23 of these lymphomas. All except one case carried chromosomal imbalances, most frequently gains in Xq28, 11q22.3-qter, and 7q32.1-qter and losses in 6q13-16.1, 15q14-22.31, and 17p. No recurrent copy-neutral losses of heterozygosity were observed. TP53 point mutations were detected in three of six cases with loss of 17p. Overall this study unravels a recurrent pattern of ...

Schizophrenia is a devastating neurodevelopmental disorder whose genetic influences remain elusive. We hypothesize that individually rare structural variants contribute to the illness. Microdeletions and microduplications ,100 kilobases were identified by microarray comparative genomic hybridization of genomic DNA from 150 individuals with schizophrenia and 268 ancestry-matched controls. All variants were validated by high-resolution platforms. Novel deletions and duplications of genes were present in 5% of controls versus 15% of cases and 20% of young-onset cases, both highly significant differences. The association was independently replicated in patients with childhood-onset schizophrenia as compared with their parents. Mutations in cases disrupted genes disproportionately from signaling networks controlling neurodevelopment, including neuregulin and glutamate pathways. These results suggest that multiple, individually rare mutations altering genes in neurodevelopmental pathways contribute to ...

Array-based comparative genomic hybridization (CGH) and gene expression profiling have become vital techniques for identifying molecular defects underlying genetic diseases. Regardless of the microarray platform, cyanine dyes (Cy3 and Cy5) are one of the most widely used fluorescent dye pairs for microarray analysis owing to their brightness and ease of incorporation, enabling high level of assay sensitivity. However, combining both dyes on arrays can become problematic during summer months when ozone levels rise to near 25 parts per billion (ppb). Under such conditions, Cy5 is known to rapidly degrade leading to loss of signal from either homebrew or commercial arrays. Cy5 can also suffer disproportionately from dye photobleaching resulting in distortion of (Cy5/Cy3) ratios used in copy number analysis. Our laboratory has been active in fluorescent dye research to find a suitable alternative to Cy5 that is stable to ozone and resistant to photo-bleaching. Here, we report on the development of such a

Acute myeloid leukemia (AML) with inv(3)(q21q26.2)/t(3;3)(q21;q26.2) is a distinct clinicopathologic entity with a poor prognosis. However, double inv(3)(q21q26.2) is extremely rare in AML. We report here 3 cases analyzed by oligonucleotide microarray comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP). Clinicopathologic, cytogenetic and molecular findings were correlated with clinical outcome to better understand the entity. The study group included one man and two women at 56-74 years of age. The AML arose from myelodysplastic syndrome in one patient and from chronic myelomonocytic leukemia in another patient. Monosomy 7 was found as additional cytogenetic finding in one patient. One patient had a single inv(3) in the initial clone and acquired double inv(3) as part of clonal evolution. EVI1 (MECOM) rearrangement was confirmed using metaphase/interphase fluorescence in situ hybridization (FISH). Microarray (aCGH + SNP) data analysis revealed that the double inv(3) was a

DNA copy number alterations in 146 bladder tumors.A) Whole genome heatmap representing relative copy number profiles of the samples. Segments of gains or deleti

Abstract: Resistance to chemotherapeutic agents and radiotherapy has kept surgery the primary treatment of uterine leiomyosarcoma (ULMS). In search of leads for potential therapeutic targets, array CGH (aCGH) was used to obtain a genomewide pattern of ULMS-specific genetic imbalances and to define the affected biological processes. Fine-resolution genomewide aCGH analysis was performed using customised 16K cDNA microarrays on 18 primary ULMS cases. Furthermore, patterns of DNA copy number changes were assessed for associations with clinical parameters, i.e., tumour grade, tumour size and patient status at last follow-up. Our aCGH results demonstrated extensive DNA copy number changes in all chromosomes. Of the 10,590 gene loci included in the analysis, 4,387 were found to be affected by DNA copy number gains and 4,518 by DNA copy number losses in at least one case. Further analyses revealed that 231 of these were commonly gained, and 265 lost in at least 20% of the cases. The gains affected loci ...

CMA-Expanded utilizes array-based comparative genomic hybridization (aCGH) and contains 400,000 oligonucleotides for copy number analysis and SNP probes for all chromosomes for detection of uniparental disomy (UPD) and consanguinity. SNP probes are also useful for the detection of triploidy. This expanded prenatal array offers exon-by-exon coverage of over 1,700 genes. It is recommended for providers and patients who want the highest level of detection possible. This option may be the best choice for fetal evaluations assessing possible copy number changes at breakpoints of de novo apparently balanced rearrangements. CMA is limited to detection of gains and losses of genomic material and will not detect low-level mosaicism, balanced translocations, inversions or point mutations in specific genes ...

article{7b211b82-b7cf-45eb-9b6c-526d9db736a8, abstract = {Chemotherapy resistance remains a major obstacle to successful treatment of ovarian cancer patients. Therefore, increased knowledge of underlying mechanisms and identification of predictive factors are of great importance. Standard treatment for ovarian carcinoma is surgery followed by platinum-based chemotherapy. In this study, we aimed to search for genes or genomic regions involved in platinum resistance in ovarian carcinoma. Array-based comparative genomic hybridization (CGH) was used to identify genetic alterations in 32 early-stage epithelial ovarian carcinomas homogeneously treated with single-agent carboplatin. The arrays contain 33,370 bacterial artificial chromosome (BAC) clones and form a contiguous and tiling coverage of the human genome with an average resolution of similar to 100 kb. We found certain genetic changes associated with carboplatin response. Gains in 1q25.1-q41 were significantly more frequent in ...

elicobacter pylori infection is associated with several gastro-duodenal inflammatory diseases of various levels of severity. To determine whether certain combinations of genetic markers can be used to predict the clinical source of the infection, we analyzed well documented and geographically homogenous clinical isolates using a comparative genomics approach. A set of 254 H. pylori genes was used to perform array-based comparative genomic hybridization among 120 French H. pylori strains associated with chronic gastritis (n = 33), duodenal ulcers (n = 27), intestinal metaplasia (n = 17) or gastric extra-nodal marginal zone B-cell MALT lymphoma (n = 43). Hierarchical cluster analyses of the DNA hybridization values allowed us to identify a homogeneous subpopulation of strains that clustered exclusively with cag PAI minus MALT lymphoma isolates. The genome sequence of B38, a representative of this MALT lymphoma strain-cluster, was completed, fully annotated, and compared with the six previously released H.

Urinary tract infections (UTIs) are caused by uropathogenic Escherichia coli (UPEC) strains. In contrast to many enteric E. coli pathogroups, no genetic signature has been identified for UPEC strains. We conducted a high-resolution comparative genomic study using E. coli isolates collected from the urine of women suffering from frequent recurrent UTIs. These isolates were genetically diverse and varied in their urovirulence, that is, their ability to infect the bladder in a mouse model of cystitis. We found no set of genes, including previously defined putative urovirulence factors (PUFs), that were predictive of urovirulence. In addition, in some patients, the E. coli strain causing a recurrent UTI had fewer PUFs than the supplanted strain. In competitive experimental infections in mice, the supplanting strain was more efficient at colonizing the mouse bladder than the supplanted strain. Despite the lack of a clear genomic signature for urovirulence, comparative transcriptomic and phenotypic ...

TY - JOUR. T1 - High-Resolution Genomic Arrays Facilitate Detection of Novel Cryptic Chromosomal Lesions in Myelodysplastic Syndromes. AU - OKeefe, Christine L.. AU - Tiu, Ramon. AU - Gondek, Lukasz P.. AU - Powers, Jennifer. AU - Theil, Karl S.. AU - Kalaycio, Matt. AU - Lichtin, Alan. AU - Sekeres, Mikkael A.. AU - Maciejewski, Jaroslaw P.. PY - 2007/2/1. Y1 - 2007/2/1. N2 - Objective: Unbalanced chromosomal aberrations are common in myelodysplastic syndromes and have prognostic implications. An increased frequency of cytogenetic changes may reflect an inherent chromosomal instability due to failure of DNA repair. Therefore, it is likely that chromosomal defects in myelodysplastic syndromes may be more frequent than predicted by metaphase cytogenetics and new cryptic lesions may be revealed by precise analysis methods. Methods: We used a novel high-resolution karyotyping technique, array-based comparative genomic hybridization, to investigate the frequency of cryptic chromosomal lesions in a ...

Grey zone. Structural genomic variants or copy number variations (CNV) can be reliably assessed using array comparative genomic hybridization (array CGH) or Single Nucleotide Polymorphism (SNP) arrays. However, for deletions or duplications smaller than 50-100 kB, these technologies have a poor detection rate with many false positive and false negative findings unless platforms are used that target specific candidate regions. Exome analysis, on the other hand, is capable of assessing genetic variation reliably on the single base-pair level. Between both technologies, there is a grey zone of structural genomic variants that are difficult to detect; CNVs smaller than 50 kB are often difficult to assess, and the extent and pathogenic role of these small CNVs is unclear. Now, a recent paper in the American Journal of Human Genetics manages to detect small CNVs through exome data. Their analysis in patients with autism, parents, and unaffected siblings suggests a contribution of small inherited CNVs ...

NSCLC-associated EGFR mutations are most frequently heterozygous. However, Paez et al. (18) reported one mutation involving exon 19 that appeared to be homozygous, and we detected two such cases. Interpretation of mutational status solely from DNA sequencing can be problematic. On the one hand, contaminating normal cells with wild-type EGFR could account for apparent heterozygosity; on the other hand, amplification of mutant EGFR, as occurs in lung cancer (23), could account for detection of only mutant sequences. Mouse models expressing mutant EGFR proteins in the lung and analysis of mutant-positive NSCLCs by fluorescence in situ hybridization and/or array-based comparative genomic hybridization may help address these issues. Interestingly, in one of these tumors (G3), we detected a heterozygous intronic polymorphism downstream of exon 19 (data not shown). In this case, it is probable that a gene conversion event occurred, encompassing the area of deletion in exon 19.. Five of 17 reported ...

A 3-month-old boy presented with decreased appetite, fatigue, and a nosebleed. Initial workup revealed hemoglobin 2.6 g/dL (10.2-12.7), hematocrit 7.7% (30.9-37.9), mean corpuscular volume 104 fL (71.3-82.6), white blood cell count 4200/μL (240 absolute neutrophil count), platelets 50 000/μL (140-400), and reticulocyte count 1.31% (1.55-2.7). Bone marrow revealed hypercellularity with cytoplasmic vacuolization of myeloid and erythroid precursors (panels A-B; original magnification ×1000, Wright-Giemsa stain). Iron staining of marrow biopsy revealed numerous ringed sideroblasts (panels C-D; original magnification ×1000, Prussian blue stain). DNA was examined by array-based comparative genomic hybridization and revealed a 4.9-kb deletion, m.11027_15950del4923, consistent with mitochondrial DNA deletion syndrome, also known as Pearson syndrome. Fecal elastase was initially normal, but now it is ,15 μg/g (normal ,200), consistent with severe pancreatic insufficiency. We have begun pancreatic ...

STUDY QUESTION: Can next-generation sequencing (NGS) techniques be used reliably for comprehensive aneuploidy screening of human embryos from patients undergoing IVF treatments, with the purpose of identifying and selecting chromosomally normal embryos for transfer?. SUMMARY ANSWER: Extensive application of NGS in clinical preimplantation genetic screening (PGS) cycles demonstrates that this methodology is reliable, allowing identification and transfer of euploid embryos resulting in ongoing pregnancies.. WHAT IS KNOWN ALREADY: The effectiveness of PGS is dependent upon the biology of the early embryo and the limitations of the technology. Fluorescence in situ hybridization, used to test for a few chromosomes, has largely been superseded by microarray techniques that test all 24 chromosomes. Array comparative genomic hybridization (array-CGH) has been demonstrated to be an accurate PGS method and has become the de facto gold standard, but new techniques, such as NGS, continue to emerge.. STUDY ...

Importantly, when creating the mimicked data sets we did not generate any simulated ratio values; rather, we formed different selections of values using real experimental data. We believe that this use of real experimental data is of significance for aCGH data. This belief is founded on that, in contrast to expression levels, copy number levels are restricted to a, by comparison, moderate dynamic range. Therefore, when a genomic region is subjected to gain or amplification, the increase of genomic material is relatively substantial. Thus, we reasoned that probes for regions of gain would yield comparably higher average intensities than those for regions of normal copy number and that this, in turn, would result in a correlation between M and A: probes measuring ratios of gain will have higher average intensities. The opposite relationship would apply for probes measuring ratios of loss. Consequently, utilizing normalization strategies based on Lowess would possibly correct for correlations ...

DNA copy number variants represent the greatest source of genetic variability in humans [1] and are the underlying cause of many human diseases. Array CGH is recognized as a first-tier test for DNA copy number variants (CNV) [2] and accordingly, many laboratories have already established their pipelines for pre-processing of array CGH data and CNV calling. In many cases these pipelines are based on software packages provided by the companies selling DNA microarrays or scanners such as BlueFuse [3], CytoSure [4] or CytoGenomics [5]. Yet, the scope of these tools is focused on the identification of CNVs and their evaluation in the context of gene content and frequency of a given variant in the healthy population. Comparative analysis, which integrates data obtained from multiple patients, or other experiment types are hardly supported, in particular when they are based on different array platforms or NGS technology.. Such kind of meta-analysis needs the implementation of additional commercial or ...

Abbreviations aCGH Array comparative genomic hybridization AF Amniotic fluid CRISPR Clustered regularly interspaced short palindromic repeat CVS Chorionic villus sampling FISH Fluorescence in situ hybridization HDR Homology directed repair ICM Inner cell mass ICSI Intracytoplasmic sperm injection mtDNA Mitochondrial DNA nDNA Nuclear DNA NGS Next-generation sequencing NHEJ Nonhomologous end joining cfDNA cell-free DNA PCR Polymerase…

We evaluated the prognostic and predictive value of a range of molecular changes in the setting of a randomised trial comparing standard PCV (procarbazine, CCNU (1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea) and vincristine) chemotherapy with the standard temozolomide (TMZ) 5-day (200 mg/m2/day) schedule and a 21-day (100 mg/m2/day) schedule in chemo-naïve, high-grade glioma (non-oligodendroglial tumours; WHO (World Health Organisation) grades III and IV) patients at first progression following radiotherapy. 354 samples (79.2%) from the first operation of the 447 randomised patients provided enough tumour DNA for some or all parts of the study. Genome-wide array comparative genomic hybridisation (aCGH), mutation analysis of IDH1/2 and TP53 and methylation analyses of the MGMT CpG-island was done. 84% of grade III tumours and 17% of grade IV had IDH1 or IDH2 mutations that conferred a better prognosis in both; MGMT methylation (defined as average value across 16 CpGs ≥ 10%) occurred in 75% of tumours

Manjegowda, D. S. and Karunakar, P. and Ramachandra, N. B. (2015) Effect of structural changes in proteins derived from GATA4 nonsynonymous single nucleotide polymorphisms in congenital heart disease. Indian Journal of Pharmaceutical Sciences, 77 (6). pp. 735-741. Avinash, M. V. and Megha, N. Murthy and Sangeetha, V. and Kusuma, L. and Suresh, R. V. and Nachappa, S. A. and Prashali, Nelchi and Sangeetha, N. Y. and Manjula, A. S. and Manjegowda, D. S. and Seshachalam, K. B. and Ramachandra, N. B. (2014) Copy Number Variations Burden on miRNA Genes Reveals Layers of Complexities Involved in the Regulation of Pathways and Phenotypic Expression. Plosone, 9 (2). Veerappa, Avinash M. and Vishweswaraiah, S. and Kusuma, L. and Megha, N. Murthy and Manjegowda, D. S. and Radhika Nayaka, and Ramachandra, N. B. (2013) Unravelling the Complexity of Human Olfactory Receptor Repertoire by Copy Number Analysis across Population Using High Resolution Arrays. PLOS ONE, 8 (7). pp. 1-14. ...

Vibrio harveyi BAA-1116 (and its derived mutants in panel MP-6) has been reclassified as Vibrio campbellii based on microarray comparative genome hybridization and multilocus sequence analysis. RefLin B, et al. Comparative genomic analyses identify the Vibrio harveyi genome sequenced strains BAA-1116 and HY01 as Vibrio campbellii. Environ. Microbiol. Rep. 2(1): 81-89, 2010. PubMed: 20686623

Roche NimbleGen, Inc. has launched NimbleGen Comparative Genomic Hybridization (CGH) microarrays in a 12x135K format for analysis of DNA copy number v

Hepatosplenic T-cell lymphoma (HSTL) is an aggressive lymphoma cytogenetically characterized by isochromosome 7q [i(7)(q10)], of which the molecular consequences remain unknown. We report here results of an integrative genomic and transcriptomic (expression microarray and RNA-sequencing) study of six i(7)(q10)-positive HSTL cases, including HSTL-derived cell line (DERL-2), and three cases with ring 7 [r(7)], the recently identified rare variant aberration. Using high resolution array CGH, we profiled all cases and mapped the common deleted region (CDR) at 7p22.1p14.1 (34.88 Mb; 3506316-38406226 bp) and the common gained region (CGR) at 7q22.11q31.1 (38.77 Mb; 86259620-124892276 bp). Interestingly, CDR spans a smaller region of 13 Mb (86259620-99271246 bp) constantly amplified in cases with r(7). In addition, we found that TCRG (7p14.1) and TCRB (7q32) are involved in formation of r(7), which seems to be a byproduct of illegitimate somatic rearrangement of both loci. Further transcriptomic ...

Rodríguez-Castillo, J. G., Pino, C., Niño, L. F., Rozo, J. C., Llerena-Polo, C., Parra-López, C. A., Tauch, A., et al. (2017). Comparative genomic analysis of Mycobacterium tuberculosis Beijing-like strains revealed specific genetic variations associated with virulence and drug resistance. Infect Genet Evol, 54, 314-323. doi:10.1016/j.meegid.2017.07. ...

We have developed ascatNgs to aid researchers in carrying out Allele-Specific Copy number Analysis of Tumours (ASCAT). ASCAT is capable of detecting DNA copy number changes affecting a tumor genome when comparing to a matched normal sample. Additionally, the algorithm estimates the amount of tumor DNA in the sample, known as Aberrant Cell Fraction (ACF). ASCAT itself is an R-package which requires the generation of many file types. Here, we present a suite of tools to help handle this for the user. Our code is available on our GitHub site (https://github.com/cancerit). This unit describes both one-shot execution and approaches more suitable for large-scale compute farms. © 2016 by John Wiley & Sons, Inc.

View the review history for Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton

Bioconductor version: Release (3.6) The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.. Author: Lei Song, Krithika Bhuvaneshwar, Yue Wang, Yuanjian Feng, Ie-Ming Shih, Subha Madhavan, Yuriy Gusev Maintainer: Yuriy Gusev ,yg63 at georgetown.edu, ...

Comparative genomic hybridization (CGH) was used to screen 83 lung adenocarcinomas of 60 patients for chromosomal imbalances. The most common alteration was DNA overrepresentation on chromosome 1q, with a peak incidence at 1q22-q23 in 73% of the primary tumours, followed by DNA overrepresentation on …

Dr Liesbeth Lenaerts talks to ecancer at ESMO 2018 about a pre-existing pre-natal test which flagged up copy number alterations and cancer in the foetus'

To assess the influence of molecular markers with potential prognostic value to groups of patients with newly diagnosed glioblastoma patients were examined: group A with 36 patients (surgical resection plus standard combined chemoradiotherapy) and group B with 36 patients (surgical resection, standard combined chemoradiotherapy plus carmustine wafer implantation). Our aim was to determine chromosomal alterations, methylation status of MGMT, p15, and p16 (CDKN2A) in order to analyse the influence on patient survival time as well as radio- and chemotherapy responses. Promoter hypermethylation of MGMT, p16, and p15 genes were determined by MS-PCR. Comparative genomic hybridisation (CGH) analyses were performed with isolated, labelled DNA of each tumor to detect genetic alterations. Age of onset of the disease showed a significant effect on overall survival (OS) (p < 0.0001). Additional treatment with carmustine wafer (group B) compared to the control group (group A) did not result in improved OS (p = 0.562

Copy number variants (CNVs) on the Breakpoint 1 to Breakpoint 2 region Ki8751 at 15q11. of publically obtainable expression data identified a relationship between expression of mRNA and FOXP2 in mind. We suggest that changed medication dosage through aberrant patterning from the lh.SMG may donate to language-related Mouse monoclonal to CD11b.4AM216 reacts with CD11b, a member of the integrin a chain family with 165 kDa MW. which is expressed on NK cells, monocytes, granulocytes and subsets of T and B cells. It associates with CD18 to form CD11b/CD18 complex.The cellular function of CD11b is on neutrophil and monocyte interactions with stimulated endothelium; Phagocytosis of iC3b or IgG coated particles as a receptor; Chemotaxis and apoptosis. Ki8751 issues connected with BP1-2 CNVs. Even more generally this process may be useful in clarifying the contribution Ki8751 of individual genes at CNV risk loci. Introduction Rare multi-gene copy number variants (CNVs) are well established to increase ...

Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We developed a method we call Sector-Ploidy-Profiling to study the clonal composition of breast tumors. SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization. Breast carcinomas display two classes of genomic structural variation: (1) monogenomic and (2) polygenomic. Monogenomic tumors appear to contain a single major clonal subpopulation with a highly stable chromosome structure. Polygenomic tumors contain multiple clonal tumor subpopulations, which may occupy the same sectors, or separate anatomic locations. In polygenomic tumors, we show that ...

Integrative and conjugative elements (ICEs) of the ICESa2603 family have been isolated from several species of Streptococcus spp.; however, the comparative genomic and evolutionary analyses of these particular ICEs are currently only at their initial stages. By investigating 13 ICEs of the ICESa2603 family and two ICESa2603 family-like ICEs derived from diverse hosts and locations, we have determined that ICEs comprised a backbone of 30 identical syntenic core genes and accessory genes that were restricted to the intergenic sites or the 3-end of the non-conserved domain of core genes to maintain its function. ICESa2603 family integrase IntICESa2603 specifically recognized a 15-bp att sequence (TTATTTAAGAGTAAC) at the 3-end of rplL, which was highly conserved in genus Streptococcus. Phylogenetic analyses suggest that extensive recombination/insertion and the occurrence of a hybrid/mosaic in the ICESa2603 family were responsible for the significant increase in ICE diversity, thereby broadening its host

Dr. Dobyns leads a broad-based research program investigating the nature and causes of a wide range of human developmental brain disorders. These include malformations of the forebrain, mid-hindbrain (brainstem and cerebellum) and cerebral cortex, as well as a wide spectrum of developmental disabilities including autism, intellectual disability, early childhood developmental forms of epilepsy, and complex developmental disorders combining several of the above. His work includes recognition and delineation of specific conditions, identification of numerous underlying genes, and detailed phenotype and genotype-phenotype analysis. The methods used in his lab include most standard molecular genetics methods plus fluorescence in situ hybridization, chromosome microarrays (comparative genome hybridization), RNA expression arrays, methylation-sensitive assays for X inactivation, standard (Sanger) sequencing, and most recently high-throughput exome sequencing.. ...

Our molecular genetics lab offers single-gene deletion and duplication analysis through comparative genomic hybridization (CGH). Learn the indications and more.

614 Taxol is one of the widely used chemotherapeutic drugs against many types of human cancer. While it is considered as one of the most effective anticancer drugs, treatment failure often occurs due to development of acquired resistance. Therefore, it is important to understand the molecular mechanisms responsible for the development of drug resistance. Although it is generally believed that taxol induces cell death through interfering with microtubules leading to mitotic arrest, recent evidence has suggested that taxol-induced cell death also occurs through pathways independent of either microtubule or mitotic arrest. In this study, we report the identification of a novel role for TWIST, a basic helix-loop-helix protein, which plays a central role in cell type determination and differentiation, during generation of acquired resistance to taxol in a nasopharyngeal carcinoma cell line, HNE1-T3, using comparative genome hybridization (CGH) and subsequent RT-PCR and Western blotting. We found that ...

The incidence of adenocarcinoma of the lung is increasing in the United States, however, the difficulties in obtaining lung cancer families and representative samples of early to late stages of the disease have lead to the intense study of mouse models for lung cancer. We used Spectral Karyotyping (SKY), mapping with fluorescently labeled genomic clones (FISH), comparative genomic hybridization (C

The frequency of disease-related large rearrangements (referred to as copy-number mutations, CNMs) varies among genes, and search for these mutations has an important place in diagnostic strategies. In recent years, CGH method using custom-designed h

Genomic instability is a hallmark of cancer resulting in widespread somatic copy number alterations. We integrated a genome-scale shRNA viability screen and copy number profiles from 179 cancer cell lines to perform an unbiased analysis of copy-number associated gene-dependency interactions. We found most copy-number associated gene dependencies result from losses of genetic material rather than gains. Strikingly, the most enriched class of these dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes. Hemizygous loss of CYCLOPS genes sensitizes cancer cells to their further suppression. One of the top hits from the analysis was the pre-mRNA splicing factor SF3B1, which is also frequently mutated in cancer. We then sought to evaluate SF3B1 as a CYCLOPS gene. Cancer cells with hemizygous SF3B1 copy-loss were uniquely sensitive to partial SF3B1 suppression by RNAi compared to cells with normal SF3B1 gene dosage. Mechanistically, cancer cells ...