Genomes and Genes
comparative genomic hybridization
Summary: A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.
- Masecchia S, Barla A, Salzo S, Verri A. Dictionary learning improves subtyping of breast cancer aCGH data. Conf Proc IEEE Eng Med Biol Soc. 2013;2013:604-7 pubmed publisherThe advent of Comparative Genomic Hybridization (CGH) data led to the development of new mathematical models and computational methods to automatically infer chromosomal alterations...
- Agostini A, Brunetti M, Davidson B, Trope C, Heim S, Panagopoulos I, et al. Genomic imbalances are involved in miR-30c and let-7a deregulation in ovarian tumors: implications for HMGA2 expression. Oncotarget. 2017;8:21554-21560 pubmed publisher..and miR-30c could be evaluated on the basis of previously generated karyotypic and high resolution comparative genomic hybridization (CGH) data on 103 tumors...
- Schumacher S, Bartenhagen C, Hoffmann M, Will D, Fischer J, Baldus S, et al. Disseminated tumour cells with highly aberrant genomes are linked to poor prognosis in operable oesophageal adenocarcinoma. Br J Cancer. 2017;117:725-733 pubmed publisher..The analysis of PAG/CIN in solitary marker-positive DTCs identifies operable EAC patients with poor prognosis, indicating a more aggressive minimal residual disease. ..
- Chen X, Wang J, Mitchell E, Guo J, Wang L, Zhang Y, et al. Recurrent 8q13.2-13.3 microdeletions associated with branchio-oto-renal syndrome are mediated by human endogenous retroviral (HERV) sequence blocks. BMC Med Genet. 2014;15:90 pubmed publisher..These findings raise the potential that HERV sequences may more commonly underlie recombination of dosage sensitive regions associated with recurrent syndromes. ..
- Grau C, Starkovich M, Azamian M, Xia F, Cheung S, Evans P, et al. Xp11.22 deletions encompassing CENPVL1, CENPVL2, MAGED1 and GSPT2 as a cause of syndromic X-linked intellectual disability. PLoS ONE. 2017;12:e0175962 pubmed publisher..Loss of GSPT2 and/or MAGED1 function may contribute to the intellectual disability and developmental delay seen in males with these deletions. ..
- McNamee K, Dawood F, Farquharson R. Evaluation of array comparative genomic hybridization in recurrent miscarriage. Br J Hosp Med (Lond). 2013;74:36-40 pubmed
- Castagnola P, Gandolfo S, Malacarne D, Aiello C, Marino R, Zoppoli G, et al. DNA aneuploidy relationship with patient age and tobacco smoke in OPMDs/OSCCs. PLoS ONE. 2017;12:e0184425 pubmed publisher..Nuclear genomic aberrations were determined in a subset of 65 patients by genome-wide array comparative genomic hybridization (aCGH) using DNA extracted from either diploid or aneuploid nuclei suspension sorted by FCM...
- Chen C, Lin S, Chern S, Tsai F, Wu P, Lee C, et al. Deletion 2q37.3->qter and duplication 15q24.3->qter characterized by array CGH in a girl with epilepsy and dysmorphic features. Genet Couns. 2010;21:263-7 pubmed
- Yon D, Park J, Kim S, Shim S, Chae K. A sibship with duplication of Xq28 inherited from the mother; genomic characterization and clinical outcomes. BMC Med Genet. 2017;18:30 pubmed publisher..We tried to analyze the information of the relationship between neuropsychiatric phenotype and the extent of duplication at Xq28 by comparing with previous reports. ..
- La Marca A, Minasi M, Sighinolfi G, Greco P, Argento C, Grisendi V, et al. Female age, serum antimÃ¼llerian hormone level, and number of oocytes affect the rate and number of euploid blastocysts in inÂ vitro fertilization/intracytoplasmic sperm injection cycles. Fertil Steril. 2017;108:777-783.e2 pubmed publisher..A strong positive age-independent relationship between AMH level and the rate of euploid blastocysts was found. This confirms that the measurement of ovarian reserve by means of AMH has high relevance when counseling infertile patients. ..
- Borlee G, Plumley B, Martin K, Somprasong N, Mangalea M, Islam M, et al. Genome-scale analysis of the genes that contribute to Burkholderia pseudomallei biofilm formation identifies a crucial exopolysaccharide biosynthesis gene cluster. PLoS Negl Trop Dis. 2017;11:e0005689 pubmed publisher..These findings will facilitate further advances in understanding the pathogenesis of B. pseudomallei and improve diagnostics and therapeutic treatment strategies. ..
- Narvaez Bravo C, Taboada E, Mutschall S, Aslam M. Epidemiology of antimicrobial resistant Campylobacter spp. isolated from retail meats in Canada. Int J Food Microbiol. 2017;253:43-47 pubmed publisher..CGF analysis showed that Campylobacter isolated from poultry meat in this study were genetically related to clinical isolates recovered from human infections and to those isolated from animals and the environment. ..
- Nacheva E, Mokretar K, Soenmez A, Pittman A, Grace C, Valli R, et al. DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation. PLoS ONE. 2017;12:e0180467 pubmed publisher..This may contribute to array "waves", and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance. ..
- Ryall S, Arnoldo A, Krishnatry R, Mistry M, Khor K, Sheth J, et al. Multiplex Detection of Pediatric Low-Grade Glioma Signature Fusion Transcripts and Duplications Using the NanoString nCounter System. J Neuropathol Exp Neurol. 2017;76:562-570 pubmed publisher..3%), KIAA1549-BRAF 15;11 (2/171, 1.2%), FAM131B-BRAF 2;9 (1/171, 0.6%), and RNF130-BRAF 3;9 (1/171, 0.6%). This work introduces NanoString as a viable clinical replacement for the detection of fusion and duplication events in pLGG. ..
- Suryawanshi V, Talke I, Weber M, Eils R, Brors B, Clemens S, et al. Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri. BMC Genomics. 2016;17:1034 pubmed publisher..Moreover our results support the hypothesis that elemental defences, which result from the hyperaccumulation of toxic metals, allow the reduction of classical defences against biotic stress as a trade-off. ..
- Aleksandrova N, Shubina E, Ekimov A, Kodyleva T, Mukosey I, Makarova N, et al. [Comparative results of preimplantation genetic screening by array comparative genomic hybridization and new-generation sequencing]. Mol Biol (Mosk). 2017;51:308-313 pubmed publisher..NGS data were collected for 38 biopsied embryos and compared with the data from array comparative genomic hybridization (array-CGH). The concordance between the NGS and array-CGH data was 94.8%...
- Wang D, Li S, Guo F, Ning K, Wang L. Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats. BMC Genomics. 2017;18:268 pubmed publisher..This suggests that the conservation of ends could possibly be a popular phenomenon in many types of chromosome rearrangement events. ..
- KELLEHER P, Bottacini F, Mahony J, Kilcawley K, van Sinderen D. Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation. BMC Genomics. 2017;18:267 pubmed publisher..Niche adaptation appears to play a significant role in governing the genetic content of each L. lactis subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted. ..
- Dagher J, Kammerer Jacquet S, Dugay F, Beaumont M, Lespagnol A, Cornevin L, et al. Clear cell renal cell carcinoma: a comparative study of histological and chromosomal characteristics between primary tumors and their corresponding metastases. Virchows Arch. 2017;471:107-115 pubmed publisher..sequencing (VHL and c-MET genes), multiplex ligation-dependent probe amplification, and array-(comparative genomic hybridization) CGH analyses were realized...
- Brisse H, Blanc T, Schleiermacher G, Mosseri V, Philippe Chomette P, Janoueix Lerosey I, et al. Radiogenomics of neuroblastomas: Relationships between imaging phenotypes, tumor genomic profile and survival. PLoS ONE. 2017;12:e0185190 pubmed publisher..Genomic profiles were assessed using array-based comparative genomic hybridization and divided into three groups: "numerical-only chromosome alterations" (NCA), "..
- Tassano E, Giacomini T, Severino M, Gamucci A, Fiorio P, Gimelli G, et al. Characterization of the Phenotype Associated with Microduplication Reciprocal to NF1 Microdeletion Syndrome. Cytogenet Genome Res. 2017;152:22-28 pubmed publisher..2 microduplications. We also analyzed the gene content of the duplicated region in order to investigate the possible role of specific genes in the clinical phenotype of our patient. ..
- Takada Y, Sakai Y, Matsushita Y, Ohkubo K, Koga Y, Akamine S, et al. Sustained endocrine profiles of a girl with WAGR syndrome. BMC Med Genet. 2017;18:117 pubmed publisher..Children with WAGR syndrome may manifest profound delay in postnatal growth through unknown mechanisms. Epigenetic factors and growth-associated genes in WAGR syndrome remain to be characterized. ..
- Berglund J, Nevalainen E, Molin A, Perloski M, Andre C, Zody M, et al. Novel origins of copy number variation in the dog genome. Genome Biol. 2012;13:R73 pubmed publisher..Here we comprehensively assay CNVs using high-density array comparative genomic hybridization in 50 dogs from 17 dog breeds and 3 gray wolves...
- Zoropogui A, Pujic P, Normand P, Barbe V, Belli P, Graindorge A, et al. The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle. BMC Genomics. 2013;14:286 pubmed publisher..GUH-2 ability at acquiring foreign DNA was found significant and to have led to functional changes likely beneficial for its environmental cycle and opportunistic colonization of a human host. ..
- Morin S, Melzer Ross K, McCulloh D, Grifo J, Munne S. A greater number of euploid blastocysts in a given cohort predicts excellent outcomes in single embryo transfer cycles. J Assist Reprod Genet. 2014;31:667-73 pubmed..Blastocysts from 437 patients underwent trophectoderm biopsy followed by array comparative genomic hybridization. Embryos were then selected for single or double embryo transfer...
- Li Y, Chang X, Yu W, Li H, Ye Z, Yu H, et al. Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains. BMC Genomics. 2013;14:523 pubmed publisher..erythraea strain and the wild-type strain. These findings help to understand the global regulation mechanisms of erythromycin biosynthesis in S. erythraea, providing useful clues for genetic and metabolic engineering in the future. ..
- . large-scale screening for targeted knockouts in the Caenorhabditis elegans genome. G3 (Bethesda). 2012;2:1415-25 pubmed publisher..This knowledge will usher in a new age of metazoan genetics in which the contribution to any biological process can be assessed for all genes. ..
- Tian M, Wang Y, Gu X, Feng C, Fang S, Hu X, et al. Copy number variants in locally raised Chinese chicken genomes determined using array comparative genomic hybridization. BMC Genomics. 2013;14:262 pubmed publisher..of the copy number variants in locally raised Chinese chicken breeds identified using a customized comparative genomic hybridization array. We identified 833 copy number variants contained within 308 copy number variant regions...
- de Castro M, Tostes C, Dávila A, Senger H, da Silva F. SparkBLAST: scalable BLAST processing using in-memory operations. BMC Bioinformatics. 2017;18:318 pubmed publisher..The superior performance of SparkBLAST is mainly due to the in-memory operations available through the Spark framework, consequently reducing the number of local I/O operations required for distributed BLAST processing. ..
- Vincent Chong V, Salahshourifar I, Woo K, Anwar A, Razali R, Gudimella R, et al. Genome wide profiling in oral squamous cell carcinoma identifies a four genetic marker signature of prognostic significance. PLoS ONE. 2017;12:e0174865 pubmed publisher..The current study aimed to identify copy number alterations (CNAs) in OSCC using array comparative genomic hybridization (array CGH) and to correlate the CNAs with clinico-pathologic parameters and clinical outcomes...
- Zhou P, Silverstein K, Ramaraj T, Guhlin J, Denny R, Liu J, et al. Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. BMC Genomics. 2017;18:261 pubmed publisher..Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation. ..
- Tan T, Aftimos S, Worgan L, Susman R, Wilson M, Ghedia S, et al. Phenotypic expansion and further characterisation of the 17q21.31 microdeletion syndrome. J Med Genet. 2009;46:480-9 pubmed publisher..These data have significant implications for the clinical diagnosis and management of other individuals with 17q21.31 deletions. ..
- Ahmed M, Shen C, Khan A, Wahid M, Shaban M, Lin Z. A comparative genomics approach revealed evolutionary dynamics of microsatellite imperfection and conservation in genus Gossypium. Hereditas. 2017;154:12 pubmed publisher..The outcome could be a directive to explore comparative evolutionary footprints of simple non-coding genetic elements i.e., repeat elements, through the evolution of genus-specific characteristics in cotton genomes. ..
- Marotta M, Chen X, Inoshita A, Stephens R, Budd G, Crowe J, et al. A common copy-number breakpoint of ERBB2 amplification in breast cancer colocalizes with a complex block of segmental duplications. Breast Cancer Res. 2012;14:R150 pubmed publisher..chain reaction (PCR)-based assays for primary breast tumors and analyzed publically available array-comparative genomic hybridization data to map a common copy-number breakpoint in ERBB2-amplified primary breast tumors...
- Creytens D, Mentzel T, Ferdinande L, Lecoutere E, van Gorp J, Atanesyan L, et al. "Atypical" Pleomorphic Lipomatous Tumor: A Clinicopathologic, Immunohistochemical and Molecular Study of 21 Cases, Emphasizing its Relationship to Atypical Spindle Cell Lipomatous Tumor and Suggesting a Morphologic Spectrum (Atypical Spindle Cell/Ple. Am J Surg Pathol. 2017;41:1443-1455 pubmed publisher..In addition, array-based comparative genomic hybridization was performed on 4 APLTs and all PLSs...
- Leushkin E, Sutormin R, Nabieva E, Penin A, Kondrashov A, Logacheva M. The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences. BMC Genomics. 2013;14:476 pubmed publisher..The gene loss is more frequent for the genes that belong to multigenic families indicating that genetic redundancy is an important prerequisite for genome size reduction. ..
- Bauer J. The Molecular Revolution in Cutaneous Biology: Era of Cytogenetics and Copy Number Analysis. J Invest Dermatol. 2017;137:e57-e59 pubmed publisher..Genome-wide copy number analysis was made possible by the development of comparative genomic hybridization. It compares an entire cancer genome to a normal genome by differential fluorescence labeling and ..
- Choi B, Madeo A, King K, Zalewski C, Pryor S, Muskett J, et al. Segregation of enlarged vestibular aqueducts in families with non-diagnostic SLC26A4 genotypes. J Med Genet. 2009;46:856-61 pubmed publisher..These results will be helpful for counselling EVA families with non-diagnostic SLC26A4 genotypes. ..
- Pettersson M, Viljakainen H, Loid P, Mustila T, Pekkinen M, Armenio M, et al. Copy Number Variants Are Enriched in Individuals With Early-Onset Obesity and Highlight Novel Pathogenic Pathways. J Clin Endocrinol Metab. 2017;102:3029-3039 pubmed publisher..We used custom high-density array comparative genomic hybridization with exon resolution in 1989 genes, including all known obesity loci...
- Santos M, Dias Pereira P, Williams C, Lopes C, Breen M. Malignant canine mammary tumours: Preliminary genomic insights using oligonucleotide array comparative genomic hybridisation analysis. Vet J. 2017;222:68-71 pubmed publisher..Analysis of adjacent samples of one tumour revealed regional differences in the number of genomic imbalances, suggesting heterogeneity within tumours. ..
- Villela D, Schlesinger D, Suemoto C, Grinberg L, Rosenberg C. A microdeletion in Alzheimer's disease disrupts NAMPT gene. J Genet. 2014;93:535-7 pubmed
- Muñoz Amatriaín M, Eichten S, Wicker T, Richmond T, Mascher M, Steuernagel B, et al. Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol. 2013;14:R58 pubmed publisher..Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild ..
- Naseer M, Faheem M, Chaudhary A, Kumosani T, Al Quaiti M, Jan M, et al. Genome wide analysis of novel copy number variations duplications/deletions of different epileptic patients in Saudi Arabia. BMC Genomics. 2015;16 Suppl 1:S10 pubmed publisher..Novel technologies, such as array comparative genomic hybridization (array-CGH), may help to uncover the pathogenic CNVs in patients with epilepsy...
- ZaldÃvar LÃ³pez S, ROWELL J, Fiala E, Zapata I, Couto C, Alvarez C. Comparative genomics of canine hemoglobin genes reveals primacy of beta subunit delta in adult carnivores. BMC Genomics. 2017;18:141 pubmed publisher..Our findings are also likely to raise new questions about the significance of human HBD. The comparative genomics of dog hemoglobin genes sets the stage for diverse research and translation. ..
- Guimaraes L, Soares S, Trost E, Blom J, Ramos R, Silva A, et al. Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology. BMC Genomics. 2015;16 Suppl 5:S7 pubmed publisher..urealyticum provide insights in the lifestyle of this opportunistic pathogen and may be useful in developing future therapeutic strategies. ..
- Liu W, Laitinen S, Khan S, Vihinen M, Kowalski J, Yu G, et al. Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nat Med. 2009;15:559-65 pubmed publisher..This study establishes that genomic archeology of multiple anatomically separate metastatic cancers in individuals can be used to define the salient genomic features of a parent cancer clone of proven lethal metastatic phenotype. ..
- Ge L, Li N, Liu M, Xu N, Wang M, Wu L. Copy number variations of neurotrophic tyrosine receptor kinase 3 (NTRK3) may predict prognosis of ovarian cancer. Medicine (Baltimore). 2017;96:e7621 pubmed publisher..Array comparative genomic hybridization (CGH) was used to test gene backgrounds between platinum-sensitive and platinum-resistant relapsed ..
- Maldonado L, Assis J, Araújo F, Salim A, Macchiaroli N, Cucher M, et al. The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases. BMC Genomics. 2017;18:204 pubmed publisher..Additional cestode genomes need to be sequenced to be able to resolve their phylogeny. ..
- Fabian I, Thaung C, AlHarby L, Sisley K, Mudhar H, Doherty R, et al. Late Solitary Extraocular Recurrence From Previously Resected Iris Melanoma. Am J Ophthalmol. 2017;181:97-105 pubmed publisher..GNA11 mutation was found in 1 case. On array-based comparative genomic hybridization (n = 3), gain of 6p was found in 2 cases and gain of 8 in 2...
- Allegrini D, Penco S, Pece A, Autelitano A, Montesano G, Paci S, et al. Cataract and optic disk drusen in a patient with glycogenosis and di George syndrome: clinical and molecular report. BMC Ophthalmol. 2017;17:107 pubmed publisher..Genetic testing by array-comparative genomic hybridization (CGH) for DGS was required because of her low levels of serum calcium...
- Coci E, Auhuber A, Langenbach A, Mrasek K, Riedel J, Leenen A, et al. Novel Unbalanced Translocations Affecting the Long Arms of Chromosomes 10 and 22 Cause Complex Syndromes with Very Severe Neurodevelopmental Delay, Speech Impairment, Autistic Behavior, and Epilepsy. Cytogenet Genome Res. 2017;151:171-178 pubmed publisher