Journal articles: 'Array hybridisation analysis'

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Bachman, Kristine K., Stephanie J. DeWard, Constantinos Chrysostomou, Ricardo Munoz, and Suneeta Madan-Khetarpal. "Array CGH as a first-tier test for neonates with congenital heart disease." Cardiology in the Young 25, no. 1 (November 6, 2013): 115–22. http://dx.doi.org/10.1017/s1047951113001868.

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AbstractObjectiveEfficient diagnosis of an underlying genetic aetiology in a patient with congenital heart disease is essential to optimising clinical care. Copy number variants are one aetiology of congenital heart disease; the majority are identifiable by targeted fluorescence in situ hybridisation or array comparative genomic hybridisation, not by classical cytogenetic analysis. This study assessed the utility of array comparative genomic hybridisation as a first-tier diagnostic test for neonates with congenital heart disease.Study designA prospective chart review of neonates with congenital heart disease in the Cardiac Intensive Care Unit at Children’s Hospital of Pittsburgh of UPMC was performed. Patients were tested by array comparative genomic hybridisation and classical cytogenetic analysis simultaneously. Data collected included all chromosome abnormalities detected, physical examination findings, and imaging results. McNemar’s test was used to compare detection of array comparative genomic hybridisation and classical cytogenetic analysis.ResultsOf 45 patients, three (6.7%) had an abnormality detected by classical cytogenetic analysis and an additional 10 (22.2%) had a copy number variant detected by array comparative genomic hybridisation, highlighting an increased detection rate (p=0.008). Several of these copy number variants had unclear clinical significance, requiring additional investigation. The prevalence of dysmorphology and/or comorbidity in this population was 72%. Identification of dysmorphic features was greater when assessed by a geneticist than by providers of different subspecialties.ConclusionsArray comparative genomic hybridisation has significant clinical utility as a first-tier test in this population, but it carries the potential for incidental findings and results of uncertain clinical significance. Collaboration between cardiologists and medical geneticists is essential to providing optimal clinical care.

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Hightower, Hannah B., Nathaniel H. Robin, Fady M. Mikhail, and Namasivayam Ambalavanan. "Array comparative genomic hybridisation testing in CHD." Cardiology in the Young 25, no. 6 (October 8, 2014): 1155–72. http://dx.doi.org/10.1017/s1047951114001838.

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AbstractBackground: CHD is the leading cause of mortality due to birth defects. Array comparative genomic hybridisation (aCGH) detects submicroscopic copy number changes and may improve identification of the genetic basis of CHD. Methods: This is a retrospective analysis of 1252 patients from a regional referral centre who had undergone aCGH. Of the patients, 173 had CHD. A whole-genome custom-designed oligonucleotide array with >44,000 probes was used to detect copy number changes. Results: Of the 1252 patients, 335 (26.76%) had abnormal aCGH results. Of the 173 patients with CHD, 50 (28.9%) had abnormal aCGH results versus 284 (26.3%) of 1079 non-cardiac patients. There were six patients with CHD who had well-described syndromes such as Wolf–Hirschhorn, trisomy 13, DiGeorge, and Williams. Of the patients with CHD, those with left-sided heart disease had the highest proportion (14/31; 45.13%) of abnormal aCGH results, followed by those with conotruncal heart disease (10/29; 34.48%), endocardial cushion defects (13/50; 26%), complex/other heart disease (12/52; 23.08%), and patent ductus arteriosus (1/11; 9.09%). Conclusions: Patients with CHD are at a substantial risk of having microdeletions and microduplications. The incidence of abnormalities on aCGH analysis is higher than identified with karyotype, and identification of copy number changes may help identify the genetic basis of the specific heart defects. However, aCGH may not have a significant diagnostic yield in those with isolated CHD. Further research using larger data sets may help identify candidate genes associated with CHD.

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Mermer, Serdar, and Derya Aydın Şahin. "Array comparative genomic hybridisation results of non-syndromic children with the conotruncal heart anomaly." Cardiology in the Young 32, no. 2 (January 20, 2022): 301–6. http://dx.doi.org/10.1017/s104795112100473x.

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AbstractThe study aimed to show the chromosomal copy number variations responsible for the aetiology in patients with isolated conotruncal heart anomaly by array comparative genomic hybridisation and identify candidate genes causing conotruncal heart disease. A total of 37 patients, 17 male, and 20 female, with isolated conotruncal heart anomalies, were included in the study. No findings indicated any syndrome in terms of dysmorphology in the patients.Results:Copy number variations were detected in the array comparative genomic hybridisation analysis of five (13.5%) of 37 patients included in the study. Three candidate genes (PRDM16, HIST1H1E, GJA5) found in these deletion and duplication regions may be associated with the conotruncal cardiac anomaly.Conclusion:CHDs can be encountered as the first and sometimes the single finding of many genetic disorders in children. It is thought that genetic tests, especially array comparative genomic hybridisation, may be beneficial for children with CHD since the diagnosis of genetic diseases in these patients as early as possible will help to prevent or reduce complications that may develop in the future. Also, it would be possible to detect candidate genes responsible for conotruncal cardiac anomalies with array comparative genomic hybridisation.

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Finn, Stephen P., Paul Smyth, Esther O’Regan, Susanne Cahill, Richard Flavin, John O’Leary, and Orla Sheils. "Array comparative genomic hybridisation analysis of gamma-irradiated human thyrocytes." Virchows Archiv 445, no. 4 (July 17, 2004): 396–404. http://dx.doi.org/10.1007/s00428-004-1070-9.

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Creytens, David, Joost van Gorp, Liesbeth Ferdinande, Nadine Van Roy, and Louis Libbrecht. "Array-based comparative genomic hybridisation analysis of a pleomorphic myxoid liposarcoma." Journal of Clinical Pathology 67, no. 9 (June 26, 2014): 834–35. http://dx.doi.org/10.1136/jclinpath-2014-202420.

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Bauersachs, S., S. Rehfeld, SE Ulbrich, S. Mallok, K. Prelle, H. Wenigerkind, R. Einspanier, H. Blum, and E. Wolf. "Monitoring gene expression changes in bovine oviduct epithelial cells during the oestrous cycle." Journal of Molecular Endocrinology 32, no. 2 (April 1, 2004): 449–66. http://dx.doi.org/10.1677/jme.0.0320449.

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The oviduct epithelium undergoes marked morphological and functional changes during the oestrous cycle. To study these changes at the level of the transcriptome we did a systematic gene expression analysis of bovine oviduct epithelial cells at oestrus and dioestrus using a combination of subtracted cDNA libraries and cDNA array hybridisation. A total of 3072 cDNA clones of two subtracted libraries were analysed by array hybridisation with cDNA probes derived from six cyclic heifers, three of them slaughtered at oestrus and three at dioestrus. Sequencing of cDNAs showing significant differences in their expression levels revealed 77 different cDNAs. Thirty-seven were expressed at a higher level at oestrus, for the other 40 genes expression levels were higher at dioestrus. The identified genes represented a variety of functional classes. During oestrus especially genes involved in the regulation of protein secretion and protein modification, and mRNAs of secreted proteins, were up-regulated, whereas during dioestrus particularly transcripts of genes involved in transcription regulation showed a slight up-regulation. The concentrations of seven selected transcripts were quantified by real-time RT-PCR to validate the cDNA array hybridisation data. For all seven transcripts, RT-PCR results were in excellent correlation (r>0.92) with the results obtained by array hybridisation. Our study is the first to analyse changes in gene expression profiles of bovine oviduct epithelial cells during different stages of the oestrous cycle, providing a starting point for the clarification of the key transcriptome changes in these cells.

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Wei, Ching Kuo, Shun Hsing Chen, and Ming Chih Chen. "An empirical analysis of intention to use array-comparative genomic hybridisation method." International Journal of Biomedical Engineering and Technology 21, no. 3 (2016): 279. http://dx.doi.org/10.1504/ijbet.2016.078291.

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Kriegshäuser, Gernot, Veronika Auner, Eva Schuster, Barbara Holzer, Christian Oberkanins, Reinhard Horvat, Paul Speiser, and Robert Zeillinger. "KRAS mutation analysis in genomic DNA isolated from formalin-fixed paraffin-embedded ovarian tissue: evaluation of a strip-based reverse-hybridisation assay." Journal of Clinical Pathology 64, no. 3 (January 22, 2011): 252–56. http://dx.doi.org/10.1136/jcp.2010.081414.

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AimsTo evaluate a reverse-hybridisation assay (strip assay) designed for the sensitive detection of 10 mutations in codons 12 and 13 of the KRAS gene. The strip assay relies on mutant-enriched PCR followed by reverse-hybridisation of biotinylated amplification products to oligonucleotide probes immobilised as an array of parallel lines on nitrocellulose test strips.MethodsThe strip assay was used to analyse genomic DNA isolated from 120 formalin-fixed paraffin-embedded (FFPE) ovarian tissue samples. The samples were analysed in parallel using a biochip-based protocol (biochip assay) covering the same mutation spectrum, and results were compared with respect to sensitivity, specificity and operational input.ResultsThe strip assay identified 19 (16%) of 120 FFPE samples to carry a KRAS mutation; results were in agreement with those obtained by biochip hybridisation. Both assays had an analytical sensitivity of 1% when performed on FFPE-extracted DNA with approximately the same operational input needed for post-PCR processing. In contrast to the biochip assay, strip assay hybridisation may be automated to a large extent.ConclusionsThe strip assay is an accurate and sensitive tool for the low to medium throughput detection of KRAS mutation in genomic DNA isolated from FFPE tissue.

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Ohguri, T. "Cytogenetic analysis of myxoid liposarcoma and myxofibrosarcoma by array-based comparative genomic hybridisation." Journal of Clinical Pathology 59, no. 9 (September 1, 2006): 978–83. http://dx.doi.org/10.1136/jcp.2005.034942.

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Lall, Meena, Pushpa Saviour, Ratna Puri, Preeti Paliwal, Surbhi Mahajan, and Ishwar Verma. "Combined classical cytogenetics and array Comparative Genomic Hybridisation for genomic copy number analysis." Molecular Cytogenetics 7, Suppl 1 (2014): P3. http://dx.doi.org/10.1186/1755-8166-7-s1-p3.

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Kawanishi, H., T. Takahashi, M. Ito, Y. Matsui, J. Watanabe, N. Ito, T. Kamoto, et al. "Genetic analysis of multifocal superficial urothelial cancers by array-based comparative genomic hybridisation." British Journal of Cancer 97, no. 2 (June 19, 2007): 260–66. http://dx.doi.org/10.1038/sj.bjc.6603850.

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Weiss, M. M. "Genome wide array comparative genomic hybridisation analysis of premalignant lesions of the stomach." Molecular Pathology 56, no. 5 (October 1, 2003): 293–98. http://dx.doi.org/10.1136/mp.56.5.293.

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McMahon, Colin J., Conall T. Morgan, and Marie T. Greally. "Chromosome 22q11.21 microduplication in association with hypoplastic left heart syndrome with hypoplastic pulmonary arteries." Cardiology in the Young 25, no. 1 (January 22, 2014): 167–70. http://dx.doi.org/10.1017/s104795111300231x.

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AbstractWe describe a case of a baby girl born with hypoplastic left heart syndrome consisting of mitral atresia, aortic atresia, hypoplastic ascending aorta, and left ventricle. The pulmonary arteries were hypoplastic, measuring 3 mm. Fluorescence in situ hybridisation analysis demonstrated a microduplication of chromosome 22q11.2. Subsequent array comparative genomic hybridisation showed a gain of 2.3 Mb in one copy of chromosome 22q at band 22q11.21. The proband underwent a successful Norwood procedure with Sano shunt and subsequently underwent bi-directional Glenn shunt and Fontan procedure. This report highlights the association between hypoplastic left heart syndrome with hypoplastic pulmonary arteries and chromosome 22q11.21 microduplication.

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Forster, T., D. Roy, and P. Ghazal. "Experiments using microarray technology: limitations and standard operating procedures." Journal of Endocrinology 178, no. 2 (August 1, 2003): 195–204. http://dx.doi.org/10.1677/joe.0.1780195.

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Microarrays are a powerful method for the global analysis of gene or protein content and expression, opening up new horizons in molecular and physiological systems. This review focuses on the critical aspects of acquiring meaningful data for analysis following fluorescence-based target hybridisation to arrays. Although microarray technology is adaptable to the analysis of a range of biomolecules (DNA, RNA, protein, carbohydrates and lipids), the scheme presented here is applicable primarily to customised DNA arrays fabricated using long oligomer or cDNA probes. Rather than provide a comprehensive review of microarray technology and analysis techniques, both of which are large and complex areas, the aim of this paper is to provide a restricted overview, highlighting salient features to provide initial guidance in terms of pitfalls in planning and executing array projects. We outline standard operating procedures, which help streamline the analysis of microarray data resulting from a diversity of array formats and biological systems. We hope that this overview will provide practical initial guidance for those embarking on microarray studies.

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Chua, E. W., S. Cree, M. L. Barclay, K. Doudney, K. Lehnert, A. Aitchison, and M. A. Kennedy. "Exome sequencing and array-based comparative genomic hybridisation analysis of preferential 6-methylmercaptopurine producers." Pharmacogenomics Journal 15, no. 5 (March 10, 2015): 414–21. http://dx.doi.org/10.1038/tpj.2015.9.

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Santos, Marta, Patrícia Dias-Pereira, Christina Williams, Carlos Lopes, and Matthew Breen. "Malignant canine mammary tumours: Preliminary genomic insights using oligonucleotide array comparative genomic hybridisation analysis." Veterinary Journal 222 (April 2017): 68–71. http://dx.doi.org/10.1016/j.tvjl.2017.03.005.

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Lundén, K., M. Eklund, R. Finlay, J. Stenlid, and F. O. Asiegbu. "Heterologous array analysis in Heterobasidion: Hybridisation of cDNA arrays with probe from mycelium of S, P or F-types." Journal of Microbiological Methods 75, no. 2 (October 2008): 219–24. http://dx.doi.org/10.1016/j.mimet.2008.06.014.

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Karimpour-Fard, Anis, Laura Dumas, Tzulip Phang, James M. Sikela, and Lawrence E. Hunter. "A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation." Human Genomics 4, no. 6 (2010): 421. http://dx.doi.org/10.1186/1479-7364-4-6-421.

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Robson, Stephen C., Lyn S. Chitty, Stephen Morris, Talitha Verhoef, Gareth Ambler, Diana G. Wellesley, Ruth Graham, Claire Leader, Jane Fisher, and John A. Crolla. "Evaluation of Array Comparative genomic Hybridisation in prenatal diagnosis of fetal anomalies: a multicentre cohort study with cost analysis and assessment of patient, health professional and commissioner preferences for array comparative genomic hybridisation." Efficacy and Mechanism Evaluation 4, no. 1 (February 2017): 1–104. http://dx.doi.org/10.3310/eme04010.

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BackgroundCurrent pathways for testing fetuses at increased risk of a chromosomal anomaly because of an ultrasound anomaly involve karyotyping after rapid aneuploidy exclusion. Chromosomal microarray (CMA) may detect more clinically significant chromosomal imbalances than karyotyping but evidence to guide UK health service providers on whether or not CMA should replace karyotyping is limited.Objectives(1) To compare detection rates of copy number variants (CNVs) and laboratory turnaround times (TATs) by karyotyping and CMA in fetuses with ultrasound anomalies, (2) to calculate test costs and the cost per additional pathogenic CNV detected by CMA relative to karyotyping and (3) to determine what factors influence parents’ and health professionals’ choice and decision-making about CMA.DesignA multicentre experimental research cohort study with an additional cost analysis.SettingA total of 20 fetal medicine units and nine cytogenetic laboratories across England and Wales.ParticipantsWomen with a fetus undergoing quantitative fluorescent polymerase chain reaction (QF-PCR) and karyotyping for clinical indications with (1) one or more structural anomalies identified on ultrasound or (2) an isolated nuchal translucency (NT) of ≥ 3.5 mm.InterventionsKaryotyping and CMA after exclusion of major chromosomal anomalies by QF-PCR. The array design consisted of 8-plex 60,000 60-mer oligonucleotides with a backbone resolution of ≈75 kb.Main outcome measuresRates of abnormal karyotypes and pathogenic CNVs and variants of unknown significance on CMA. Laboratory TATs for karyotyping and CMA. Costs of karyotyping and CMA and cost per additional pathogenic CNV detected by CMA. Parent and health professional attitudes to CMA.ResultsOut of the 1718 probands recruited, 1123 cases with normal QF-PCR and both karyotype and CMA were available for analysis. In the group with structural anomalies (n = 629), CMA detected more CNVs [6.8%, 95% confidence interval (CI) 4.4% to 9.3%] and more pathogenic CNVs (3.5%, 95% CI 1.5% to 5.5%) than karyotyping. In the increased NT group (n = 494), CMA detected more CNVs (4.5%, 95% CI 1.8% to 7.1%) than karyotyping but not more pathogenic CNVs. Compared with karyotyping, median TAT was 3 days [interquartile range (IQR) 0–13 days] longer with CMA but when actual set-up to reporting times were compared, CMA was 5 days (IQR 2–8 days) quicker. Cost calculations of the respective pathways indicated that, per patient, CMA is on average £113 more costly than karyotyping. The incremental cost per extra pathogenic CNV detected by CMA was greater in the increased NT than the structural anomaly group (£9439 vs. £3635). Qualitative evaluation suggested that parents find CMA acceptable, despite the uncertainties it may introduce, and that in the main it is acceptable to health professionals and commissioners.ConclusionsCMA is a robust, acceptable and probably cost-effective method to detect more clinically significant chromosomal imbalances in the anomalous fetus. The results suggest that CMA should replace karyotyping in these care pathways.Future workThe application of CMA (and exome sequencing) on cell-free DNA in maternal plasma.Trial registrationCurrent Controlled Trials ISRCTN01058191.FundingThis project was funded by the Efficacy and Mechanism Evaluation programme, a MRC and NIHR partnership. The funder had no role in the identification, design and conduct of the study and the reporting of the analysis. The funder did recommend the inclusion of the cell-free DNA aspects of the EACH study. Funding was also received from the Great Ormond Street Biomedical Research Centre.

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Hallor, K. H., J. Staaf, G. Jönsson, M. Heidenblad, F. Vult von Steyern, H. C. F. Bauer, M. IJszenga, et al. "Frequent deletion of the CDKN2A locus in chordoma: analysis of chromosomal imbalances using array comparative genomic hybridisation." British Journal of Cancer 98, no. 2 (December 11, 2007): 434–42. http://dx.doi.org/10.1038/sj.bjc.6604130.

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Sirard, Marc-André, Isabelle Dufort, Maud Vallée, Lyne Massicotte, Catherine Gravel, Hélène Reghenas, Andrew J. Watson, W. Allan King, and Claude Robert. "Potential and limitations of bovine-specific arrays for the analysis of mRNA levels in early development: preliminary analysis using a bovine embryonic array." Reproduction, Fertility and Development 17, no. 2 (2005): 47. http://dx.doi.org/10.1071/rd04113.

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New insights into the early development of large mammals are becoming available through the measurement of differential mRNA levels in oocytes and preimplantation embryos. These advances in knowledge are rapidly picking up in pace, mainly owing to the advantages brought by new molecular biology approaches being developed. The possibility of amplifying the starting material and therefore making measurements in single embryo units is now feasible. With these tools, the evaluation of variations in gene expression patterns during the preimplantation period or the impact of culture on mRNA levels is now possible. However, it is important to keep in mind that these methods still have limitations associated with sample preparation or the use of the appropriate controls. Even proper methods of analysis are very important to achieve the full benefit of the application of these tools. The present paper describes some of the potential, as well as limitations, of mRNA level analysis in early embryos, especially for microarray analysis. We have generated a bovine cDNA array (>2000 clones) that contains expressed sequence tags (ESTs) collected from various preimplantation development stages. Using this chip, we have initiated the characterisation of global mRNA level patterns of several key developmental stages from the immature oocyte to the blastocyst stage. As expected, the hybridisation results indicate very different expression profiles involving hundreds of genes when comparing oocyte and blastocyst samples to a reference mRNA sample made from a pool of ESTs from pooled somatic tissues. Although this array is still in its preliminary stage and the EST bank has not been processed to contain only unigenes, it is already a very useful tool for discovering candidate genes that may play important roles during early embryonic life.

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Bersinger, Nick A., Markus Eisenhut, Petra Stute, and Michael von Wolff. "Gonadotropin Stimulation Has Only a Limited Effect on the Concentration of Follicular Fluid Signalling Proteins: An Antibody Array Analysis." International Journal of Reproductive Medicine 2021 (January 27, 2021): 1–7. http://dx.doi.org/10.1155/2021/2906164.

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Objective. The follicular fluid (FF) plays an essential role in the physiology of the follicle and the oocyte. Gonadotropin stimulation affects the FF steroid hormone and anti-Mullerian hormone (AMH) concentrations, which has been suggested to be the reason for lower oocyte competence in conventional gonadotropin stimulated in vitro fertilisation (cIVF) compared to natural cycle IVF (NC-IVF). To analyse the effect of gonadotropin stimulation on a broad spectrum of signalling proteins, we ran proteomic antibody arrays on FF of women undergoing both treatments NC-IVF and cIVF. Method. Twenty women underwent one NC-IVF and one cIVF treatment cycle. Follicular fluids of the first aspirated follicle were compared between the two groups using a protein microarray which included antibodies against 224 proteins related to cell signalling and reference proteins. Each of the 40 albumin-stripped, matched-pair samples was labelled in the reverse-dye (Cy3/Cy5) procedure before undergoing array hybridisation. Signal analysis was performed using normalisation algorithms in dedicated software. Five proteins yielding a value of P < 0.05 in the array experiment (Cystatin A, Caspase-3, GAD65/67, ERK-1, and ERK-2) were then submitted to quantitative determination by ELISA in the same follicular fluids. Results. Array analysis yielded only a small number of differentially expressed signalling markers by unadjusted P values. Adjustment as a consequence of multiple determinations resulted in the absence of any significant differential marker expression on the array. Five unadjusted differentially expressed proteins were quantified immunometrically with antibodies from different sources. Follicular fluid concentrations of Cystatin A and MAP kinase ERK-1 concentrations were significantly higher in the cIVF than in the NC-IVF follicles, while GAD-2 (GAD65/67) did not differ. The assays for Caspase-3 and MAP kinase ERK-2 did not have the required sensitivities. Conclusion. In contrast to FF steroid hormones and AMH, FF concentrations of signalling proteins are not or only marginally altered by gonadotropin stimulation.

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Roberts, Ian, Stephanie A. Carter, Cinzia G. Scarpini, Konstantina Karagavriilidou, Jenny C. J. Barna, Mark Calleja, and Nicholas Coleman. "A High-Throughput Computational Framework for Identifying Significant Copy Number Aberrations from Array Comparative Genomic Hybridisation Data." Advances in Bioinformatics 2012 (September 13, 2012): 1–12. http://dx.doi.org/10.1155/2012/876976.

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Reliable identification of copy number aberrations (CNA) from comparative genomic hybridization data would be improved by the availability of a generalised method for processing large datasets. To this end, we developed swatCGH, a data analysis framework and region detection heuristic for computational grids. swatCGH analyses sequentially displaced (sliding) windows of neighbouring probes and applies adaptive thresholds of varying stringency to identify the 10% of each chromosome that contains the most frequently occurring CNAs. We used the method to analyse a published dataset, comparing data preprocessed using four different DNA segmentation algorithms, and two methods for prioritising the detected CNAs. The consolidated list of the most commonly detected aberrations confirmed the value of swatCGH as a simplified high-throughput method for identifying biologically significant CNA regions of interest.

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Nakamura, Akie, Koji Muroya, Hiroko Ogata-Kawata, Kazuhiko Nakabayashi, Keiko Matsubara, Tsutomu Ogata, Kenji Kurosawa, Maki Fukami, and Masayo Kagami. "A case of paternal uniparental isodisomy for chromosome 7 associated with overgrowth." Journal of Medical Genetics 55, no. 8 (February 17, 2018): 567–70. http://dx.doi.org/10.1136/jmedgenet-2017-104986.

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BackgroundPaternal uniparental disomy for chromosome 7 (upd(7)pat) is extremely rare, and only four cases have been previously reported. As these cases were accompanied by autosomal-recessive disorders which are likely to be involved in growth restriction, the relevance of upd(7)pat to the overgrowth phenotype remains unclear. Here we describe one case of upd(7)pat with no additional genetic diseases, which may answer the question.MethodsA 5-year-old Japanese boy presented with a tall stature of unknown causes. To detect the genetic cause of the tall stature, we performed Sanger sequencing, targeted resequencing, comparative genomic hybridisation and single-nucleotide polymorphism (SNP) array analyses, methylation analysis and microsatellite analysis.ResultsWe could not detect pathogenic variants in causative genes for overgrowth syndrome or apparent copy number alterations. DNA methylation analysis revealed hypomethylation at the GRB10, PEG1 and PEG10 differentially methylated regions. SNP array and microsatellite analyses suggested paternal uniparental isodisomy for chromosome 7. Furthermore, we could not identify homozygous mutations of known causative genes for inherited disorders on chromosome 7.ConclusionWe report the first case of upd(7)pat with an overgrowth phenotype.

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Sun, Lijuan, Qingqing Wu, Shi-Wen Jiang, Yani Yan, Xin Wang, Juan Zhang, Yan Liu, Ling Yao, Yuqing Ma, and Li Wang. "Prenatal Diagnosis of Central Nervous System Anomalies by High-Resolution Chromosomal Microarray Analysis." BioMed Research International 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/426379.

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The aims of this study were to evaluate the contribution of chromosomal microarray analysis (CMA) in the prenatal diagnosis of fetuses with central nervous system (CNS) anomalies but normal chromosomal karyotype. A total of 46 fetuses with CNS anomalies with or without other ultrasound anomalies but normal karyotypes were evaluated by array-based comparative genomic hybridisation (aCGH) or single-nucleotide polymorphism (SNP) array. The result showed that CNVs were detected in 17 (37.0%) fetuses. Of these, CNVs identified in 5 (5/46, 10.9%) fetuses were considered to be likely pathogenic, and CNVs detected in 3 (3/46, 6.5%) fetuses were defined as being of uncertain clinical significance. Fetuses with CNS malformations plus other ultrasound anomalies had a higher rate of pathogenic CNVs than those with isolated CNS anomalies (13.6% versus 8.3%), but there was no significant difference (Fisher’s exact test,P>0.05). Pathogenic CNVs were detected most frequently in fetuses with Dandy-Walker syndrome (2/6, 33.3%) when compared with other types of neural malformations, and holoprosencephaly (2/7, 28.6%) ranked the second. CMA is valuable in prenatal genetic diagnosis of fetuses with CNS anomalies. It should be considered as part of prenatal diagnosis in fetuses with CNS malformations and normal karyotypes.

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Somenzi, Elisa, Paolo Ajmone-Marsan, and Mario Barbato. "Identification of Ancestry Informative Marker (AIM) Panels to Assess Hybridisation between Feral and Domestic Sheep." Animals 10, no. 4 (March 30, 2020): 582. http://dx.doi.org/10.3390/ani10040582.

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Hybridisation of wild populations with their domestic counterparts can lead to the loss of wildtype genetic integrity, outbreeding depression, and loss of adaptive features. The Mediterranean island of Sardinia hosts one of the last extant autochthonous European mouflon (Ovis aries musimon) populations. Although conservation policies, including reintroduction plans, have been enforced to preserve Sardinian mouflon, crossbreeding with domestic sheep has been documented. We identified panels of single nucleotide polymorphisms (SNPs) that could act as ancestry informative markers able to assess admixture in feral x domestic sheep hybrids. The medium-density SNP array genotyping data of Sardinian mouflon and domestic sheep (O. aries aries) showing pure ancestry were used as references. We applied a two-step selection algorithm to this data consisting of preselection via Principal Component Analysis followed by a supervised machine learning classification method based on random forest to develop SNP panels of various sizes. We generated ancestry informative marker (AIM) panels and tested their ability to assess admixture in mouflon x domestic sheep hybrids both in simulated and real populations of known ancestry proportions. All the AIM panels recorded high correlations with the ancestry proportion computed using the full medium-density SNP array. The AIM panels proposed here may be used by conservation practitioners as diagnostic tools to exclude hybrids from reintroduction plans and improve conservation strategies for mouflon populations.

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Heyning, F. H., P. M. Jansen, P. C. W. Hogendoorn, and K. Szuhai. "Array-based comparative genomic hybridisation analysis reveals recurrent chromosomal alterations in primary diffuse large B cell lymphoma of bone." Journal of Clinical Pathology 63, no. 12 (October 20, 2010): 1095–100. http://dx.doi.org/10.1136/jcp.2010.078915.

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Cui, Yushan, Yang Liu, Danyang Wang, Yuzhang Liu, Lina Liu, and Baijun Fang. "Comparative Analysis of miRNA Expression Profiles of Multiple Myeloma with 1q21 Gains and Normal FISH." Acta Haematologica 139, no. 2 (2018): 96–100. http://dx.doi.org/10.1159/000486662.

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Background: Multiple myeloma (MM) with 1q21 gains invariably has a poor prognosis. Many recent studies have reported the relationship between micro (mi)RNA expression and MM prognosis. However, there is little information on the association between miRNA alterations and 1q21 gains. Methods: We compared the miRNA expression profiles of MM with 1q21 gains and MM with normal fluorescence in situ hybridisation (FISH) by gene expression array. Differentially expressed miRNAs were identified using Affymetrix TAC software. Thresholds were defined as a false discovery rate <0.05, p value <0.05, and n-fold change >2. Results: Six miRNAs (let-7f-5p and -7g-5p, and miR-29a-3p, -29b-1-5p, -331-3p, and -223-3p) were downregulated and 4 (miR-30e-5p, -17-3p, -18b-5p, and -19a-3p) were upregulated in MM with 1q21 gains relative to MM with normal FISH. Conclusions: The identified set of miRNAs can serve as biomarkers for distinguishing MM with 1q21 gains from MM with normal FISH.

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Hillman, S., S. Pretlove, A. Coomarasamy, D. McMullan, E. Davison, E. Maher, and M. Kilby. "Additional information from array comparative genomic hybridisation technology over conventional karyotyping in prenatal diagnosis-a systematic review and meta-analysis." Archives of Disease in Childhood - Fetal and Neonatal Edition 95, Supplement 1 (June 1, 2010): Fa4. http://dx.doi.org/10.1136/adc.2010.192310.1.1.

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Guemann, Anne-Sophie, Joris Andrieux, Florence Petit, Emmanuel Halimi, Sonia Bouquillon, Sylvie Manouvrier-Hanu, Jiddeke Van De Kamp, et al. "ELN gene triplication responsible for familial supravalvular aortic aneurysm." Cardiology in the Young 25, no. 4 (June 17, 2014): 712–17. http://dx.doi.org/10.1017/s1047951114000766.

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AbstractSupravalvular aortic aneurysms are less frequent than abdominal ones. Among Supravalvular aortic aneurysm aetiologies, we focused on dystrophic lesions as they can be secondary to genetic causes such as elastin anomaly. We report on a familial 7q11.23 triplication – including the ELN gene – segregating with a supravalvular aortic aneurysm. During her first pregnancy, our index patient was diagnosed with tuberous sclerosis and with a Supravalvular aortic aneurysm. The foetus was affected equally. For the second pregnancy, parents applied for preimplantation diagnosis, and a subsequent prenatal diagnosis was offered to the couple, comprising TSC1 molecular analysis, karyotype, and multiplex ligation probe amplification. TSC1 mutation was not found on foetal deoxyribo nucleic acid. Foetal karyotype was normal, but multiplex ligation probe amplification detected a 7q11.23 duplication. Quantitative-polymerase chain reaction and array-comparative genomic hybridisation carried out to further assess this chromosome imbalance subsequently identified a 7q11.23 triplication involving ELN and LIMK1. Foetal heart ultrasound identified a Supravalvular aortic aneurysm. A familial screening was offered for the 7q11.23 triplication and, when found, heart ultrasound was performed. The triplication was diagnosed in our index case as well as in her first child. Of the 17 individuals from this family, 11 have the triplication. Of the 11 individuals with the triplication, 10 were identified to have a supravalvular aortic aneurysm. Of them, two individuals received a medical treatment and one individual needed surgery. We provide evidence of supravalvular aortic aneurysm segregating with 7q11.23 triplication in this family. We would therefore recommend cardiac surveillance for individuals with 7q11.23 triplication. It would also be interesting to offer a quantitative-polymerase chain reaction or an array-comparative genomic hybridisation to a larger cohort of patients presenting with isolated supravalvular aortic aneurysm, as it may provide further information.

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Pryor, LD, ER Williams, and BV Gunn. "A morphometric analysis of Eucalyptus urophylla and related taxa with descriptions of two new species." Australian Systematic Botany 8, no. 1 (1995): 57. http://dx.doi.org/10.1071/sb9950057.

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Over 400 specimens from 26 locations, mainly in the Lesser Sunda Islands and some from New Guinea and northern Cape York, were examined. These were representative of an array of forms ordinarily assigned to Eucalyptus urophylla, E. pellita and an undescribed species as well as those considered by some to be hybrid between E. alba and E. urophylla. The latter has long been considered to show considerable polymorphism. Re-examination of the available material and records suggest that interspecific hybridisation is not significantly involved in this variability. Although this examination pointed to the existence of some differentiation at the level of species in this array, there was still a core of material which could not be separated readily into subgroups. Measurements were taken of selected floral and foliar morphological features which were then subject to statistical analysis to ascertain if subgroups were discernible on this basis. As a result, the separation of two species, Eucalyptus orophila sp. nov. and Eucalyptus wetarensis sp. nov. from Eucalyptus urophylla sensu lato in the Lesser Sunda Islands, is supported. The related populations called species A by Pinyopusarerk et al. (1993), from New Guinea and northern Cape York, were to a somewhat lesser extent separated on these criteria. These results were paralleled by evidence from seedling morphology and oil characteristics. Isozyme analysis gave a similar grouping for the material from Wetar, but did not indicate other separations from the core E. urophylla.

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Bianco, Bianca, Denise Maria Christofolini, Gabriel Seixas Conceição, and Caio Parente Barbosa. "Preimplantation genetic diagnosis associated to Duchenne muscular dystrophy." Einstein (São Paulo) 15, no. 4 (September 21, 2017): 489–91. http://dx.doi.org/10.1590/s1679-45082017rc3994.

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ABSTRACT Duchenne muscular dystrophy is the most common muscle disease found in male children. Currently, there is no effective therapy available for Duchenne muscular dystrophy patients. Therefore, it is essential to make a prenatal diagnosis and provide genetic counseling to reduce the birth of such boys. We report a case of preimplantation genetic diagnosis associated with Duchenne muscular dystrophy. The couple E.P.R., 38-year-old, symptomatic patient heterozygous for a 2 to 47 exon deletion mutation in DMD gene and G.T.S., 39-year-old, sought genetic counseling about preimplantation genetic diagnosis process. They have had a 6-year-old son who died due to Duchenne muscular dystrophy complications. The couple underwent four cycles of intracytoplasmic sperm injection (ICSI) and eight embryos biopsies were analyzed by polymerase chain reaction (PCR) for specific mutation analysis, followed by microarray-based comparative genomic hybridisation (array CGH) for aneuploidy analysis. Preimplantation genetic diagnosis revealed that two embryos had inherited the maternal DMD gene mutation, one embryo had a chromosomal alteration and five embryos were normal. One blastocyst was transferred and resulted in successful pregnancy. The other embryos remain vitrified. We concluded that embryo analysis using associated techniques of PCR and array CGH seems to be safe for embryo selection in cases of X-linked disorders, such as Duchenne muscular dystrophy.

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Unger, Kristian, Johannes Wienberg, Andrew Riches, Ludwig Hieber, Axel Walch, Andreas Brown, Patricia C. M. O'Brien, et al. "Novel gene rearrangements in transformed breast cells identified by high-resolution breakpoint analysis of chromosomal aberrations." Endocrine-Related Cancer 17, no. 1 (March 2010): 87–98. http://dx.doi.org/10.1677/erc-09-0065.

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Chromosomal copy number alterations and chromosomal rearrangements are frequent mutations in human cancer. Unlike copy number alterations, little is known about the role and occurrence of chromosomal rearrangements in breast cancer. This may be due to the fact that chromosome-based breakpoint analysis is widely restricted to cultured cells. In order to identify gene rearrangements in breast cancer, we studied the chromosomal breakpoints in radiation-transformed epithelial breast cell lines using a high-resolution array-based approach using 1 Mb bacterial artificial chromosome (BAC) arrays. The breakpoints were further narrowed down by fluorescence in situ hybridisation (FISH) with clones from the 32 k BAC library. The analysis of the cell lines B42-11 and B42-16 revealed rearrangements of chromosomes 7, 8, 10 and 12. We identified the genes Has2, Grid1, Ret, Cpm, Tbx3, Tbx5, Tuba1a, Wnt1 and Arf3 within the breakpoint regions. Quantitative RT-PCR showed a deregulated expression of all of these candidate genes except for Tbx5 and Tbx3. This is the first study demonstrating gene rearrangements and their deregulated mRNA expression in radiation-transformed breast cells. Since the gene rearrangements occurred in the transformed and tumourigenic cell lines only, it is likely that these were generated in conjunction with malignant transformation of the epithelial breast cells and therefore might reflect early molecular events in breast carcinogenesis. Initial studies indicate that these gene alterations are also found in sporadic breast cancers.

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Carvalho, Beatriz, Tineke E. Buffart, Rui M. Reis, Thomas Mons, Cátia Moutinho, Paula Silva, Nicole C. T. van Grieken, et al. "Mixed Gastric Carcinomas Show Similar Chromosomal Aberrations in Both their Diffuse and Glandular Components." Analytical Cellular Pathology 28, no. 5-6 (January 1, 2006): 283–94. http://dx.doi.org/10.1155/2006/650620.

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Gastric cancer is one of the most frequent malignancies in the world. Nonetheless, the knowledge of the molecular events involved in the development of gastric carcinoma is far from complete. One of the hallmarks of gastric cancer is chromosomal instability resulting in abnormal DNA copy number changes throughout the genome. Mixed gastric carcinomas constitute a rare histological entity, containing the two main histological phenotypes (diffuse and intestinal). Very little is known about the underlying mechanisms of phenotypic divergence in these mixed tumours. To the best of our knowledge only E-Cadherin mutations were implicated so far in the divergence of these tumours and nothing is known about the involvement of chromosome copy number changes in the two divergent histological components. In this study, we compared the DNA copy number changes, in the two different components (diffuse and intestinal) of mixed gastric carcinomas by microarray – comparative genomic hybridisation (array CGH). The analysis of 12 mixed gastric carcinomas showed no significant differences in array CGH profiles between the diffuse and intestinal components of mixed carcinomas. This supports the idea that the phenotypic divergence within mixed gastric carcinomas is not caused by DNA chromosomal aberrations.

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van Zijll de Jong, Eline, Kathryn M. Guthridge, German C. Spangenberg, and John W. Forster. "Sequence Analysis of SSR-Flanking Regions Identifies Genome Affinities between Pasture Grass Fungal Endophyte Taxa." International Journal of Evolutionary Biology 2011 (January 12, 2011): 1–11. http://dx.doi.org/10.4061/2011/921312.

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Fungal species of the Neotyphodium and Epichloë genera are endophytes of pasture grasses showing complex differences of life-cycle and genetic architecture. Simple sequence repeat (SSR) markers have been developed from endophyte-derived expressed sequence tag (EST) collections. Although SSR array size polymorphisms are appropriate for phenetic analysis to distinguish between taxa, the capacity to resolve phylogenetic relationships is limited by both homoplasy and heteroploidy effects. In contrast, nonrepetitive sequence regions that flank SSRs have been effectively implemented in this study to demonstrate a common evolutionary origin of grass fungal endophytes. Consistent patterns of relationships between specific taxa were apparent across multiple target loci, confirming previous studies of genome evolution based on variation of individual genes. Evidence was obtained for the definition of endophyte taxa not only through genomic affinities but also by relative gene content. Results were compatible with the current view that some asexual Neotyphodium species arose following interspecific hybridisation between sexual Epichloë ancestors. Phylogenetic analysis of SSR-flanking regions, in combination with the results of previous studies with other EST-derived SSR markers, further permitted characterisation of Neotyphodium isolates that could not be assigned to known taxa on the basis of morphological characteristics.

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Solomon, N. M. "Array comparative genomic hybridisation analysis of boys with X linked hypopituitarism identifies a 3.9 Mb duplicated critical region at Xq27 containing SOX3." Journal of Medical Genetics 41, no. 9 (September 1, 2004): 669–78. http://dx.doi.org/10.1136/jmg.2003.016949.

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Solomon, N. M., S. A. Ross, S. M. Forrest, P. Q. Thomas, T. Morgan, J. L. Belsky, F. A. Hol, et al. "Array comparative genomic hybridisation analysis of boys with X-linked hypopituitarism identifies a 3.9 Mb duplicated critical region at Xq27 containing SOX3." Journal of Medical Genetics 44, no. 4 (April 1, 2007): e75-e75. http://dx.doi.org/10.1136/jmg.2007.049049.

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38

Aston, E., H. Whitby, T. Maxwell, N. Glaus, B. Cowley, D. Lowry, X. L. Zhu, B. Issa, S. T. South, and A. R. Brothman. "Comparison of targeted and whole genome analysis of postnatal specimens using a commercially available array based comparative genomic hybridisation (aCGH) microarray platform." Journal of Medical Genetics 45, no. 5 (January 4, 2008): 268–74. http://dx.doi.org/10.1136/jmg.2007.055319.

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Goh, X. Y., J. R. E. Rees, A. L. Paterson, S. F. Chin, J. C. Marioni, V. Save, M. O'Donovan, et al. "Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma." Gut 60, no. 10 (April 8, 2011): 1317–26. http://dx.doi.org/10.1136/gut.2010.234179.

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40

Varma, G., R. Varma, H. Huang, A. Pryshchepava, J. Groth, D. Fleming, N. J. Nowak, et al. "Array comparative genomic hybridisation (aCGH) analysis of premenopausal breast cancers from a nuclear fallout area and matched cases from Western New York." British Journal of Cancer 93, no. 6 (September 2005): 699–708. http://dx.doi.org/10.1038/sj.bjc.6602784.

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41

Esoof, Noor, Aristoteles Giagounidis, Mario Cazzola, Luca Malcovati, Carlo Aul, Andrea Pellagatti, Carrie Fidler, et al. "High-Resolution Genomic Profiling of Myelodysplasia (MDS) by Microarray Comparative Genomic Hybridization (CGH)." Blood 108, no. 11 (November 16, 2006): 2645. http://dx.doi.org/10.1182/blood.v108.11.2645.2645.

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Abstract Myelodysplasia (MDS) is a heterogeneous group of clonal disorders of hematopoietic stem cells characterised by ineffective hematopoiesis and a variable risk of transformation to acute myelogenous leukaemia. We have used Comparative Genomic Hybridisation (CGH) microarray analysis, a technology that represents a significant improvement in resolution over conventional cytogenetic analysis, to screen genomic DNA from MDS patients for the identification of genome-wide Copy-Number Changes (CNCs). We have studied genomic DNA obtained from the neutrophil population of 48 MDS patients and 40 normal controls. Of the 48 MDS patients 10 had the 5q- syndrome, 32 were assigned normal karyotype and 6 had complex karyotypes. Comparative Genomic Hybridisation (CGH) microarray analysis was performed using microarrays containing 3500 BAC clones at 1Mb intervals over the whole human genome. Furthermore we used a whole genome tiling-path (27 000 overlapping BAC clones) array to profile 9 5q-syndrome patients and for 3 of those patients the T-cell DNA were also profiled to act as constitutional control. The patient DNA and a pool of normal reference DNA was labelled with different fluorochromes and cohybridised to the microarray. The normalised ratio of signal intensities was calculated and log2 ratios between −0.4 and 0.4 were considered normal. Ratios below or above the normal range were interpreted as loss or gain of genetic material, respectively. The deletions on chromosome 5q were precisely mapped by array-CGH in the patients with the 5q- syndrome but no additional CNCs were detected. One of the 5q deletions, however, displayed a discontiguous pattern with the tiling resolution array. Copy-number changes (CNCs) that escaped conventional cytogenetic detection were identified in the MDS patients originally reported with normal bone marrow karyotypes. 8 out of those 32 patients displayed CNCs that were not detected in the 40 normal controls and as such were considered as disease-related changes (non-polymorphic). Many of those CNCs were single-clone abberrations that were validated by dye-swap experiments and some were confirmed by quantitative PCR. Microarray CGH data confirmed all abnormalities reported by conventional cytogenetic analysis in the MDS patients with complex karyotypes and previously undetected abnormalities were uncovered. Several genes involved in either the initiation or progression of hematological malignancies are known to map within the cryptic abnormalities identified in the patients studied. For example, one patient with an apparently normal karyotype showed a small deletion at 17q11 which encompasses the NF1 gene. Further work will determine whether particular abnormalities detected by microarray CGH are recurrent and the nature of the genes involved. However, the promise of microarray CGH in the diagnostic work up of MDS particularly in those patients with normal karyotypes is clear.

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Zeng, Sheng, Mei-yun Zhang, Xue-jing Wang, Zheng-mao Hu, Jin-chen Li, Nan Li, Jun-ling Wang, et al. "Long-read sequencing identified intronic repeat expansions inSAMD12from Chinese pedigrees affected with familial cortical myoclonic tremor with epilepsy." Journal of Medical Genetics 56, no. 4 (September 7, 2018): 265–70. http://dx.doi.org/10.1136/jmedgenet-2018-105484.

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BackgroundThe locus for familial cortical myoclonic tremor with epilepsy (FCMTE) has long been mapped to 8q24 in linkage studies, but the causative mutations remain unclear. Recently, expansions of intronic TTTCA and TTTTA repeat motifs withinSAMD12were found to be involved in the pathogenesis of FCMTE in Japanese pedigrees. We aim to identify the causative mutations of FCMTE in Chinese pedigrees.MethodsWe performed genetic linkage analysis by microsatellite markers in a five-generation Chinese pedigree with 55 members. We also used array-comparative genomic hybridisation (CGH) and next-generation sequencing (NGS) technologies (whole-exome sequencing, capture region deep sequencing and whole-genome sequencing) to identify the causative mutations in the disease locus. Recently, we used low-coverage (~10×) long-read genome sequencing (LRS) on the PacBio Sequel and Oxford Nanopore platforms to identify the causative mutations, and used repeat-primed PCR for validation of the repeat expansions.ResultsLinkage analysis mapped the disease locus to 8q23.3–24.23. Array-CGH and NGS failed to identify causative mutations in this locus. LRS identified the intronic TTTCA and TTTTA repeat expansions inSAMD12as the causative mutations, thus corroborating the recently published results in Japanese pedigrees.ConclusionsWe identified the pentanucleotide repeat expansion inSAMD12as the causative mutation in Chinese FCMTE pedigrees. Our study also suggested that LRS is an effective tool for molecular diagnosis of genetic disorders, especially for neurological diseases that cannot be positively diagnosed by conventional clinical microarray and NGS technologies.

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Raghavan, Manoj, Debra Lillington, Spyros Skoulakis, Silvana Debernardi, Tracy Chaplin, Nicola J. Foot, T. Andrew Lister, and Bryan D. Young. "Genome Wide SNP Analysis Reveals Frequent Uniparental Disomy (UPD) Due to Somatic Recombination in Acute Myeloid Leukemias." Blood 104, no. 11 (November 16, 2004): 139. http://dx.doi.org/10.1182/blood.v104.11.139.139.

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Abstract Many cases of AML have either a normal karyotype or non-recurrent chromosomal abnormalities and hence their pathogenesis remains obscure. The introduction of array-based analysis of single nucleotide polymorphisms (SNPs) allows the rapid determination of genome-wide allelic information at a high density for a DNA sample. High-resolution SNP genotype analysis was performed on 64 presentation AML samples with full karyotype information as follows: normal karyotype [40], t(8;21) [5], t(15;17) [4], inv16 [3], 11q23 [2],−7 [3],+8 [2] and other structural abnormalities [7]. Using the 10K SNP array (Affymetrix, Inc., Santa Clara) 9, a mean call rate of 93.3% yielded more than 10,000 SNP genotype calls per sample. Large unexpected regions of homozygosity were observed in 12 AMLs (18.75%). These regions ranged in size from 16 million base pairs to 113 million base pairs and would have been visible in the karyotypes if due to deletion. Remission bone marrow samples from 5 of those patients were subjected to SNP genotype analysis. The SNP call data demonstrated clearly that the homozygosity seen in the leukemic DNA was not present in the respective remission bone marrow DNA. Fluorescence in situ hybridisation (FISH) demonstrated 2 signals for probes within regions of homozygosity. Furthermore, hybridisation signal values on the SNP arrays demonstrated that regions of homozygosity did not differ from the rest of the chromosome. It was therefore concluded that such homozygous regions corresponded to uniparental disomy (UPD) due to somatic recombination events occurring during development of the leukemias. There appears to be a non-random distribution of UPD with 5 events on chromosome 11, 2 on chromosome 6, 2 on chromosome 9 and 1 on chromosomes 13, 19 and 21. As expected for somatic recombination, homozygosity continued to the telomere in most cases. Any parental bias in UPD could be evidence of a role for imprinted genes. This issue was investigated using the H19 gene, which is located at 11p15 and is normally methylated only on the paternal allele. Two leukemias exhibited UPD including 11p15 and the methylation status of the H19 gene was therefore determined by bisulfite sequencing. One leukemia with UPD11p exhibited a homozygous methylated paternal pattern, while the other example of UPD11p showed a homozygous non-methylated maternal pattern. These data show that the UPD seen on 11p is not restricted to a single parental origin. In a previous analysis, the leukemia with UPD19q was shown to be homozygous for a CEBPA mutation and FISH demonstrated 2 copies of the CEBPA gene. This gene is located at 19q13.1, within the area of UPD and we conclude that the mutation occurred prior to the UPD. We can therefore speculate that an important consequence of UPD could be to unmask pre-existing mutations. A total of 8 different chromosomal regions have been shown to be affected by UPD in this study and this may suggest that there are at least this number of mutational targets. The discovery of widespread, somatically acquired, UPD in leukemias has potentially important clinical implications. 20% of the normal karyotype AMLs was found to have UPD, and this could offer a valuable new approach to the classification of this important subgroup of AML. The prognostic consequences of such cryptic abnormalities for the patient are uncertain, and larger studies will be required to assess the clinical significance of this phenomenon.

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Saida, Myriam, David Iles, Abdul Elnefati, Martin Brinkworth, and David Miller. "Key gene regulatory sequences with distinctive ontological signatures associate with differentially endonuclease-accessible mouse sperm chromatin." REPRODUCTION 142, no. 1 (July 2011): 73–86. http://dx.doi.org/10.1530/rep-10-0536.

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Using a well-established endonuclease-based chromatin dissection procedure in conjunction with both experimental comparative genome hybridisation (CGH) array profiling andin silicodata mining, we show that mouse spermatozoa contain chromatin that is sensitive and resistant to digestion with micrococcal nuclease (MNase). Sequences represented in the micrococcal nuclease digestion solubilised (MNDS) but not the MND insoluble (MNDI) chromatin are strongly enriched in chromosomal regions of high gene density. Furthermore, by fluorescencein situhybridisation (FISH) analysis, we show that MNDS and MNDI DNAs occupy distinct domains of decondensed mouse sperm nuclei that may also retain abundant histones. More detailedin silicoanalysis of CGH probe location in relation to known promoters and sequences recognised by CCCTC binding factor (CTCF) shows a significant excess of both in MNDS chromatin. A functional analysis of gene promoters reveals strong ontological signatures for ion transport on methylated promoters associated with CTCF binding sequences in MNDS chromatin. Sensory perception is the only strong ontological signature present in MNDI chromatin, driven by promoters that are not associated with CTCF regardless of their methylation status.

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Salmela, M. T. "Upregulation of matrix metalloproteinases in a model of T cell mediated tissue injury in the gut: analysis by gene array and in situ hybridisation." Gut 51, no. 4 (October 1, 2002): 540–47. http://dx.doi.org/10.1136/gut.51.4.540.

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Dohner, Konstanze, Marianne Habdank, Frank G. Rucker, Simone Miller, Stefan Frohling, Stephen W. Scherer, Lars Bullinger, and Hartmut Dohner. "Molecular Characterization of Distinct Hot Spot Regions on Chromosome 7q in Myeloid Leukemias." Blood 108, no. 11 (November 1, 2006): 2349. http://dx.doi.org/10.1182/blood.v108.11.2349.2349.

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Abstract In recent years several groups initiated the molecular characterization of deletion and translocation breakpoints affecting the long arm of chromosome 7 (7q−) to identify genes that are involved in the pathogenesis of myeloid leukemias. Based on these studies a commonly deleted segment (CDS) of approximately 2 Mb in size was identified in chromosomal band 7q22 flanked by the microsatellite markers D7S1503 and D7S1841. Recently, the MLL5 gene (mixed lineage leukemia 5) has been cloned and mapped to the CDS as an interesting candidate gene for chromosome 7q associated leukemias. However, the pathogenic role of MLL5 in myeloid leukemias has not been demonstrated yet. In addition, for the less frequent deletion/translocation breakpoints affecting the distal part of chromosome 7q a 4 to 5 Mb sized CDS was defined encompassing chromosomal bands 7q35 to q36. The heterogeneity of deletion/translocation breakpoints on 7q suggests the existence of more than one disease-related gene. We aimed to identify and characterize translocation and deletion breakpoints in a large series of myeloid leukemias with chromosome 7q aberrations using fluorescence in situ hybridisation (FISH) and array-based comparative genomic hybridization (array CGH). Once, novel hot spot regions were identified, transcriptional map(s) were constructed allowing the identification of candidate genes, expressed sequences or miR-sites. FISH with a physical map of well defined YAC/BAC/PAC clones covering the long arm of chromosome 7 was performed on a series of 105 myeloid leukemias [acute myeloid leukaemia, (AML); myelodysplastic syndrome (MDS); myeloproliferative disorders, (MPD)] exhibiting chromosome 7q aberrations on banding analysis. Selected patients were analysed by array CGH and results were confirmed by hybridisation of the corresponding DNA clones. Transcriptional map(s) were constructed using public databases. While most of the deletions were large encompassing the previously published CDS, we identified a distinct 2 Mb sized CDS in the proximal part of 7q22 that was defined by five patients all exhibiting small deletions. This segment contains several candidate genes including the putative tumor-suppressor genes CUTL1, RASA4, EPO and FBXL13. Interestingly, this CDS is located close to multiple miR-sites, which usually indicate common fragile sites in the human genome. In chromosomal bands 7q35–q36 we localized the breakpoint of an unbalanced translocation from a patient with secondary AML between the markers D7S1925 and D7S1395. This region was recently characterized as a common fragile site in the human genome, named FRA7I. Furthermore, the translocation breakpoint t(3;7)(p13;q35) of a second patient with therapy-related AML was cloned into a 100 kb sized genomic segment located centromeric the CNTNAP2-gene close to the proximal border of the CDS. Our data further indicate the remarkable heterogeneity of deletion and translocation breakpoints on 7q supporting the hypothesis of multiple genes involved in 7q-associated myeloid leukemias. Using techniques such as FISH and array CGH known CDS as well as novel hot spot regions were identified. Transcriptional maps from those regions may serve as important starting points for the identification of pathogenetically relevant genes.

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Schaub, Franz, Ralph Tiedt, Sylvie Hermouet, François Girodon, Robert Kralovics, André Tichelli, and Radek C. Skoda. "Characterization of del20q in Peripheral Blood of MPD Patients Using Copy Number Analysis and High Resolution Oligonucleotide CGH Array." Blood 110, no. 11 (November 16, 2007): 1530. http://dx.doi.org/10.1182/blood.v110.11.1530.1530.

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Abstract Previous studies showed that deletions of the long arm of chromosome 20 (del20q) are the most common chromosomal aberration in myeloproliferative disorders (MPD) and can be found in up to 10% of patients with polycythemia vera (PV). We screened 447 MPD patients (177 PV, 228 essential thrombocythemia (ET), 42 primary myelofibrosis (PMF)) for loss of gene copy number in the del20q region. Granulocyte DNA was assayed using a quantitative PCR assay for two different exons of the L3MBTL gene, which is located in the common deleted region. Since deletions can only be detected if the majority of granulocytes have lost a copy of L3MBTL, this method selects for del20q events that provided a selective advantage for the clone. Samples that showed a decrease in copy number in the initial screen were validated using primers in neighbouring genes. We found del20q in peripheral blood of 29/447 patients (6%), including 9/177 PV (5%), 12/228 ET (5%), and 8/42 PMF (19%). The observed frequency of del20q in peripheral blood is lower than reported in previous studies for bone marrow analysis. The patients positive for del20q in this screen were chosen for mapping of the deleted region by high density oligonucleotide comparative genomic hybridisation (CGH) array. A custom chip was designed with 94’000 probes from chromosome 20q, with an average resolution of 500bp. We have so far analyzed 6 patients and confirmed del20q by CGH in all of them. The deleted regions in these patients overlapped with the published common deleted region. We will use CGH to map the remaining 23 patients. Since the majority of the del20q positive patients also carried the Jak2-V617F mutation, we performed clonogenic assays and analyzed single colonies. In one patient all 94 colonies were double positive for del20q and JAK2-V617F. In a second patient 54 colonies were double positive and 10 colonies only carried del20q, but not JAK2-V617F, indicating that del20q occurred before the acquisition of JAK2-V617F.

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Hopkins, Stephen, Jeremy Turk, Adeniyi Daramola, and Marinos Kyriakopoulos. "Autism spectrum mixed neurodevelopmental disorder associated with 6q27 deletion and multiple copies within 20q11.23: a case study." Advances in Mental Health and Intellectual Disabilities 8, no. 3 (April 29, 2014): 210–15. http://dx.doi.org/10.1108/amhid-07-2013-0050.

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Purpose – Copy Number Variations (CNVs) are not infrequently observed in aberrant neurodevelopment. CNVs can alter gene expression and have been linked to a wide range of neuropsychiatric disorders. The purpose of this case study is to report the association of CNVs with a mixed neurodevelopmental disorder. Design/methodology/approach – Array-Comparative Genomic Hybridisation analysis was carried out in a case of an eight-year-old boy presenting with a mixed neurodevelopmental disorder including autism spectrum disorder, intellectual disability, tic disorder, anxiety and severe aggression. The child's parents also underwent the same investigation. Findings – A 6q27 deletion and multiple copies within 20q11.23 were identified. The boy's father shared the 6q27 deletion and his mother also had multiple copies within 20q11.23. Originality/value – This is the first report linking the combination of 6p27 and 20q11 CNVs with a mixed neurodevelopmental presentation. Identifying CNVs that may underlie aberrant neurodevelopment is likely to assist in unravelling the aetiology of neurodevelopmental and psychiatric disorders and lead to more effective strategies for their characterisation and management.

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Cottrell, Emily, Claudia P. Cabrera, Miho Ishida, Sumana Chatterjee, James Greening, Neil Wright, Artur Bossowski, et al. "Rare CNVs provide novel insights into the molecular basis of GH and IGF-1 insensitivity." European Journal of Endocrinology 183, no. 6 (December 2020): 581–95. http://dx.doi.org/10.1530/eje-20-0474.

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Objective Copy number variation (CNV) has been associated with idiopathic short stature, small for gestational age and Silver-Russell syndrome (SRS). It has not been extensively investigated in growth hormone insensitivity (GHI; short stature, IGF-1 deficiency and normal/high GH) or previously in IGF-1 insensitivity (short stature, high/normal GH and IGF-1). Design and methods Array comparative genomic hybridisation was performed with ~60 000 probe oligonucleotide array in GHI (n = 53) and IGF-1 insensitivity (n = 10) subjects. Published literature, mouse models, DECIPHER CNV tracks, growth associated GWAS loci and pathway enrichment analyses were used to identify key biological pathways/novel candidate growth genes within the CNV regions. Results Both cohorts were enriched for class 3–5 CNVs (7/53 (13%) GHI and 3/10 (30%) IGF-1 insensitivity patients). Interestingly, 6/10 (60%) CNV subjects had diagnostic/associated clinical features of SRS. 5/10 subjects (50%) had CNVs previously reported in suspected SRS: 1q21 (n = 2), 12q14 (n = 1) deletions and Xp22 (n = 1), Xq26 (n = 1) duplications. A novel 15q11 deletion, previously associated with growth failure but not SRS/GHI was identified. Bioinformatic analysis identified 45 novel candidate growth genes, 15 being associated with growth in GWAS. The WNT canonical pathway was enriched in the GHI cohort and CLOCK was identified as an upstream regulator in the IGF-1 insensitivity cohorts. Conclusions Our cohort was enriched for low frequency CNVs. Our study emphasises the importance of CNV testing in GHI and IGF-1 insensitivity patients, particularly GHI subjects with SRS features. Functional experimental evidence is now required to validate the novel candidate growth genes, interactions and biological pathways identified.

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Rudenko, Hannah C., Monica Else, Claire Dearden, Vasantha Brito-Babapulle, Chris Jones, Tim Dexter, Kerry Fenwick, et al. "Characterising the TP53-deleted subgroup of chronic lymphocytic leukemia: an analysis of additional cytogenetic abnormalities detected by interphase fluorescencein situhybridisation and array-based comparative genomic hybridisation." Leukemia & Lymphoma 49, no. 10 (January 2008): 1879–86. http://dx.doi.org/10.1080/10428190802345902.

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Journal articles on the topic 'Array hybridisation analysis'

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