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Abstract
Although Prader-Willi syndrome (PWS) is a well-described clinical dysmorphic syndrome, DNA testing is required for a definitive diagnosis. A definitive diagnosis can be made in approximately 99% of cases using DNA testing; there are a number of DNA tests that can be used for this purpose, although there is no set standard algorithm of testing. The dilemma arises because of the complex genetic mechanisms at the basis of PWS, which need to be elucidated. To establish the molecular mechanism with a complete work up, involves at least 2 tests. Here we discuss the commonly used tests currently available and suggest a cost-effective approach to diagnostic testing.
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Affiliation(s)
- Arabella Smith
- University of Sydney Clinical School, Children's Hospital at Westmead, Westmead, Australia
| | - Dorothy Hung
- Children's Hospital at Westmead, Sydney Genome Diagnostics (Cytogenetics), Children's Hospital Network, PO Box 4001, Westmead, Australia
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2
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Daugaard I, Kjeldsen TE, Hager H, Hansen LL, Wojdacz TK. The influence of DNA degradation in formalin-fixed, paraffin-embedded (FFPE) tissue on locus-specific methylation assessment by MS-HRM. Exp Mol Pathol 2015; 99:632-40. [PMID: 26551081 DOI: 10.1016/j.yexmp.2015.11.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/04/2015] [Indexed: 11/19/2022]
Abstract
Readily accessible formalin-fixed paraffin embedded (FFPE) tissues are a highly valuable source of genetic material for molecular analyses in both research and in vitro diagnostics but frequently genetic material in those samples is highly degraded. With locus-specific methylation changes being widely investigated for use as biomarkers in various aspects of clinical disease management, we aimed to evaluate to what extent standard laboratory procedures can approximate the quality of the DNA extracted from FFPE samples prior to methylation analyses. DNA quality in 107 FFPE non-small cell lung cancer (NSCLC) samples was evaluated using spectrophotometry and gel electrophoresis. Subsequently, the quality assessment results were correlated with the results of locus specific methylation assessment with methylation sensitive high resolution melting (MS-HRM). The correlation of template quality with PCR amplification performance and HRM based methylation detection indicated a significant influence of DNA quality on PCR amplification but not on methylation assessment. In conclusion, standard laboratory procedures fairly well approximate DNA degradation of FFPE samples and DNA degradation does not seem to considerably affect locus-specific methylation assessment by MS-HRM.
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Affiliation(s)
- Iben Daugaard
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Build. 1230, DK-8000 Aarhus C, Denmark.
| | - Tina E Kjeldsen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Build. 1230, DK-8000 Aarhus C, Denmark
| | - Henrik Hager
- Department of Pathology, Aarhus University Hospital, Nørrebrogade 45, DK-8000 Aarhus C, Denmark
| | - Lise Lotte Hansen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Build. 1230, DK-8000 Aarhus C, Denmark
| | - Tomasz K Wojdacz
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Build. 1230, DK-8000 Aarhus C, Denmark; Aarhus Institute of Advanced Studies, Høegh-Guldbergs Gade 6B, DK-8000 Aarhus C, Denmark
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3
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Gstir R, Schafferer S, Scheideler M, Misslinger M, Griehl M, Daschil N, Humpel C, Obermair GJ, Schmuckermair C, Striessnig J, Flucher BE, Hüttenhofer A. Generation of a neuro-specific microarray reveals novel differentially expressed noncoding RNAs in mouse models for neurodegenerative diseases. RNA (NEW YORK, N.Y.) 2014; 20:1929-43. [PMID: 25344396 PMCID: PMC4238357 DOI: 10.1261/rna.047225.114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/27/2014] [Indexed: 05/24/2023]
Abstract
We have generated a novel, neuro-specific ncRNA microarray, covering 1472 ncRNA species, to investigate their expression in different mouse models for central nervous system diseases. Thereby, we analyzed ncRNA expression in two mouse models with impaired calcium channel activity, implicated in Epilepsy or Parkinson's disease, respectively, as well as in a mouse model mimicking pathophysiological aspects of Alzheimer's disease. We identified well over a hundred differentially expressed ncRNAs, either from known classes of ncRNAs, such as miRNAs or snoRNAs or which represented entirely novel ncRNA species. Several differentially expressed ncRNAs in the calcium channel mouse models were assigned as miRNAs and target genes involved in calcium signaling, thus suggesting feedback regulation of miRNAs by calcium signaling. In the Alzheimer mouse model, we identified two snoRNAs, whose expression was deregulated prior to amyloid plaque formation. Interestingly, the presence of snoRNAs could be detected in cerebral spine fluid samples in humans, thus potentially serving as early diagnostic markers for Alzheimer's disease. In addition to known ncRNAs species, we also identified 63 differentially expressed, entirely novel ncRNA candidates, located in intronic or intergenic regions of the mouse genome, genomic locations, which previously have been shown to harbor the majority of functional ncRNAs.
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Affiliation(s)
- Ronald Gstir
- Division of Genomics and RNomics, Innsbruck Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Simon Schafferer
- Division of Genomics and RNomics, Innsbruck Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Marcel Scheideler
- RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, 8010 Graz, Austria
| | - Matthias Misslinger
- Division of Genomics and RNomics, Innsbruck Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Matthias Griehl
- Division of Genomics and RNomics, Innsbruck Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Daschil
- Department of Psychiatry and Psychotherapy, University Clinic of General and Social Psychiatry, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Christian Humpel
- Department of Psychiatry and Psychotherapy, University Clinic of General and Social Psychiatry, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Gerald J Obermair
- Division of Physiology, Department of Physiology and Medical Physics, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Claudia Schmuckermair
- Pharmacology and Toxicology, Institute of Pharmacy, and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Joerg Striessnig
- Pharmacology and Toxicology, Institute of Pharmacy, and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Bernhard E Flucher
- Division of Physiology, Department of Physiology and Medical Physics, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Alexander Hüttenhofer
- Division of Genomics and RNomics, Innsbruck Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
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4
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Abstract
Mammalian development involves significant interactions between offspring and mother. But is this interaction a carefully coordinated effort by two individuals with a common goal--offspring survival? Or is it an evolutionary battleground (a central idea in our understanding of reproduction). The conflict between parents and offspring extends to an offspring's genes, where paternally inherited genes favor demanding more from the mother, while maternally inherited genes favor restraint. This "intragenomic conflict" (among genes within a genome) is the dominant evolutionary explanation for "genomic imprinting." But a new study in PLOS Biology provides support for a different perspective: that imprinting might facilitate coordination between mother and offspring. According to this "coadaptation theory," paternally inherited genes might be inactivated because maternally inherited genes are adapted to function harmoniously with the mother. As discussed in this article, the growth effects associated with the imprinted gene Grb10 are consistent with this idea, but it remains to be seen just how general the pattern is.
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Affiliation(s)
- Jon F. Wilkins
- Ronin Institute, Montclair, New Jersey, United States of America
- * E-mail:
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5
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Wilkins JF, Úbeda F. Diseases associated with genomic imprinting. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:401-45. [PMID: 21507360 DOI: 10.1016/b978-0-12-387685-0.00013-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genomic imprinting is the phenomenon where the expression of a locus differs between the maternally and paternally inherited alleles. Typically, this manifests as transcriptional silencing of one of the alleles, although many genes are imprinted in a tissue- or isoform-specific manner. Diseases associated with imprinted genes include various cancers, disorders of growth and metabolism, and disorders in neurodevelopment, cognition, and behavior, including certain major psychiatric disorders. In many cases, the disease phenotypes associated with dysfunction at particular imprinted loci can be understood in terms of the evolutionary processes responsible for the origin of imprinting. Imprinted gene expression represents the outcome of an intragenomic evolutionary conflict, where natural selection favors different expression strategies for maternally and paternally inherited alleles. This conflict is reasonably well understood in the context of the early growth effects of imprinted genes, where paternally inherited alleles are selected to place a greater demand on maternal resources than are maternally inherited alleles. Less well understood are the origins of imprinted gene expression in the brain, and their effects on cognition and behavior. This chapter reviews the genetic diseases that are associated with imprinted genes, framed in terms of the evolutionary pressures acting on gene expression at those loci. We begin by reviewing the phenomenon and evolutionary origins of genomic imprinting. We then discuss diseases that are associated with genetic or epigenetic defects at particular imprinted loci, many of which are associated with abnormalities in growth and/or feeding behaviors that can be understood in terms of the asymmetric pressures of natural selection on maternally and paternally inherited alleles. We next described the evidence for imprinted gene effects on adult cognition and behavior, and the possible role of imprinted genes in the etiology of certain major psychiatric disorders. Finally, we conclude with a discussion of how imprinting, and the evolutionary-genetic conflicts that underlie it, may enhance both the frequency and morbidity of certain types of diseases.
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Zeschnigk M, Tschentscher F, Lich C, Brandt B, Horsthemke B, Lohmann DR. Methylation analysis of several tumour suppressor genes shows a low frequency of methylation of CDKN2A and RARB in uveal melanomas. Comp Funct Genomics 2010; 4:329-36. [PMID: 18629284 PMCID: PMC2448448 DOI: 10.1002/cfg.295] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2003] [Indexed: 11/10/2022] Open
Abstract
We have investigated the frequency of methylation of several tumour suppressor genes in uveal melanoma. As the loss of one copy of chromosome 3 (monosomy 3), which is found in about half of these tumours, is tightly associated with metastatic disease, a special emphasis was laid on genes located on this chromosome, including the fragile histidine triad (FHIT), von Hippel-Lindau (VHL), beta-catenin (CTNNB1), activated leukocyte cell adhesion molecule (ALCAM) and retinoic acid receptor-beta2 (RARB) genes. In addition, the methylation patterns of the CpG-rich regions 5' of the E-cadherin (CDH1), p16/cyclin-dependent kinase inhibitor 2 A (CDKN2A) and retinoblastoma (RB1) genes were analysed by bisulphite genomic sequencing or methylation-specific PCR (MSP). Furthermore, the SNRPN and D15S63 loci, which are located in the imprinted region of chromosome 15, were included in the study. Aberrant methylation was detected in nine of 40 tumours analysed: The imprinted SNRPN and D15S63 loci were hypermethylated in three tumours, all of which retained both copies of chromosome 3. Methylated RARB alleles were detected in three tumours, whereas in three other tumours CDKN2A was found to be methylated. As we did not find RARB and CDKN2A preferentially methylated in tumours with monosomy 3, which is a significant predictor of metastatic disease, we suggest that these genes may play a causative role in the formation of uveal melanoma but not in the development of metastases.
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Affiliation(s)
- Michael Zeschnigk
- Institut für Humangenetik, Universitätsklinikum Essen, Hufelandstrasse 55, Essen 45122, Germany.
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Hirst M, Marra MA. Epigenetics and human disease. Int J Biochem Cell Biol 2008; 41:136-46. [PMID: 18852064 DOI: 10.1016/j.biocel.2008.09.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2008] [Revised: 09/13/2008] [Accepted: 09/16/2008] [Indexed: 01/29/2023]
Abstract
Changes to covalent modifications of DNA and histones can be induced via environmental stimuli such as nutrients, hormones and drugs. These changes can be both transient and heritable in nature and provide a framework in which to investigate how environment and lifestyle choices impact disease susceptibility and progression. Furthermore, these modifications are central to chromatin dynamics and, as such, play key roles in many biological processes involving chromatin, such as DNA replication and repair, transcription and development. In this review we provide an overview of recent advances in our understanding of the roles that DNA and histone modification play in the onset and progression of human disease.
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Affiliation(s)
- Martin Hirst
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
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Ninomiya S, Yokoyama Y, Kawakami M, Une T, Maruyama H, Morishima T. Unique maternal deletion of 15q in a patient with some symptoms of Prader-Willi syndrome. Pediatr Int 2005; 47:541-5. [PMID: 16190961 DOI: 10.1111/j.1442-200x.2005.02116.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Human chromosome 15q11-q13 is a critical region for Prader-Willi syndrome (PWS) and Angelman syndrome (AS) and most of the genes are under the condition of imprinting mechanism. PWS results from the loss of expression of paternally expressed genes and AS of maternally expressed genes. In this study molecular studies about a patient with congenital anomalies and mental retardation are analyzed. METHODS Highly polymorphic microsatellite markers were analyzed by PCR. These markers exist within 15q11-q13 and distal to 15q13. RESULTS Only the maternal D15S986 locus within 15q11-q13 was deleted and other markers were biallelic. CONCLUSIONS The result of maternal small region deletion in this patient is different from the typical PWS with paternal chromosome deletion and it suggests that nearby the deleted region there exists a gene (genes) which is not imprinted but needs biallelic expression.
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Affiliation(s)
- Shinsuke Ninomiya
- Department of Pediatrics, Okayama University Graduate School of Medicine and Dentistry, Shikata-cyo, Okayama, Japan.
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Abstract
DNA methylation is a crucial epigenetic modification of the genome that is involved in regulating many cellular processes. These include embryonic development, transcription, chromatin structure, X chromosome inactivation, genomic imprinting and chromosome stability. Consistent with these important roles, a growing number of human diseases have been found to be associated with aberrant DNA methylation. The study of these diseases has provided new and fundamental insights into the roles that DNA methylation and other epigenetic modifications have in development and normal cellular homeostasis.
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Affiliation(s)
- Keith D Robertson
- Department of Biochemistry and Molecular Biology, Shands Cancer Center, University of Florida, Gainesville, Florida 32610, USA.
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Use of two FISH probes provides a cost-effective, simple protocol to exclude an imprinting centre defect in routine laboratory testing for suspected Prader-Willi and Angelman syndrome. ANNALES DE GENETIQUE 2002; 45:189-91. [PMID: 12668166 DOI: 10.1016/s0003-3995(02)01136-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
From among the many suspected patients with Prader-Willi (PWS) or Angelman (AS) syndromes received for diagnosis in a routine genetics laboratory, we present our protocol for the exclusion of a possible, rare imprinting centre (IC) defect. Deletion detection utilising two FISH probes-SNRPN within the IC, and another probe outside the IC, on the same suspension remaining from the cytogenetic harvest, provides a simple, quick and cost-effective system for exclusion of an IC defect, for patients with an abnormal methylation analysis.
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