301
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Copy-number variation: the end of the human genome? Trends Biotechnol 2009; 27:448-54. [PMID: 19576644 DOI: 10.1016/j.tibtech.2009.05.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2009] [Revised: 05/13/2009] [Accepted: 05/14/2009] [Indexed: 12/20/2022]
Abstract
Copy-number variation (CNV)--the presence of additional or missing segments of chromosomes in some individuals--has been found to be abundant in humans and adds another dimension of variation to the genome. Copy-number variants have already been associated with some diseases and disease susceptibilities and are likely to prove as significant as sequence polymorphisms in this respect. Changes in copy number of parts of the genome are known to be a feature of many cancers, and their analysis is expected to reveal genes involved in carcinogenesis. This article will present a somewhat biased and occasionally speculative discussion of the current and future significance of CNV with a particular focus on the potential of molecular copy-number counting in the analysis of small, damaged or heterogeneous samples.
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302
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Vitaro F, Brendgen M, Arseneault L. The discordant MZ-twin method: One step closer to the holy grail of causality. INTERNATIONAL JOURNAL OF BEHAVIORAL DEVELOPMENT 2009. [DOI: 10.1177/0165025409340805] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Twin studies are well known for their value in quantifying the contribution of genes to population variation in behaviors and personality traits. Twin studies also provide a unique opportunity to untangle the contribution of environmental experiences to emotional and behavioral development. This is particularly true when examining monozygotic (MZ) twins since they represent a pair of individuals naturally matched on both their genetic background and their shared environment, thus allowing the identification of environmental experiences unique to each twin which may impact developmental outcome. This article presents two analytical strategies based on the discordant MZ-twin method. It stresses the power of this method to establish plausible causal pathways between environmental factors and developmental outcomes, and provides examples from the socio-developmental literature to illustrate its application. It also describes the limitations of this method and its requirements for optimal utilization.
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Affiliation(s)
- Frank Vitaro
- Department of Psycho-Education, University of Montreal,
Canada,
| | - Mara Brendgen
- Department of Psychology, University of Quebec in Montreal,
Canada
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303
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Geigl JB, Obenauf AC, Waldispuehl-Geigl J, Hoffmann EM, Auer M, Hörmann M, Fischer M, Trajanoski Z, Schenk MA, Baumbusch LO, Speicher MR. Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays. Nucleic Acids Res 2009; 37:e105. [PMID: 19541849 PMCID: PMC2731907 DOI: 10.1093/nar/gkp526] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Clinical DNA is often available in limited quantities requiring whole-genome amplification for subsequent genome-wide assessment of copy-number variation (CNV) by array-CGH. In pre-implantation diagnosis and analysis of micrometastases, even merely single cells are available for analysis. However, procedures allowing high-resolution analyses of CNVs from single cells well below resolution limits of conventional cytogenetics are lacking. Here, we applied amplification products of single cells and of cell pools (5 or 10 cells) from patients with developmental delay, cancer cell lines and polar bodies to various oligo tiling array platforms with a median probe spacing as high as 65 bp. Our high-resolution analyses reveal that the low amounts of template DNA do not result in a completely unbiased whole genome amplification but that stochastic amplification artifacts, which become more obvious on array platforms with tiling path resolution, cause significant noise. We implemented a new evaluation algorithm specifically for the identification of small gains and losses in such very noisy ratio profiles. Our data suggest that when assessed with sufficiently sensitive methods high-resolution oligo-arrays allow a reliable identification of CNVs as small as 500 kb in cell pools (5 or 10 cells), and of 2.6–3.0 Mb in single cells.
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Affiliation(s)
- Jochen B Geigl
- Institute of Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010 Graz, Austria
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304
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Vossen RHAM, Aten E, Roos A, den Dunnen JT. High-Resolution Melting Analysis (HRMA)-More than just sequence variant screening. Hum Mutat 2009; 30:860-6. [PMID: 19418555 DOI: 10.1002/humu.21019] [Citation(s) in RCA: 357] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rolf H A M Vossen
- Leiden Genome Technology Center (LGTC), Human and Clincal Genetics, Leiden University Medical Center, Leiden, The Netherlands
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305
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Novara F, Beri S, Bernardo ME, Bellazzi R, Malovini A, Ciccone R, Cometa AM, Locatelli F, Giorda R, Zuffardi O. Different molecular mechanisms causing 9p21 deletions in acute lymphoblastic leukemia of childhood. Hum Genet 2009; 126:511-20. [PMID: 19484265 PMCID: PMC2762534 DOI: 10.1007/s00439-009-0689-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 05/19/2009] [Indexed: 12/03/2022]
Abstract
Deletion of chromosome 9p21 is a crucial event for the development of several cancers including acute lymphoblastic leukemia (ALL). Double strand breaks (DSBs) triggering 9p21 deletions in ALL have been reported to occur at a few defined sites by illegitimate action of the V(D)J recombination activating protein complex. We have cloned 23 breakpoint junctions for a total of 46 breakpoints in 17 childhood ALL (9 B- and 8 T-lineages) showing different size deletions at one or both homologous chromosomes 9 to investigate which particular sequences make the region susceptible to interstitial deletion. We found that half of 9p21 deletion breakpoints were mediated by ectopic V(D)J recombination mechanisms whereas the remaining half were associated to repeated sequences, including some with potential for non-B DNA structure formation. Other mechanisms, such as microhomology-mediated repair, that are common in other cancers, play only a very minor role in ALL. Nucleotide insertions at breakpoint junctions and microinversions flanking the breakpoints have been detected at 20/23 and 2/23 breakpoint junctions, respectively, both in the presence of recombination signal sequence (RSS)-like sequences and of other unspecific sequences. The majority of breakpoints were unique except for two cases, both T-ALL, showing identical deletions. Four of the 46 breakpoints coincide with those reported in other cases, thus confirming the presence of recurrent deletion hotspots. Among the six cases with heterozygous 9p deletions, we found that the remaining CDKN2A and CDKN2B alleles were hypermethylated at CpG islands.
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Affiliation(s)
- Francesca Novara
- Biologia Generale e Genetica Medica, Università degli Studi di Pavia, Via Forlanini, 14, 27100 Pavia, Italy
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306
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Machin G. Non-identical monozygotic twins, intermediate twin types, zygosity testing, and the non-random nature of monozygotic twinning: A review. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2009; 151C:110-27. [DOI: 10.1002/ajmg.c.30212] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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307
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Singh SM, O'Reilly R. (Epi)genomics and neurodevelopment in schizophrenia: monozygotic twins discordant for schizophrenia augment the search for disease-related (epi)genomic alterations. Genome 2009; 52:8-19. [PMID: 19132067 DOI: 10.1139/g08-095] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Unlike stunning breakthroughs in the identification of genes for Mendelian disorders during the last three decades, gene identification in most complex disorders has been full of twists and turns and little progress. Doing more of the same will not guarantee success. The lessons learned argue for a need to reconsider genetic models that are appropriate for the disorder in question along with an interdisciplinary, systematic approach using genomic methods that have now become possible. We will use schizophrenia as an example to review the genetic progress to date that has been disappointing. We will argue that the causation of this complex disease may involve heterogeneous genomic changes of major effect. We will provide three approaches, retroviral transpositions, methylation, and copy number variations, to test this hypothesis. We will present arguments to suggest that such experiments will be most effective if undertaken on monozygotic twins. It will include our experience with associated experiments on the monozygotic twins discordant for schizophrenia. The results support that (epi)genomic changes of major effect, rather than accumulation of mutations of small effect, underlie the causation of this complex disease. More important, this experimental strategy will be an effective strategy for studies on other complex (behavioural) disorders as well.
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Affiliation(s)
- Shiva M Singh
- Molecular Genetics Laboratories, Department of Biology, and Division of Medical Genetics, The University of Western Ontario, London, ON N6A5B7, Canada.
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308
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Trobridge P, Knoblaugh S, Washington MK, Munoz NM, Tsuchiya KD, Rojas A, Song X, Ulrich CM, Sasazuki T, Shirasawa S, Grady WM. TGF-beta receptor inactivation and mutant Kras induce intestinal neoplasms in mice via a beta-catenin-independent pathway. Gastroenterology 2009; 136:1680-8.e7. [PMID: 19208363 PMCID: PMC2782436 DOI: 10.1053/j.gastro.2009.01.066] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 01/19/2009] [Accepted: 01/29/2009] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS During colorectal cancer pathogenesis, mutations and epigenetic events cause neoplastic behavior in epithelial cells by deregulating the Wnt, Ras-Raf-extracellular signal-regulated kinase (ERK), and transforming growth factor (TGF)-beta-signaling pathways, among others. The TGF-beta-signaling pathway is often inactivated in colon cancer cells by mutations in the gene encoding the TGF-beta receptor TGFBR2. The RAS-RAF-ERK pathway is frequently up-regulated in colon cancer via mutational activation of KRAS or BRAF. We assessed how these pathways interact in vivo and affect formation of colorectal tumors. METHODS We analyzed intestinal tumors that arose in mice that express an oncogenic (active) form of Kras and that have Tgfbr2 inactivations-2 common molecular events observed in human colorectal tumors. LSL-KrasG12D mice were crossed with Villin-Cre;Tgfbr2E2flx/E2flx mice, which do not express Tgfbr2 in the intestinal epithelium. RESULTS Neither inactivation of Tgfbr2 nor expression of oncogenic Kras alone was sufficient to induce formation of intestinal neoplasms. Histologic abnormalities arose in mice that expressed Kras, but only the combination of Tgfbr2 inactivation and Kras activation led to intestinal neoplasms and metastases. The cancers arose via a beta-catenin-independent mechanism; the epidermal growth factor-signaling pathway was also activated. Cells in the resulting tumors proliferated at higher rates, expressed decreased levels of p15, and expressed increased levels of cyclin D1 and cdk4, compared with control cells. CONCLUSIONS A combination of inactivation of the TGF-beta-signaling pathway and expression of oncogenic Kras leads to formation of invasive intestinal neoplasms through a beta-catenin-independent pathway; these adenocarcinomas have the capacity to metastasize.
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Affiliation(s)
- Patty Trobridge
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Sue Knoblaugh
- Experimental Histopathology, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - M. Kay Washington
- Department of Pathology, Vanderbilt University School of Medicine Nashville, TN
| | - Nina M. Munoz
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Karen D. Tsuchiya
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, Department of Laboratory Medicine, University of Washington Medical School, Department of Laboratories, Seattle Children’s Hospital, Seattle, WA
| | - Andres Rojas
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, Cancer Biology Department, Nashville, TN
| | - Xiaoling Song
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Cornelia M. Ulrich
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Takehiko Sasazuki
- Department of Cell Biology, School of Medicine Fukuoka University, Fukuoka, Japan
| | - Senji Shirasawa
- Department of Cell Biology, School of Medicine Fukuoka University, Fukuoka, Japan
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, Dept of Veterans Affairs R&D Service, Puget Sound Healthcare system, Seattle, WA, Department of Medicine, University of Washington Medical School, Seattle, WA
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309
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Abstract
It is now becoming generally accepted that a significant amount of human genetic variation is due to structural changes of the genome rather than to base-pair changes in the DNA. As for base-pair changes, knowledge of gene and genome function has been informed by structural alterations that convey clinical phenotypes. Genomic disorders are a class of human conditions that result from structural changes of the human genome that convey traits or susceptibility to traits. The path to the delineation of genomic disorders is intertwined with the evolving technologies that have enabled the resolution of human genome analyses to continue increasing. Similarly, the ability to perform high-resolution human genome analysis has fueled the current and future clinical implementation of such discoveries in the evolving field of genome medicine.
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Affiliation(s)
- James R Lupski
- Departments of Molecular and Human Genetics, and Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, TX 77030, USA.
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310
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311
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Cobb JE, White SJ, Harrap SB, Ellis JA. Androgen receptor copy number variation and androgenetic alopecia: a case-control study. PLoS One 2009; 4:e5081. [PMID: 19340294 PMCID: PMC2659771 DOI: 10.1371/journal.pone.0005081] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 03/06/2009] [Indexed: 11/18/2022] Open
Abstract
Background The functional polymorphism that explains the established association of the androgen receptor (AR) with androgenetic alopecia (AGA) remains unidentified, but Copy Number Variation (CNV) might be relevant. CNV involves changes in copy number of large segments of DNA, leading to the altered dosage of gene regulators or genes themselves. Two recent reports indicate regions of CNV in and around AR, and these have not been studied in relation to AGA. The aim of this preliminary case-control study was to determine if AR CNV is associated with AGA, with the hypothesis that CNV is the functional AR variant contributing to this condition. Methodology/Principal Findings Multiplex Ligation-dependent Probe Amplification was used to screen for CNV in five AR exons and a conserved, non-coding region upstream of AR in 85 men carefully selected as cases and controls for maximal phenotypic contrast. There was no evidence of CNV in AR in any of the cases or controls, and thus no evidence of significant association between AGA and AR CNV. Conclusions/Significance The results suggest this form of genomic variation at the AR locus is unlikely to predispose to AGA.
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Affiliation(s)
- Joanna E. Cobb
- Department of Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Stefan J. White
- Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Stephen B. Harrap
- Department of Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Justine A. Ellis
- Department of Physiology, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Childrens Research Institute, Parkville, Victoria, Australia
- * E-mail:
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312
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Singh SM, Castellani CA, O'Reilly RL. Copy number variation showers in schizophrenia: an emerging hypothesis. Mol Psychiatry 2009; 14:356-8. [PMID: 19139749 DOI: 10.1038/mp.2008.149] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic discoveries on Schizophrenia remain challenging. Traditional approaches have provided clues, but no genes. Novel theories that must account for extensive heterogeneity, including high discordance of monozygotic (MZD) twins, are needed. To this end, the extensive repeats of the human genome may provide the predisposition for DNA replication errors operational at every cell cycle during meiosis and mitosis. These errors will shower the genome with replication errors including copy number variations. Depending on the timing and the genes involved, this will contribute to the mutational load and disease. The evidence for such a mechanism in schizophrenia is emerging.
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Affiliation(s)
- S M Singh
- University of Western Ontario, London, ON, Canada.
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313
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Genes, Environments, and Adolescent Substance Use: Retrospect and Prospect from the <I>FinnTwin</I> Studies. ACTA PSYCHOLOGICA SINICA 2009. [DOI: 10.3724/sp.j.1041.2008.01062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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314
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de Smith AJ, Walters RG, Froguel P, Blakemore AI. Human genes involved in copy number variation: mechanisms of origin, functional effects and implications for disease. Cytogenet Genome Res 2009; 123:17-26. [PMID: 19287135 DOI: 10.1159/000184688] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2008] [Indexed: 11/19/2022] Open
Abstract
Copy number variants (CNVs) overlap over 7000 genes, many of which are pivotal in biological pathways. The implications of this are profound, with consequences for evolutionary studies, population genetics, gene function and human phenotype, including elucidation of genetic susceptibility to major common diseases, the heritability of which has thus far defied full explanation. Even though this research is still in its infancy, CNVs have already been associated with a number of monogenic, syndromic and complex diseases: the development of high throughput and high resolution techniques for CNV screening is likely to bring further new insights into the contribution of copy number variation to common diseases. Amongst genes overlapped by CNVs, significant enrichments for certain gene ontology categories have been identified, including those related to immune responses and interactions with the environment. Genes in both of these categories are thought to be important in evolutionary adaptation and to be particular targets of natural selection. Thus, a full appreciation of copy number variation may be important for our understanding of human evolution.
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Affiliation(s)
- A J de Smith
- Section of Genomic Medicine, Imperial College London, Hammersmith Hospital, London, UK
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315
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Oikawa T, Yasuda K. Inclusion of genetically identical animals to a numerator relationship matrix and modification of its inverse. Genet Sel Evol 2009; 41:25. [PMID: 19284529 PMCID: PMC2674412 DOI: 10.1186/1297-9686-41-25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 03/03/2009] [Indexed: 01/09/2023] Open
Abstract
In the field of animal breeding, estimation of genetic parameters and prediction of breeding values are routinely conducted by analyzing quantitative traits. Using an animal model and including the direct inverse of a numerator relationship matrix (NRM) into a mixed model has made these analyses possible. However, a method including a genetically identical animal (GIA) in NRM if genetic relationships between pairs of GIAs are not perfect, is still lacking. Here, we describe a method to incorporate GIAs into NRM using a K matrix in which diagonal elements are set to 1.0, off-diagonal elements between pairs of GIAs to (1-x) and the other elements to 0, where x is a constant less than 0.05. The inverse of the K matrix is then calculated directly by a simple formula. Thus, the inverse of the NRM is calculated by the products of the lower triangular matrix that identifies the parents of each individual, its transpose matrix, the inverse of the K matrix and the inverse of diagonal matrix D, in which the diagonal elements comprise a number of known parents and their inbreeding coefficients. The computing method is adaptable to the analysis of a data set including pairs of GIAs with imperfect relationships.
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Affiliation(s)
- Takuro Oikawa
- Graduate School of Natural Science and Technology, Okayama University, Okayama-shi, Japan.
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316
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Arlt MF, Mulle JG, Schaibley VM, Ragland RL, Durkin SG, Warren ST, Glover TW. Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants. Am J Hum Genet 2009; 84:339-50. [PMID: 19232554 PMCID: PMC2667984 DOI: 10.1016/j.ajhg.2009.01.024] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 01/23/2009] [Accepted: 01/30/2009] [Indexed: 11/28/2022] Open
Abstract
Copy number variants (CNVs) are an important component of genomic variation in humans and other mammals. Similar de novo deletions and duplications, or copy number changes (CNCs), are now known to be a major cause of genetic and developmental disorders and to arise somatically in many cancers. A major mechanism leading to both CNVs and disease-associated CNCs is meiotic unequal crossing over, or nonallelic homologous recombination (NAHR), mediated by flanking repeated sequences or segmental duplications. Others appear to involve nonhomologous end joining (NHEJ) or aberrant replication suggesting a mitotic cell origin. Here we show that aphidicolin-induced replication stress in normal human cells leads to a high frequency of CNCs of tens to thousands of kilobases across the human genome that closely resemble CNVs and disease-associated CNCs. Most deletion and duplication breakpoint junctions were characterized by short (<6 bp) microhomologies, consistent with the hypothesis that these rearrangements were formed by NHEJ or a replication-coupled process, such as template switching. This is a previously unrecognized consequence of replication stress and suggests that replication fork stalling and subsequent error-prone repair are important mechanisms in the formation of CNVs and pathogenic CNCs in humans.
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Affiliation(s)
- Martin F. Arlt
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer G. Mulle
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | | | - Ryan L. Ragland
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sandra G. Durkin
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephen T. Warren
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Thomas W. Glover
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
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317
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Mukherjee N, Kang C, Wolfe HM, Hertzberg BS, Smith JK, Lin W, Gerig G, Hamer RM, Gilmore JH. Discordance of prenatal and neonatal brain development in twins. Early Hum Dev 2009; 85:171-5. [PMID: 18804925 PMCID: PMC2696044 DOI: 10.1016/j.earlhumdev.2008.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 07/21/2008] [Accepted: 07/23/2008] [Indexed: 11/28/2022]
Abstract
BACKGROUND Discordance of birth weight has been observed in twin pairs, though little is known about prenatal and early neonatal discordance of head and brain size, and the role that zygosity and chorionicity play in discordances of early brain development in twins. AIMS To compare prenatal and neonatal discordances of head size in monozygotic-monochorionic (MZ-MC), monozygotic-dichorionic (MZ-DC), and same-sex dizygotic-dichorionic twin pairs (DZ). STUDY DESIGN Subjects prospectively had ultrasounds at 22 and 32 weeks gestational age, and magnetic resonance imaging (MRI) of the brain MRI after birth. SUBJECTS 88 twin pairs recruited from two university hospital prenatal diagnostic clinics; 22 MZ-MC, 17 MZ-DC, and 49 same-sex DZ pairs. OUTCOME MEASURES Discordance of head circumference (HC) and weight at 22 weeks, 32 weeks and birth, as well as intracranial volume (ICV) on neonatal MRI. RESULTS There were no group differences in discordance of head circumference and weight on the 22 or 32 week ultrasounds, or at birth. MZ-MC twins tended to have numerically greater discordances of HC and weight. There was a significant group difference in ICV on neonatal MRI (ANOVA, p=0.0143), with DZ twins having significantly greater discordance than MZ-MC (p=0.028) or MZ-DC (p=0.0131) twins. CONCLUSIONS This study indicates that zygosity and chorionicity do not contribute to significant discordances of head size in late prenatal development. DZ twins do have significantly greater discordances of ICV on neonatal MRI, suggesting a relatively greater genetic influence on brain growth in the first weeks after birth.
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Affiliation(s)
- Niyati Mukherjee
- Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Chaeryon Kang
- Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Honor M. Wolfe
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
| | | | - J. Keith Smith
- Department of Radiology, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Weili Lin
- Department of Radiology, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Guido Gerig
- Scientific Computing and Imaging, University of Utah, Salt Lake City, UT
| | - Robert M. Hamer
- Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, NC
| | - John H. Gilmore
- Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, NC
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318
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Goodin DS. The causal cascade to multiple sclerosis: a model for MS pathogenesis. PLoS One 2009; 4:e4565. [PMID: 19242548 PMCID: PMC2644781 DOI: 10.1371/journal.pone.0004565] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 12/22/2008] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND MS pathogenesis seems to involve both genetic susceptibility and environmental risk factors. Three sequential factors are implicated in the environmental risk. The first acts near birth, the second acts during childhood, and the third acts long thereafter. Two candidate factors (vitamin D deficiency and Epstein-Barr viral infection) seem well suited to the first two environmental events. METHODOLOGY/PRINCIPAL FINDINGS A mathematical Model for MS pathogenesis is developed, incorporating these environmental and genetic factors into a causal scheme that can explain some of the recent changes in MS-epidemiology (e.g., increasing disease prevalence, a changing sex-ratio, and regional variations in monozygotic twin concordance rates). CONCLUSIONS/SIGNIFICANCE This Model suggests that genetic susceptibility is overwhelmingly the most important determinant of MS pathogenesis. Indeed, over 99% of individuals seem genetically incapable of developing MS, regardless of what environmental exposures they experience. Nevertheless, the contribution of specific genes to MS-susceptibility seems only modest. Thus, despite HLA DRB1*1501 being the most consistently identified genetic marker of MS-susceptibility (being present in over 50% of northern MS patient populations), only about 1% of individuals with this allele are even genetically susceptible to getting MS. Moreover, because genetic susceptibility seems so similar throughout North America and Europe, environmental differences principally determine the regional variations in disease characteristics. Additionally, despite 75% of MS-patients being women, men are 60% more likely to be genetically-susceptible than women. Also, men develop MS at lower levels of environmental exposure than women. Nevertheless, women are more responsive to the recent changes in environmental-exposure (whatever these have been). This explains both the changing sex-ratio and the increasing disease prevalence (which has increased by a minimum of 32% in Canada over the past 35 years). As noted, environmental risk seems to result from three sequential components of environmental exposure. The potential importance of this Model for MS pathogenesis is that, if correct, a therapeutic strategy, designed to interrupt one or more of these sequential factors, has the potential to markedly reduce or eliminate disease prevalence in the future.
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Affiliation(s)
- Douglas S Goodin
- Department of Neurology, University of California San Francisco, San Francisco, California, USA.
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319
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Abstract
In this review we will evaluate evidence that altered gene dosage and structure impacts neurodevelopment and neural connectivity through deleterious effects on synaptic structure and function, and evidence that the latter are key contributors to the risk for autism. We will review information on alterations of structure of mitochondrial DNA and abnormal mitochondrial function in autism and indications that interactions of the nuclear and mitochondrial genomes may play a role in autism pathogenesis. In a final section we will present data derived using Affymetrix SNP 6.0 microarray analysis of DNA of a number of subjects and parents recruited to our autism spectrum disorders project. We include data on two sets of monozygotic twins. Collectively these data provide additional evidence of nuclear and mitochondrial genome imbalance in autism and evidence of specific candidate genes in autism. We present data on dosage changes in genes that map on the X chromosomes and the Y chromosome. Precise analyses of Y located genes are often difficult because of the high degree of homology of X- and Y-related genes. However, continued efforts to analyze the latter are important, given the consistent evidence for a 4:1 ratio of males to females affected by autism. It is also important to consider whether environmental factors play a role in generating the nuclear and mitochondrial genomic instability we have observed. The study of autism will benefit from a move to analysis of pathways and multigene clusters for identification of subtypes that share a specific genetic etiology.
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Affiliation(s)
- Moyra Smith
- Department of Pediatrics, University of California-Irvine, Irvine, CA 92697, USA.
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320
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A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 2009; 5:e1000327. [PMID: 19180184 PMCID: PMC2621351 DOI: 10.1371/journal.pgen.1000327] [Citation(s) in RCA: 615] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Chromosome structural changes with nonrecurrent endpoints associated with genomic disorders offer windows into the mechanism of origin of copy number variation (CNV). A recent report of nonrecurrent duplications associated with Pelizaeus-Merzbacher disease identified three distinctive characteristics. First, the majority of events can be seen to be complex, showing discontinuous duplications mixed with deletions, inverted duplications, and triplications. Second, junctions at endpoints show microhomology of 2–5 base pairs (bp). Third, endpoints occur near pre-existing low copy repeats (LCRs). Using these observations and evidence from DNA repair in other organisms, we derive a model of microhomology-mediated break-induced replication (MMBIR) for the origin of CNV and, ultimately, of LCRs. We propose that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR). Under these circumstances, single-strand 3′ tails from broken replication forks will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.
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321
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Kaminsky ZA, Tang T, Wang SC, Ptak C, Oh GHT, Wong AHC, Feldcamp LA, Virtanen C, Halfvarson J, Tysk C, McRae AF, Visscher PM, Montgomery GW, Gottesman II, Martin NG, Petronis A. DNA methylation profiles in monozygotic and dizygotic twins. Nat Genet 2009; 41:240-5. [DOI: 10.1038/ng.286] [Citation(s) in RCA: 536] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 10/10/2008] [Indexed: 01/07/2023]
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322
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Abstract
Two developments have sparked new directions in the genetics-to-genomics transition for research and medical applications: the advance of whole-genome assays by array or DNA sequencing technologies, and the discovery among human genomes of extensive submicroscopic genomic structural variation, including copy number variation. For health care to benefit from interpretation of genomic data, we need to know how these variants contribute to the phenotype of the individual. Research is revealing the spectrum, both in size and complexity, of structural genotypic variation, and its association with a broad range of human phenotypes. Genomic disorders associated with relatively large, recurrent contiguous variants have been recognized for some time, as have certain Mendelian traits associated with functional disruption of single genes by structural variation. More recent examples from phenotype- and genotype-driven studies demonstrate a greater level of complexity, with evidence of incremental dosage effects, gene interaction networks, buffering and modifiers, and position effects. Mechanisms underlying such variation are emerging to provide a handle on the bulk of human variation, which is associated with complex traits and adaptive potential. Interpreting genotypes for personalized health care and communicating knowledge to the individual will be significant challenges for genomics professionals.
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323
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Shanks N, Greek R, Greek J. Are animal models predictive for humans? Philos Ethics Humanit Med 2009; 4:2. [PMID: 19146696 PMCID: PMC2642860 DOI: 10.1186/1747-5341-4-2] [Citation(s) in RCA: 431] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 01/15/2009] [Indexed: 05/20/2023] Open
Abstract
It is one of the central aims of the philosophy of science to elucidate the meanings of scientific terms and also to think critically about their application. The focus of this essay is the scientific term predict and whether there is credible evidence that animal models, especially in toxicology and pathophysiology, can be used to predict human outcomes. Whether animals can be used to predict human response to drugs and other chemicals is apparently a contentious issue. However, when one empirically analyzes animal models using scientific tools they fall far short of being able to predict human responses. This is not surprising considering what we have learned from fields such evolutionary and developmental biology, gene regulation and expression, epigenetics, complexity theory, and comparative genomics.
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Affiliation(s)
- Niall Shanks
- Wichita State University, Department of History, 1845 N Fairmont, Fiske Hall, Wichita KS 67260, USA
| | - Ray Greek
- Americans For Medical Advancement, 2251 Refugio Rd Goleta, CA 93117, USA
| | - Jean Greek
- Americans For Medical Advancement, 2251 Refugio Rd Goleta, CA 93117, USA
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324
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Abstract
The genetic make-up of an organism, established at fertilization, is not conventionally expected to change during development unless mutation occurs. However, there is actually evidence that considerable variation can arise. Some of these changes may occur in response to the environment. This article reviews such variations in genome size or DNA content (excluding ploidy-level changes). The variation can be generated by processes, including high-frequency chromosomal recombination, transposition, cis-element-enhanced gene amplification and repetitive-sequence-based changes in nuclear DNA content. Environmentally induced and developmentally regulated genomic variation (ED-genomic variation or ED-genetic variation) can be found in both coding and non-coding sequences, and is often non-Mendelian in its inheritance pattern. Changes can depend on development (for example, propagation method, seed/fruit position on plants, embryo stage, etc.) and occur in response to the environment (for example, light, temperature, herbicide, salinity, fertilizer, land slope direction, pathogen infection, etc.). Some plants have meiotic (or rejuvenation) corrections, which restore their genome sizes to a certain degree. However, Mendelian inheritance and acquired inheritance of the variants occur, and both inheritance types may be different expressions evolved for the same adaptive responses. With this perspective, the terms 'pure-breeding line' or 'stable cultivar' may only be appropriate for a given mode of reproduction or propagation, and for a given environment. ED-genomic variation appears to be an essential component of differentiation, development and adaptation. Consequently, modern molecular biology tools, such as microarray hybridization and new sequencing technology, should be directed towards a more comprehensive evaluation of ED-genomic variation.
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325
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Abstract
Extraordinary technical advances in the field of human genetics over the past few years have catalyzed an explosion of new information about the genetics of human autoimmunity. In particular, the ability to scan the entire genome for common polymorphisms that associate with disease has led to the identification of numerous new risk genes involved in autoimmune phenotypes. Several themes are emerging. Autoimmune disorders have a complex genetic basis; multiple genes contribute to disease risk, each with generally modest effects independently. In addition, it is now clear that common genes underlie multiple autoimmune disorders. There is also heterogeneity among subphenotypes within a disease and across major racial groups. The current crop of genetic associations are only the start of a complete catalog of genetic factors for autoimmunity, and it remains unclear to what extent common variation versus multiple rare variants contribute to disease susceptibility. The current review focuses on recent discoveries within functionally related groups of genes that provide clues to novel pathways of pathogenesis for human autoimmunity.
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Affiliation(s)
- Peter K. Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, New York 11030
| | - Lina M. Olsson
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, New York 11030
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326
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Genotype-phenotype mapping developmental biology confronts the toolkit paradox. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 278:119-48. [PMID: 19815178 DOI: 10.1016/s1937-6448(09)78003-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The quest to understand the relationship between an organism's DNA sequence and three-dimensional form is an interdisciplinary task, integrating diverse fields of the life sciences. The relevance of the metaphor of a genotype-phenotype map is explored from a developmental perspective, in light of the recent concept of a "molecular toolkit" of protein-coding genes, and the widespread view that analyzing the logic and mechanics of gene regulation at multiple levels is key to explaining how morphology is genetically encoded. We discuss the challenges of decoding genomes despite variable genetic backgrounds, the dynamically changing physical and molecular contexts of the internal environment during development, and the impact of external forces on morphogenesis.
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327
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Joober R, Boksa P. A new wave in the genetics of psychiatric disorders: the copy number variant tsunami. J Psychiatry Neurosci 2009; 34:55-9. [PMID: 19125213 PMCID: PMC2612076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Affiliation(s)
- Ridha Joober
- Department of Psychiatry, McGill University, Douglas Mental Health University Institute, Montréal, QC, Canada.
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328
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Fadista J, Nygaard M, Holm LE, Thomsen B, Bendixen C. A snapshot of CNVs in the pig genome. PLoS One 2008; 3:e3916. [PMID: 19079605 PMCID: PMC2596487 DOI: 10.1371/journal.pone.0003916] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Accepted: 11/14/2008] [Indexed: 11/18/2022] Open
Abstract
Recent studies of mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report a first account of CNVs in the pig genome covering part of the chromosomes 4, 7, 14, and 17 already sequenced and assembled. A custom tiling oligonucleotide array was used with a median probe spacing of 409 bp for screening 12 unrelated Duroc boars that are founders of a large family material. After a strict CNV calling pipeline, 37 copy number variable regions (CNVRs) across all four chromosomes were identified, with five CNVRs overlapping segmental duplications, three overlapping pig unigenes and one overlapping a RefSeq pig mRNA. This CNV snapshot analysis is the first of its kind in the porcine genome and constitutes the basis for a better understanding of porcine phenotypes and genotypes with the prospect of identifying important economic traits.
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Affiliation(s)
- João Fadista
- Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark
| | - Marianne Nygaard
- Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark
| | - Lars-Erik Holm
- Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark
| | - Bo Thomsen
- Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark
| | - Christian Bendixen
- Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark
- * E-mail:
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329
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Murphy EL, Murtagh FEM, Carey I, Sheerin NS. Understanding symptoms in patients with advanced chronic kidney disease managed without dialysis: use of a short patient-completed assessment tool. Nephron Clin Pract 2008; 111:c74-80. [PMID: 19088482 DOI: 10.1159/000183177] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Accepted: 09/12/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND It is often believed that patients with advanced chronic kidney disease (CKD) stage 4-5 have few symptoms, and that dying with renal disease is relatively symptom-free. But the symptom burden of patients managed conservatively (without dialysis), with potentially high levels of comorbidity and poor functional status, is unknown. This clinical audit evaluated the prevalence and severity of symptoms in conservatively managed CKD stage 4-5 patients. METHODS Symptom data was collected from all conservatively managed patients from 2 renal units referred to a new renal palliative care service over a 10-month period between April 2005 and January 2006. Data on symptom prevalence and severity was collected as part of their routine clinical care, using a modified version of the Patient Outcome Scale--symptom module (POSs). This patient-completed instrument identifies the presence and severity of 17 symptoms. Demographic data was also collected, including estimated glomerular filtration rate (eGFR) using the MDRD formula, primary renal diagnosis and comorbidity. RESULTS Symptoms were evaluated in 55 patients, with a mean age of 82 years (SD 5.5, range 66-96). eGFR ranged from 3 to 30 ml/min (median 11, mean 12.75). In patients with CKD stage 4-5, managed without dialysis, the symptom burden is high. The most prevalent symptoms reported were weakness (75%), poor mobility (75%), poor appetite (58%), pain (56%), pruritus (56%) and dyspnoea (49%). The total number of symptoms each individual patient experienced ranged from 1 to 14 (median 7, mean 6.8). Symptoms were frequently reported as moderate, severe, or overwhelming; in 54% of patients with poor mobility, 48% with weakness, 30% with itching, 31% with anorexia and 27% with pain. No significant association was demonstrated between the number of symptoms experienced and either severity of renal disease or comorbidity score. CONCLUSIONS This structured clinical evaluation demonstrates the extent and severity of symptom burden in conservatively managed patients with CKD stage 4-5, and demonstrates the use of an appropriate clinical tool that can be used to assess the efficacy of treatment.
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Affiliation(s)
- Emma L Murphy
- Florence Nightingale School of Nursing and Midwifery, King's College London, London, UK.
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330
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Affiliation(s)
- D A Collier
- Division of Psychological Medicine and Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, UK.
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331
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Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature 2008. [PMID: 19043404 DOI: 10.1038/nature07540 19043404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides. Studies of a few unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is used and stored. Here we characterize the faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers, to address how host genotype, environmental exposure and host adiposity influence the gut microbiome. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person's gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable 'core microbiome' at the gene, rather than at the organismal lineage, level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean).
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Affiliation(s)
- Peter J Turnbaugh
- Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
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332
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Abstract
The human distal gut harbors a vast ensemble of microbes (the microbiota) that provide us with important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides1–6. Studies of a small number of unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes6–8, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is utilized and stored3–5. To address the question of how host genotype, environmental exposures, and host adiposity influence the gut microbiome, we have characterized the fecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person’s gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable ‘core microbiome’ at the gene, rather than at the organismal lineage level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity, and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiologic states (obese versus lean).
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333
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Piotrowski A, Bruder CEG, Andersson R, Diaz de Ståhl T, Menzel U, Sandgren J, Poplawski A, von Tell D, Crasto C, Bogdan A, Bartoszewski R, Bebok Z, Krzyzanowski M, Jankowski Z, Partridge EC, Komorowski J, Dumanski JP. Somatic mosaicism for copy number variation in differentiated human tissues. Hum Mutat 2008; 29:1118-24. [PMID: 18570184 DOI: 10.1002/humu.20815] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Two major types of genetic variation are known: single nucleotide polymorphisms (SNPs), and a more recently discovered structural variation, involving changes in copy number (CNVs) of kilobase- to megabase-sized chromosomal segments. It is unknown whether CNVs arise in somatic cells, but it is, however, generally assumed that normal cells are genetically identical. We tested 34 tissue samples from three subjects and, having analyzed for each tissue < or =10(-6) of all cells expected in an adult human, we observed at least six CNVs, affecting a single organ or one or more tissues of the same subject. The CNVs ranged from 82 to 176 kb, often encompassing known genes, potentially affecting gene function. Our results indicate that humans are commonly affected by somatic mosaicism for stochastic CNVs, which occur in a substantial fraction of cells. The majority of described CNVs were previously shown to be polymorphic between unrelated subjects, suggesting that some CNVs previously reported as germline might represent somatic events, since in most studies of this kind, only one tissue is typically examined and analysis of parents for the studied subjects is not routinely performed. A considerable number of human phenotypes are a consequence of a somatic process. Thus, our conclusions will be important for the delineation of genetic factors behind these phenotypes. Consequently, biobanks should consider sampling multiple tissues to better address mosaicism in the studies of somatic disorders.
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Affiliation(s)
- Arkadiusz Piotrowski
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294-0024, USA
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334
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Zukunft der Zytogenetik. MED GENET-BERLIN 2008. [DOI: 10.1007/s11825-008-0129-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Zusammenfassung
Der Themenschwerpunkt dieser Ausgabe der Zeitschrift „Medizinische Genetik“ ist der gegenwärtigen Entwicklung der Zytogenetik gewidmet. Die klassische Bänderungsanalyse, die seit Jahrzehnten in der humangenetischen Routinediagnostik eine zentrale Position einnimmt, wird anhand qualitätssichernder Maßnahmen dargestellt. Verschiedene Beiträge beschreiben die molekulare Zytogenetik, die im Wesentlichen auf der Fluoreszenz-in-situ-Hybridisierung (FISH) beruht. Die Einführung der vergleichenden genomischen Hybridisierung [“comparative genomic hybridization“ (CGH)], speziell auf Arrayplattformen, hat die Zytogenetik revolutioniert und erlaubt die Bearbeitung völlig neuer Fragestellungen. Ein besonderer Schwerpunkt der Zytogenetik, der sie von vielen anderen molekularen Techniken unterscheidet, ist, dass sie Analysen auf Einzelzellniveau ermöglichen. Mit dem vorliegenden Heft wird auch versucht, mögliche zukünftige Entwicklungen der Zytogenetik aufzuzeichnen.
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335
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Cook EH, Scherer SW. Copy-number variations associated with neuropsychiatric conditions. Nature 2008; 455:919-23. [PMID: 18923514 DOI: 10.1038/nature07458] [Citation(s) in RCA: 503] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Neuropsychiatric conditions such as autism and schizophrenia have long been attributed to genetic alterations, but identifying the genes responsible has proved challenging. Microarray experiments have now revealed abundant copy-number variation--a type of variation in which stretches of DNA are duplicated, deleted and sometimes rearranged--in the human population. Genes affected by copy-number variation are good candidates for research into disease susceptibility. The complexity of neuropsychiatric genetics, however, dictates that assessment of the biomedical relevance of copy-number variants and the genes that they affect needs to be considered in an integrated context.
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Affiliation(s)
- Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois, 1747 West Roosevelt Road, Chicago, Illinois 60608, USA
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336
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Geigl J, Speicher M. Neue Verfahren für Einzelzellanalysen in Forschung und Diagnostik. MED GENET-BERLIN 2008. [DOI: 10.1007/s11825-008-0138-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zusammenfassung
Die traditionelle Zytogenetik ist ein Paradebeispiel für eine Einzelzelldiagnostik, weil mit jeder gebänderten Metaphase das gesamte Genom einer Zelle – bei relativ niedriger Auflösung – untersucht wird. Dies repräsentierte über mehrere Jahrzehnte einen wichtigen Unterschied zu molekulargenetischen Untersuchungstechniken, die in der Mehrheit der Fälle auf DNA oder RNA basieren, die aus hunderten oder tausenden von Zellen extrahiert wurden. Viele Fragestellungen können jedoch nur durch Analysen auf dem Niveau einzelner oder weniger Zellen beantwortet werden. Deshalb wurden besonders in den letzten Jahren neue Einzelzelltechniken mit dem Ziel entwickelt, immer mehr Loci mit verbessertem Auflösungsvermögen simultan analysieren zu können. In dieser Übersichtsarbeit werden die diesbezüglich wichtigsten Entwicklungen der letzten Jahre zusammengefasst.
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Affiliation(s)
- J. Geigl
- Aff1_138 grid.11598.34 0000000089882476 Institut für Humangenetik Medizinische Universität Graz Harrachgasse 21/8 A-8010 Graz Österreich
| | - M. Speicher
- Aff1_138 grid.11598.34 0000000089882476 Institut für Humangenetik Medizinische Universität Graz Harrachgasse 21/8 A-8010 Graz Österreich
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337
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Extensive genomic copy number variation in embryonic stem cells. Proc Natl Acad Sci U S A 2008; 105:17453-6. [PMID: 18988746 DOI: 10.1073/pnas.0805638105] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Recent analysis of the human and mouse genomes has revealed that highly identical duplicated elements account for >5% of the sequence content. These elements vary in copy number between individuals. Copy number variations (CNVs) contribute significantly to genetic differences among individuals and are increasingly recognized as a causal factor in human diseases with different etiologies. In inbred mouse strains, CNVs have been fixed by inbreeding, but they are highly variable among strains. Within strains, de novo germ-line CNVs can occur, leading to interindividual variation. By analyzing the genome of clonal isolates of mouse ES cells derived from common parental lines, we have uncovered extensive and recurrent CNVs. This variation arises during mitosis and can be cotransmitted into the mouse germ line along with engineered alleles, contributing to genetic variability. The frequency and extent of these genomic changes in ES cells suggests that all somatic tissues in individuals will be mosaics composed of variants of the zygotic genome. Human ES (hES) cells and derived somatic lineages may be similarly affected, challenging the concept of a stable somatic genome.
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338
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Gu W, Zhang F, Lupski JR. Mechanisms for human genomic rearrangements. PATHOGENETICS 2008; 1:4. [PMID: 19014668 PMCID: PMC2583991 DOI: 10.1186/1755-8417-1-4] [Citation(s) in RCA: 432] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 11/03/2008] [Indexed: 02/08/2023]
Abstract
Genomic rearrangements describe gross DNA changes of the size ranging from a couple of hundred base pairs, the size of an average exon, to megabases (Mb). When greater than 3 to 5 Mb, such changes are usually visible microscopically by chromosome studies. Human diseases that result from genomic rearrangements have been called genomic disorders. Three major mechanisms have been proposed for genomic rearrangements in the human genome. Non-allelic homologous recombination (NAHR) is mostly mediated by low-copy repeats (LCRs) with recombination hotspots, gene conversion and apparent minimal efficient processing segments. NAHR accounts for most of the recurrent rearrangements: those that share a common size, show clustering of breakpoints, and recur in multiple individuals. Non-recurrent rearrangements are of different sizes in each patient, but may share a smallest region of overlap whose change in copy number may result in shared clinical features among different patients. LCRs do not mediate, but may stimulate non-recurrent events. Some rare NAHRs can also be mediated by highly homologous repetitive sequences (for example, Alu, LINE); these NAHRs account for some of the non-recurrent rearrangements. Other non-recurrent rearrangements can be explained by non-homologous end-joining (NHEJ) and the Fork Stalling and Template Switching (FoSTeS) models. These mechanisms occur both in germ cells, where the rearrangements can be associated with genomic disorders, and in somatic cells in which such genomic rearrangements can cause disorders such as cancer. NAHR, NHEJ and FoSTeS probably account for the majority of genomic rearrangements in our genome and the frequency distribution of the three at a given locus may partially reflect the genomic architecture in proximity to that locus. We provide a review of the current understanding of these three models.
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Affiliation(s)
- Wenli Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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339
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The 'fractionable autism triad': a review of evidence from behavioural, genetic, cognitive and neural research. Neuropsychol Rev 2008; 18:287-304. [PMID: 18956240 DOI: 10.1007/s11065-008-9076-8] [Citation(s) in RCA: 282] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 09/13/2008] [Indexed: 10/21/2022]
Abstract
Autism is diagnosed on the basis of a triad of impairments in social interaction, communication, and flexible imaginative functions (with restricted and repetitive behaviors and interests; RRBIs). There has been a strong presumption that these different features of the syndrome are strongly intertwined and proceed from a common cause at the genetic, cognitive and neural levels. In this review we examine evidence for an alternative approach, considering the triad as largely 'fractionable'. We present evidence from our own twin studies, and review relevant literature on autism and autistic-like traits in other groups. We suggest that largely independent genes may operate on social skills/impairments, communication abilities, and RRBIs, requiring a change in molecular-genetic research approaches. At the cognitive level, we suggest that satisfactory accounts exist for each of the triad domains, but no single unitary account can explain both social and nonsocial features of autism. We discuss the implications of the fractionable-triad approach for both diagnosis and future research directions.
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340
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Woldringh G, Janssen I, Hehir-Kwa J, van den Elzen C, Kremer J, de Boer P, Schoenmakers E. Constitutional DNA copy number changes in ICSI children. Hum Reprod 2008; 24:233-40. [DOI: 10.1093/humrep/den323] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Recent discoveries in the science of ageing indicate that lifespan in model organisms such as yeast, nematodes, flies and mice is plastic and can be manipulated by genetic, nutritional or pharmacological intervention. A better understanding of the targets of such interventions, as well as the proximate causes of ageing-related degeneration and disease, is essential before we can evaluate if abrogation of human senescence is a realistic prospect.
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342
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Carvalho CMB, Lupski JR. Copy number variation at the breakpoint region of isochromosome 17q. Genome Res 2008; 18:1724-32. [PMID: 18714090 DOI: 10.1101/gr.080697.108] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Isochromosome 17q, or i(17q), is one of the most frequent nonrandom changes occurring in human neoplasia. Most of the i(17q) breakpoints cluster within a approximately 240-kb interval located in the Smith-Magenis syndrome common deletion region in 17p11.2. The breakpoint cluster region is characterized by a complex architecture with large ( approximately 38-49 kb), inverted and directly oriented, low-copy repeats (LCRs), known as REPA and REPB that apparently lead to genomic instability and facilitate somatic genetic rearrangements. Through the analysis of bacterial artificial chromosome (BAC) clones, pulsed-field gel electrophoresis (PFGE), and public array comparative genomic hybridization (array CGH) data, we show that the REPA/B structure is also susceptible to frequent meiotic rearrangements. It is a highly dynamic genomic region undergoing deletions, inversions, and duplications likely produced by non-allelic homologous recombination (NAHR) mediated by the highly identical SNORD3@, also known as U3, gene cluster present therein. We detected at least seven different REPA/B structures in samples from 29 individuals of which six represented potentially novel structures. Two polymorphic copy-number variation (CNV) variants, detected in 20% of samples, could be structurally described along with the likely underlying molecular mechanism for formation. Our data show the high susceptibility to rearrangements at the i(17q) breakpoint cluster region in the general population and exemplifies how large genomic regions laden with LCRs still represent a technical challenge for both determining specific structure and assaying population variation. The variant REPA/B structures identified may have different susceptibilities for inducing i(17q), thus potentially representing important risk alleles for tumor progression.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Abstract
Recent years have seen great advances in generating and analyzing data to identify the genetic architecture of biological traits. Human disease has understandably received intense research focus, and the genes responsible for most Mendelian diseases have successfully been identified. However, the same advances have shown a consistent if less satisfying pattern, in which complex traits are affected by variation in large numbers of genes, most of which have individually minor or statistically elusive effects, leaving the bulk of genetic etiology unaccounted for. This pattern applies to diverse and unrelated traits, not just disease, in basically all species, and is consistent with evolutionary expectations, raising challenging questions about the best way to approach and understand biological complexity.
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Affiliation(s)
- Kenneth M Weiss
- Department of Anthropology and Integrated Biosciences Genetics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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344
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Morgan DK, Whitelaw E. The case for transgenerational epigenetic inheritance in humans. Mamm Genome 2008; 19:394-7. [PMID: 18663528 DOI: 10.1007/s00335-008-9124-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Accepted: 05/28/2008] [Indexed: 11/28/2022]
Abstract
Work in the laboratory mouse has identified a group of genes, called metastable epialleles, that are informing us about the mechanisms by which the epigenetic state is established in the embryo. At these alleles, transcriptional activity is dependent on the epigenetic state and this can vary from cell to cell in the one tissue type. The decision to be active or inactive is probabilistic and sensitive to environmental influences. Moreover, in some cases the epigenetic state at these alleles can survive across generations, termed transgenerational epigenetic inheritance. Together these findings raise the spectre of Lamarckism and epigenetics is now being touted as an explanation for some intergenerational effects in human populations. In this review we will discuss the evidence so far.
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Affiliation(s)
- Daniel K Morgan
- Division of Population Studies and Human Genetics, Queensland Institute of Medical Research, 300 Herston Road, Herston, Brisbane 4006, Australia
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347
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Derijck A, van der Heijden G, Giele M, Philippens M, de Boer P. DNA double-strand break repair in parental chromatin of mouse zygotes, the first cell cycle as an origin of de novo mutation. Hum Mol Genet 2008; 17:1922-37. [PMID: 18353795 DOI: 10.1093/hmg/ddn090] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In the human, the contribution of the sexes to the genetic load is dissimilar. Especially for point mutations, expanded simple tandem repeats and structural chromosome mutations, the contribution of the male germline is dominant. Far less is known about the male germ cell stage(s) that are most vulnerable to mutation contraction. For the understanding of de novo mutation induction in the germline, mechanistic insight of DNA repair in the zygote is mandatory. At the onset of embryonic development, the parental chromatin sets occupy one pronucleus (PN) each and DNA repair can be regarded as a maternal trait, depending on proteins and mRNAs provided by the oocyte. Repair of DNA double-strand breaks (DSBs) is executed by non-homologous end joining (NHEJ) and homologous recombination (HR). Differentiated somatic cells often resolve DSBs by NHEJ, whereas embryonic stem cells preferably use HR. We show NHEJ and HR to be both functional during the zygotic cell cycle. NHEJ is already active during replacement of sperm protamines by nucleosomes. The kinetics of G1 repair is influenced by DNA-PK(cs) hypomorphic activity. Both HR and NHEJ are operative in S-phase, HR being more active in the male PN. DNA-PK(cs) deficiency upregulates the HR activity. Both after sperm remodeling and at first mitosis, spontaneous levels of gammaH2AX foci (marker for DSBs) are high. All immunoflurescent indices of DNA damage and DNA repair point at greater spontaneous damage and induced repair activity in paternal chromatin in the zygote.
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Affiliation(s)
- Alwin Derijck
- Department of Obstetrics and Gynaecology, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
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Lenroot RK, Giedd JN. The changing impact of genes and environment on brain development during childhood and adolescence: initial findings from a neuroimaging study of pediatric twins. Dev Psychopathol 2008; 20:1161-75. [PMID: 18838036 PMCID: PMC2892674 DOI: 10.1017/s0954579408000552] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Human brain development is created through continuing complex interactions of genetic and environmental influences. The challenge of linking specific genetic or environmental risk factors to typical or atypical behaviors has led to interest in using brain structural features as an intermediate phenotype. Twin studies in adults have found that many aspects of brain anatomy are highly heritable, demonstrating that genetic factors provide a significant contribution to variation in brain structures. Less is known about the relative impact of genes and environment while the brain is actively developing. We summarize results from the ongoing National Institute of Mental Health child and adolescent twin study that suggest that heritability of different brain areas changes over the course of development in a regionally specific fashion. Areas associated with more complex reasoning abilities become increasingly heritable with maturation. The potential mechanisms by which gene-environment interactions may affect heritability values during development is discussed.
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349
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Wineinger NE, Kennedy RE, Erickson SW, Wojczynski MK, Bruder CE, Tiwari HK. Statistical issues in the analysis of DNA Copy Number Variations. INTERNATIONAL JOURNAL OF COMPUTATIONAL BIOLOGY AND DRUG DESIGN 2008; 1:368-95. [PMID: 19774103 PMCID: PMC2747762 DOI: 10.1504/ijcbdd.2008.022208] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Approaches to assess copy number variation have advanced rapidly and are being incorporated into genetic studies. While the technology exists for CNV genotyping, a further understanding and discussion of how to use the CNV data for association analyses is warranted. We present the options available for processing and analysing CNV data. We break these steps down into choice of genotyping platform, normalisation of the array data, calling algorithm, and statistical analysis.
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Affiliation(s)
- Nathan E. Wineinger
- Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA, Fax: 205-975-2540, E-mail:
| | - Richard E. Kennedy
- Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA, Fax: 205-975-2540, E-mail:
| | - Stephen W. Erickson
- Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA, Fax: 205-975-2540, E-mail:
| | - Mary K. Wojczynski
- Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA, Fax: 205-975-2540, E-mail:
| | - Carl E. Bruder
- Viral Biochemistry, Division of Drug Discovery, Southern Research Institute, Birmingham, Alabama 35205, USA, Fax: (205) 581-2097, E-mail:
| | - Hemant K. Tiwari
- Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA, Fax: 205-975-2541, E-mail:
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