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Affiliation(s)
| | - Michael P. Blair
- Retinal Consultants, Des Plaines, IL, USA
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, USA
| | - Harry Dietz
- Howard Hughes Medical Institute and The McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Pediatric Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Michael J. Shapiro
- Retinal Consultants, Des Plaines, IL, USA
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
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2
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Abstract
With more than 10 million genotyped customers, the consumer genomics industry is maturing and becoming a mainstream phenomenon. At last, innovations and applications, some unforeseen, are being brought to the masses.
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Affiliation(s)
| | - David Mittelman
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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3
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Fang H, Wu Y, Yang H, Yoon M, Jiménez-Barrón LT, Mittelman D, Robison R, Wang K, Lyon GJ. Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine. BMC Med Genomics 2017; 10:10. [PMID: 28228131 PMCID: PMC5322674 DOI: 10.1186/s12920-017-0246-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/14/2017] [Indexed: 12/18/2022] Open
Abstract
Background Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, there have been relatively few reports combining whole genome sequencing (WGS) and HPO, especially in the context of structural variants. Methods We illustrate an integrative analysis of WGS and HPO using an extended pedigree, which involves Prader–Willi Syndrome (PWS), hereditary hemochromatosis (HH), and dysautonomia-like symptoms. A comprehensive WGS pipeline was used to ensure reliable detection of genomic variants. Beyond variant filtering, we pursued phenotypic prioritization of candidate genes using Phenolyzer. Results Regarding PWS, WGS confirmed a 5.5 Mb de novo deletion of the parental allele at 15q11.2 to 15q13.1. Phenolyzer successfully returned the diagnosis of PWS, and pinpointed clinically relevant genes in the deletion. Further, Phenolyzer revealed how each of the genes is linked with the phenotypes represented by HPO terms. For HH, WGS identified a known disease variant (p.C282Y) in HFE of an affected female. Analysis of HPO terms alone fails to provide a correct diagnosis, but Phenolyzer successfully revealed the phenotype-genotype relationship using a disease-centric approach. Finally, Phenolyzer also revealed the complexity behind dysautonomia-like symptoms, and seven variants that might be associated with the phenotypes were identified by manual filtering based on a dominant inheritance model. Conclusions The integration of WGS and HPO can inform comprehensive molecular diagnosis for patients, eliminate false positives and reveal novel insights into undiagnosed diseases. Due to extreme heterogeneity and insufficient knowledge of human diseases, it is also important that phenotypic and genomic data are standardized and shared simultaneously. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0246-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Han Fang
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA.,Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yiyang Wu
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA
| | - Hui Yang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, USA.,Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
| | - Margaret Yoon
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Laura T Jiménez-Barrón
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, MX, Mexico
| | | | - Reid Robison
- Tute, Genomics Inc., 150 S 100 W, Provo, UT, USA.,Utah Foundation for Biomedical Research, Salt Lake City, UT, USA
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, USA.,Department of Psychiatry, University of Southern California, Los Angeles, CA, USA.,Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA.,Present Address: Department of Biomedical Informatics and Institute for Genomic Medicine, Columbia University Medical Center, New York, 10032, NY, USA
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .,Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA. .,Utah Foundation for Biomedical Research, Salt Lake City, UT, USA.
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4
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Quilez J, Guilmatre A, Garg P, Highnam G, Gymrek M, Erlich Y, Joshi RS, Mittelman D, Sharp AJ. Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans. Nucleic Acids Res 2016; 44:3750-62. [PMID: 27060133 PMCID: PMC4857002 DOI: 10.1093/nar/gkw219] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/22/2016] [Indexed: 01/23/2023] Open
Abstract
Despite representing an important source of genetic variation, tandem repeats (TRs) remain poorly studied due to technical difficulties. We hypothesized that TRs can operate as expression (eQTLs) and methylation (mQTLs) quantitative trait loci. To test this we analyzed the effect of variation at 4849 promoter-associated TRs, genotyped in 120 individuals, on neighboring gene expression and DNA methylation. Polymorphic promoter TRs were associated with increased variance in local gene expression and DNA methylation, suggesting functional consequences related to TR variation. We identified >100 TRs associated with expression/methylation levels of adjacent genes. These potential eQTL/mQTL TRs were enriched for overlaps with transcription factor binding and DNaseI hypersensitivity sites, providing a rationale for their effects. Moreover, we showed that most TR variants are poorly tagged by nearby single nucleotide polymorphisms (SNPs) markers, indicating that many functional TR variants are not effectively assayed by SNP-based approaches. Our study assigns biological significance to TR variations in the human genome, and suggests that a significant fraction of TR variations exert functional effects via alterations of local gene expression or epigenetics. We conclude that targeted studies that focus on genotyping TR variants are required to fully ascertain functional variation in the genome.
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Affiliation(s)
- Javier Quilez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Audrey Guilmatre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gareth Highnam
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Melissa Gymrek
- Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA New York Genome Center, New York, NY 10038, USA
| | - Yaniv Erlich
- Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY 10027, USA
| | - Ricky S Joshi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Mittelman
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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5
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O’Rawe J, Wu Y, Dörfel M, Rope A, Au P, Parboosingh J, Moon S, Kousi M, Kosma K, Smith C, Tzetis M, Schuette J, Hufnagel R, Prada C, Martinez F, Orellana C, Crain J, Caro-Llopis A, Oltra S, Monfort S, Jiménez-Barrón L, Swensen J, Ellingwood S, Smith R, Fang H, Ospina S, Stegmann S, Den Hollander N, Mittelman D, Highnam G, Robison R, Yang E, Faivre L, Roubertie A, Rivière JB, Monaghan K, Wang K, Davis E, Katsanis N, Kalscheuer V, Wang E, Metcalfe K, Kleefstra T, Innes A, Kitsiou-Tzeli S, Rosello M, Keegan C, Lyon G. TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations. Am J Hum Genet 2015; 97:922-32. [PMID: 26637982 PMCID: PMC4678794 DOI: 10.1016/j.ajhg.2015.11.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/05/2015] [Indexed: 11/30/2022] Open
Abstract
We describe an X-linked genetic syndrome associated with mutations in TAF1 and manifesting with global developmental delay, intellectual disability (ID), characteristic facial dysmorphology, generalized hypotonia, and variable neurologic features, all in male individuals. Simultaneous studies using diverse strategies led to the identification of nine families with overlapping clinical presentations and affected by de novo or maternally inherited single-nucleotide changes. Two additional families harboring large duplications involving TAF1 were also found to share phenotypic overlap with the probands harboring single-nucleotide changes, but they also demonstrated a severe neurodegeneration phenotype. Functional analysis with RNA-seq for one of the families suggested that the phenotype is associated with downregulation of a set of genes notably enriched with genes regulated by E-box proteins. In addition, knockdown and mutant studies of this gene in zebrafish have shown a quantifiable, albeit small, effect on a neuronal phenotype. Our results suggest that mutations in TAF1 play a critical role in the development of this X-linked ID syndrome.
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Bilgin Sonay T, Carvalho T, Robinson MD, Greminger MP, Krützen M, Comas D, Highnam G, Mittelman D, Sharp A, Marques-Bonet T, Wagner A. Tandem repeat variation in human and great ape populations and its impact on gene expression divergence. Genome Res 2015; 25:1591-1599. [PMID: 26290536 DOI: 10.1101/015784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 08/14/2015] [Indexed: 05/25/2023]
Abstract
Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation in humans and closely related species have been scarce due to technical difficulties derived from short-read technology. Here we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, in a total of six different species, and studied their impact on gene expression evolution. We found that population diversity patterns can be efficiently captured with short TRs (repeat unit length, 1-5 bp). We examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length, 2-50 bp). Genes that contained TRs in the promoters, in their 3' untranslated region, in introns, and in exons had higher expression divergence than genes without repeats in the regions. Polymorphic small repeats (1-5 bp) had also higher expression divergence compared with genes with fixed or no TRs in the gene promoters. Our findings highlight the potential contribution of TRs to human evolution through gene regulation.
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Affiliation(s)
- Tugce Bilgin Sonay
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-805 Zurich, Switzerland; The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tiago Carvalho
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Mark D Robinson
- The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Maja P Greminger
- Evolutionary Genetics Group, Anthropological Institute and Museum, University of Zurich, CH-8057 Zurich, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Anthropological Institute and Museum, University of Zurich, CH-8057 Zurich, Switzerland
| | - David Comas
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Gareth Highnam
- Department of Biological Science and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - David Mittelman
- Department of Biological Science and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Andrew Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai School, New York, New York 10029, USA
| | - Tomàs Marques-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain; Centro Nacional de Análisis Genómico (CNAG), PCB, Barcelona, 08028 Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-805 Zurich, Switzerland; The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; The Santa Fe Institute, Santa Fe, New Mexico 87501, USA
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7
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Bilgin Sonay T, Carvalho T, Robinson MD, Greminger MP, Krützen M, Comas D, Highnam G, Mittelman D, Sharp A, Marques-Bonet T, Wagner A. Tandem repeat variation in human and great ape populations and its impact on gene expression divergence. Genome Res 2015; 25:1591-9. [PMID: 26290536 PMCID: PMC4617956 DOI: 10.1101/gr.190868.115] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 08/14/2015] [Indexed: 12/20/2022]
Abstract
Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation in humans and closely related species have been scarce due to technical difficulties derived from short-read technology. Here we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, in a total of six different species, and studied their impact on gene expression evolution. We found that population diversity patterns can be efficiently captured with short TRs (repeat unit length, 1–5 bp). We examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length, 2–50 bp). Genes that contained TRs in the promoters, in their 3′ untranslated region, in introns, and in exons had higher expression divergence than genes without repeats in the regions. Polymorphic small repeats (1–5 bp) had also higher expression divergence compared with genes with fixed or no TRs in the gene promoters. Our findings highlight the potential contribution of TRs to human evolution through gene regulation.
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Affiliation(s)
- Tugce Bilgin Sonay
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-805 Zurich, Switzerland; The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tiago Carvalho
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Mark D Robinson
- The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Maja P Greminger
- Evolutionary Genetics Group, Anthropological Institute and Museum, University of Zurich, CH-8057 Zurich, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Anthropological Institute and Museum, University of Zurich, CH-8057 Zurich, Switzerland
| | - David Comas
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Gareth Highnam
- Department of Biological Science and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - David Mittelman
- Department of Biological Science and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Andrew Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai School, New York, New York 10029, USA
| | - Tomàs Marques-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain; Centro Nacional de Análisis Genómico (CNAG), PCB, Barcelona, 08028 Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-805 Zurich, Switzerland; The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; The Santa Fe Institute, Santa Fe, New Mexico 87501, USA
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8
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Abstract
Scientific publishers must shake off three centuries of publishing on paper and embrace 21st century technology to make scientific communication more intelligible, reproducible, engaging and rapidly available.
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9
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Santillan BA, Moye C, Mittelman D, Wilson JH. GFP-based fluorescence assay for CAG repeat instability in cultured human cells. PLoS One 2014; 9:e113952. [PMID: 25423602 PMCID: PMC4244167 DOI: 10.1371/journal.pone.0113952] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 11/03/2014] [Indexed: 12/13/2022] Open
Abstract
Trinucleotide repeats can be highly unstable, mutating far more frequently than point mutations. Repeats typically mutate by addition or loss of units of the repeat. CAG repeat expansions in humans trigger neurological diseases that include myotonic dystrophy, Huntington disease, and several spinocerebellar ataxias. In human cells, diverse mechanisms promote CAG repeat instability, and in mice, the mechanisms of instability are varied and tissue-dependent. Dissection of mechanistic complexity and discovery of potential therapeutics necessitates quantitative and scalable screens for repeat mutation. We describe a GFP-based assay for screening modifiers of CAG repeat instability in human cells. The assay exploits an engineered intronic CAG repeat tract that interferes with expression of an inducible GFP minigene. Like the phenotypes of many trinucleotide repeat disorders, we find that GFP function is impaired by repeat expansion, in a length-dependent manner. The intensity of fluorescence varies inversely with repeat length, allowing estimates of repeat tract changes in live cells. We validate the assay using transcription through the repeat and engineered CAG-specific nucleases, which have previously been reported to induce CAG repeat instability. The assay is relatively fast and should be adaptable to large-scale screens of chemical and shRNA libraries.
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Affiliation(s)
- Beatriz A. Santillan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Christopher Moye
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Mittelman
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - John H. Wilson
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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10
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Abstract
Short tandem repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across more than 1000 individuals in Phase 1 of the 1000 Genomes Project. Extensive quality controls show that reliable allelic spectra can be obtained for close to 90% of the STR loci in the genome. We utilize this call set to analyze determinants of STR variation, assess the human reference genome's representation of STR alleles, find STR loci with common loss-of-function alleles, and obtain initial estimates of the linkage disequilibrium between STRs and common SNPs. Overall, these analyses further elucidate the scale of genetic variation beyond classical point mutations.
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Affiliation(s)
- Thomas Willems
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA; Computational and Systems Biology Program, MIT, Cambridge, Massachusetts 02139, USA
| | - Melissa Gymrek
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA; Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; Department of Molecular Biology and Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Gareth Highnam
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - David Mittelman
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA; Gene by Gene, Ltd., Houston, Texas 77008, USA
| | - Yaniv Erlich
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
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12
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Loufakis DN, Cao Z, Ma S, Mittelman D, Lu C. Focusing of mammalian cells under an ultrahigh pH gradient created by unidirectional electropulsation in a confined microchamber†Electronic supplementary information (ESI) available: Figures S1-S5 and videos S1-S2. See DOI: 10.1039/c4sc00319eClick here for additional data file.Click here for additional data file.Click here for additional data file. Chem Sci 2014; 5:3331-3337. [PMID: 25750708 PMCID: PMC4348711 DOI: 10.1039/c4sc00319e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 05/28/2014] [Indexed: 01/09/2023] Open
Abstract
A new method is demonstrated for focusing mammalian cells in free solution in a closed microfluidic chamber by applying unidirectional electric pulses.
The transport and manipulation of cells in microfluidic structures are often critically required in cellular analysis. Cells typically make consistent movement in a dc electric field in a single direction, due to their electrophoretic mobility or electroosmotic flow or the combination of the two. Here we demonstrate that mammalian cells focus to the middle of a closed microfluidic chamber under the application of unidirectional direct current pulses. With experimental and computational data, we show that under the pulses electrochemical reactions take place in the confined microscale space and create an ultrahigh and nonlinear pH gradient (∼2 orders of magnitude higher than the ones in protein isoelectric focusing) at the middle of the chamber. The varying local pH affects the cell surface charge and the electrophoretic mobility, leading to focusing in free solution. Our approach provides a new and simple method for focusing and concentrating mammalian cells at the microscale.
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Affiliation(s)
- Despina Nelie Loufakis
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , USA . ; ; Tel: +1 540 231 8681
| | - Zhenning Cao
- School of Biomedical Engineering and Sciences , Virginia Tech-Wake Forest University , Blacksburg , Virginia 24061 , USA
| | - Sai Ma
- School of Biomedical Engineering and Sciences , Virginia Tech-Wake Forest University , Blacksburg , Virginia 24061 , USA
| | - David Mittelman
- Virginia Bioinformatics Institute and Department of Biological Sciences , Virginia Tech , Blacksburg , Virginia 24061 , USA
| | - Chang Lu
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , USA . ; ; Tel: +1 540 231 8681 ; School of Biomedical Engineering and Sciences , Virginia Tech-Wake Forest University , Blacksburg , Virginia 24061 , USA
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13
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Porter SN, Baker LC, Mittelman D, Porteus MH. Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo. Genome Biol 2014; 15:R75. [PMID: 24886633 PMCID: PMC4073073 DOI: 10.1186/gb-2014-15-5-r75] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 05/30/2014] [Indexed: 12/03/2022] Open
Abstract
Background Cell lines are often regarded as clonal, even though this simplifies what is known about mutagenesis, transformation and other processes that destabilize them over time. Monitoring these clonal dynamics is important for multiple areas of biomedical research, including stem cell and cancer biology. Tracking the contributions of individual cells to large populations, however, has been constrained by limitations in sensitivity and complexity. Results We utilize cellular barcoding methods to simultaneously track the clonal contributions of tens of thousands of cells. We demonstrate that even with optimal culturing conditions, common cell lines including HeLa, K562 and HEK-293 T exhibit ongoing clonal dynamics. Starting a population with a single clone diminishes but does not eradicate this phenomenon. Next, we compare lentiviral and zinc-finger nuclease barcode insertion approaches, finding that the zinc-finger nuclease protocol surprisingly results in reduced clonal diversity. We also document the expected reduction in clonal complexity when cells are challenged with genotoxic stress. Finally, we demonstrate that xenografts maintain clonal diversity to a greater extent than in vitro culturing of the human non-small-cell lung cancer cell line HCC827. Conclusions We demonstrate the feasibility of tracking and quantifying the clonal dynamics of entire cell populations within multiple cultured cell lines. Our results suggest that cell heterogeneity should be considered in the design and interpretation of in vitro culture experiments. Aside from clonal cell lines, we propose that cellular barcoding could prove valuable in modeling the clonal behavior of heterogeneous cell populations over time, including tumor populations treated with chemotherapeutic agents.
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14
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Huang W, Massouras A, Inoue Y, Peiffer J, Ràmia M, Tarone AM, Turlapati L, Zichner T, Zhu D, Lyman RF, Magwire MM, Blankenburg K, Carbone MA, Chang K, Ellis LL, Fernandez S, Han Y, Highnam G, Hjelmen CE, Jack JR, Javaid M, Jayaseelan J, Kalra D, Lee S, Lewis L, Munidasa M, Ongeri F, Patel S, Perales L, Perez A, Pu L, Rollmann SM, Ruth R, Saada N, Warner C, Williams A, Wu YQ, Yamamoto A, Zhang Y, Zhu Y, Anholt RRH, Korbel JO, Mittelman D, Muzny DM, Gibbs RA, Barbadilla A, Johnston JS, Stone EA, Richards S, Deplancke B, Mackay TFC. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Res 2014; 24:1193-208. [PMID: 24714809 PMCID: PMC4079974 DOI: 10.1101/gr.171546.113] [Citation(s) in RCA: 403] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.
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Affiliation(s)
- Wen Huang
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Andreas Massouras
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Yutaka Inoue
- Center for Education in Liberal Arts and Sciences, Osaka University, Osaka-fu, 560-0043 Japan
| | - Jason Peiffer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Miquel Ràmia
- Genomics, Bioinformatics and Evolution Group, Institut de Biotecnologia i de Biomedicina (IBB), Department of Genetics and Microbiology, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Aaron M Tarone
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - Lavanya Turlapati
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Thomas Zichner
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Dianhui Zhu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Richard F Lyman
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Michael M Magwire
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Kerstin Blankenburg
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Mary Anna Carbone
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Kyle Chang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Lisa L Ellis
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - Sonia Fernandez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Gareth Highnam
- Virginia Tech Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Carl E Hjelmen
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - John R Jack
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Mehwish Javaid
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Joy Jayaseelan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Sandy Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Lora Lewis
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Mala Munidasa
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Fiona Ongeri
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Shohba Patel
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Lora Perales
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Agapito Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - LingLing Pu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Stephanie M Rollmann
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Robert Ruth
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Nehad Saada
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Crystal Warner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Aneisa Williams
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Yuan-Qing Wu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Akihiko Yamamoto
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Yiqing Zhang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Yiming Zhu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Robert R H Anholt
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - David Mittelman
- Virginia Tech Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Antonio Barbadilla
- Genomics, Bioinformatics and Evolution Group, Institut de Biotecnologia i de Biomedicina (IBB), Department of Genetics and Microbiology, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - Eric A Stone
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Trudy F C Mackay
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
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Guilmatre A, Highnam G, Borel C, Mittelman D, Sharp AJ. Rapid multiplexed genotyping of simple tandem repeats using capture and high-throughput sequencing. Hum Mutat 2013; 34:1304-11. [PMID: 23696428 DOI: 10.1002/humu.22359] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 05/07/2013] [Indexed: 11/12/2022]
Abstract
Although simple tandem repeats (STRs) comprise ~2% of the human genome and represent an important source of polymorphism, this class of variation remains understudied. We have developed a cost-effective strategy for performing targeted enrichment of STR regions that utilizes capture probes targeting the flanking sequences of STR loci, enabling specific capture of DNA fragments containing STRs for subsequent high-throughput sequencing. Utilizing a capture design targeting 6,243 STR loci <94 bp and multiplexing eight individuals in a single Illumina HiSeq2000 sequencing lane we were able to call genotypes in at least one individual for 67.5% of the targeted STRs. We observed a strong relationship between (G+C) content and genotyping rate. STRs with moderate (G+C) content were recovered with >90% success rate, whereas only 12% of STRs with ≥ 80% (G+C) were genotyped in our assay. Analysis of a parent-offspring trio, complete hydatidiform mole samples, repeat analyses of the same individual, and Sanger sequencing-based validation indicated genotyping error rates between 7.6% and 12.4%. The majority of such errors were a single repeat unit at mono- or dinucleotide repeats. Altogether, our STR capture assay represents a cost-effective method that enables multiplexed genotyping of thousands of STR loci suitable for large-scale population studies.
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Affiliation(s)
- Audrey Guilmatre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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18
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Abstract
Whole-genome sequencing of the widely used HeLa cell line provides a nucleotide-resolution view of a greatly mutated and in some places shattered genome.
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19
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Abstract
A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012.
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20
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Highnam G, Franck C, Martin A, Stephens C, Puthige A, Mittelman D. Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles. Nucleic Acids Res 2012; 41:e32. [PMID: 23090981 PMCID: PMC3592458 DOI: 10.1093/nar/gks981] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping microsatellite repeats called RepeatSeq, which uses Bayesian model selection guided by an empirically derived error model that incorporates sequence and read properties. Next, we apply RepeatSeq to high-coverage genomes from the 1000 Genomes Project to evaluate performance and accuracy. The software uses common formats, such as VCF, for compatibility with existing genome analysis pipelines. Source code and binaries are available at http://github.com/adaptivegenome/repeatseq.
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Affiliation(s)
- Gareth Highnam
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
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21
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Abstract
Summary: The affordability of high-throughput sequencing has created an unprecedented surge in the use of genomic data in basic, translational and clinical research. The rapid evolution of sequencing technology, coupled with its broad adoption across biology and medicine, necessitates fast, collaborative interdisciplinary discussion. SEQanswers provides a real-time knowledge-sharing resource to address this need, covering experimental and computational aspects of sequencing and sequence analysis. Developers of popular analysis tools are among the >4000 active members, and ~40 peer-reviewed publications have referenced SEQanswers. Availability: The SEQanswers community is freely accessible at http://SEQanswers.com/ Contact:david.mittelman@vt.edu; ecolivares@gmail.com Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jing-Woei Li
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR
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22
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Fondon JW, Martin A, Richards S, Gibbs RA, Mittelman D. Analysis of microsatellite variation in Drosophila melanogaster with population-scale genome sequencing. PLoS One 2012; 7:e33036. [PMID: 22427938 PMCID: PMC3299726 DOI: 10.1371/journal.pone.0033036] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/07/2012] [Indexed: 11/29/2022] Open
Abstract
Genome sequencing technologies promise to revolutionize our understanding of genetics, evolution, and disease by making it feasible to survey a broad spectrum of sequence variation on a population scale. However, this potential can only be realized to the extent that methods for extracting and interpreting distinct forms of variation can be established. The error profiles and read length limitations of early versions of next-generation sequencing technologies rendered them ineffective for some sequence variant types, particularly microsatellites and other tandem repeats, and fostered the general misconception that such variants are inherently inaccessible to these platforms. At the same time, tandem repeats have emerged as important sources of functional variation. Tandem repeats are often located in and around genes, and frequent mutations in their lengths exert quantitative effects on gene function and phenotype, rapidly degrading linkage disequilibrium between markers and traits. Sensitive identification of these variants in large-scale next-gen sequencing efforts will enable more comprehensive association studies capable of revealing previously invisible associations. We present a population-scale analysis of microsatellite repeats using whole-genome data from 158 inbred isolates from the Drosophila Genetics Reference Panel, a collection of over 200 extensively phenotypically characterized isolates from a single natural population, to uncover processes underlying repeat mutation and to enable associations with behavioral, morphological, and life-history traits. Analysis of repeat variation from next-generation sequence data will also enhance studies of genome stability and neurodegenerative diseases.
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Affiliation(s)
- John W. Fondon
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Andy Martin
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Mittelman
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
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23
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Abstract
Evolution hinges on the ability of organisms to adapt to their environment. A key regulator of adaptability is mutation rate, which must be balanced to maintain genome fidelity while permitting sufficient plasticity to cope with environmental changes. Multiple mechanisms govern an organism's mutation rate. Constitutive mechanisms include mutator alleles that drive global, permanent increases in mutation rates, but these changes are confined to the subpopulation that carries the mutator allele. Other mechanisms focus mutagenesis in time and space to improve the chances that adaptive mutations can spread through the population. For example, environmental stress can induce mechanisms that transiently relax the fidelity of DNA repair to bring about a temporary increase in mutation rates during times when an organism experiences a reduced fitness for its surroundings, as has been demonstrated for double-strand break repair in Escherichia coli. Still, other mechanisms control the spatial distribution of mutations by directing changes to especially mutable sequences in the genome. In eukaryotic cells, for example, the stress-sensitive chaperone Hsp90 can regulate the length of trinucleotide repeats to fine-tune gene function and can regulate the mobility of transposable elements to enable larger functional changes. Here, we review the regulation of mutation rate, with special emphasis on the roles of tandem repeats and environmental stress in genome evolution.
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Abstract
PURPOSE To study the effects of bilateral medial rectus recession for the management of adult onset age-related distance esotropia. METHODS Ten patients with adult onset age-related distance esotropia measuring 14 prism diopters or greater underwent bilateral medial rectus recession to eliminate the need for prism glasses. RESULTS In all but one case, the diplopia completely resolved postoperatively, with a median residual deviation of 1 prism diopter esophoria for distance and 2 prism diopters exophoria at near. CONCLUSION Bilateral medial rectus recession is a useful technique for the management of adult onset age-related distance esotropia.
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Affiliation(s)
- David Mittelman
- Department of Ophthalmology, Rush University Medical Center and Advocate Lutheran General Children’s Hospital, Chicago, Illinois, USA.
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25
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Mittelman D, Sykoudis K, Hersh M, Lin Y, Wilson JH. Hsp90 modulates CAG repeat instability in human cells. Cell Stress Chaperones 2010; 15:753-9. [PMID: 20373063 PMCID: PMC3006633 DOI: 10.1007/s12192-010-0191-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 03/16/2010] [Accepted: 03/18/2010] [Indexed: 12/30/2022] Open
Abstract
The Hsp90 molecular chaperone has been implicated as a contributor to evolution in several organisms by revealing cryptic variation that can yield dramatic phenotypes when the chaperone is diverted from its normal functions by environmental stress. In addition, as a cancer drug target, Hsp90 inhibition has been documented to sensitize cells to DNA-damaging agents, suggesting a function for Hsp90 in DNA repair. Here we explore the potential role of Hsp90 in modulating the stability of nucleotide repeats, which in a number of species, including humans, exert subtle and quantitative consequences for protein function, morphological and behavioral traits, and disease. We report that impairment of Hsp90 in human cells induces contractions of CAG repeat tracks by tenfold. Inhibition of the recombinase Rad51, a downstream target of Hsp90, induces a comparable increase in repeat instability, suggesting that Hsp90-enabled homologous recombination normally functions to stabilize CAG repeat tracts. By contrast, Hsp90 inhibition does not increase the rate of gene-inactivating point mutations. The capacity of Hsp90 to modulate repeat-tract lengths suggests that the chaperone, in addition to exposing cryptic variation, might facilitate the expression of new phenotypes through induction of novel genetic variation.
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Affiliation(s)
- David Mittelman
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Kristen Sykoudis
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Megan Hersh
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Yunfu Lin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - John H. Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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26
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Abstract
Evolutionary change, whether in populations of organisms or malignant tumor cells, is contingent on the availability of inherited variation for natural selection to act upon. It is becoming clear that the Hsp90 chaperone, which normally functions to buffer client proteins against the effects of genetic variation, plays a central role in this process. Severe environmental stress can overwhelm the chaperone's buffering capacity, causing previously cryptic genetic variation to be expressed. Recent studies now indicate that in addition to exposing existing variation, Hsp90 can induce novel epigenetic and genetic changes. We discuss key findings that suggest a rich set of pathways by which Hsp90 can mediate the influences of the environment on the genome.
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Affiliation(s)
- David Mittelman
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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27
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Melnikova VO, Davis DW, Mittelman D, Zhang Y, Holz GS, Doshi GK, Cen P, Amato RJ. Development of a new, sensitive assay for circulating tumor cell detection in prostate cancer. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.e15015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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28
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Davis DW, Mittelman D, Copper G, Zhang Y, Sukumaran S, Yutzy W, Ji JJ. Sensitive detection of gamma-H2AX induction as a pharmacodynamic marker for profiling patients with cancer treated with topotecan. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.3093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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29
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Mittelman D, Moye C, Morton J, Sykoudis K, Lin Y, Carroll D, Wilson JH. Zinc-finger directed double-strand breaks within CAG repeat tracts promote repeat instability in human cells. Proc Natl Acad Sci U S A 2009; 106:9607-12. [PMID: 19482946 PMCID: PMC2701052 DOI: 10.1073/pnas.0902420106] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Indexed: 01/12/2023] Open
Abstract
Expanded triplet repeats have been identified as the genetic basis for a growing number of neurological and skeletal disorders. To examine the contribution of double-strand break repair to CAG x CTG repeat instability in mammalian systems, we developed zinc finger nucleases (ZFNs) that recognize and cleave CAG repeat sequences. Engineered ZFNs use a tandem array of zinc fingers, fused to the FokI DNA cleavage domain, to direct double-strand breaks (DSBs) in a site-specific manner. We first determined that the ZFNs cleave CAG repeats in vitro. Then, using our previously described tissue culture assay for identifying modifiers of CAG repeat instability, we found that transfection of ZFN-expression vectors induced up to a 15-fold increase in changes to the CAG repeat in human and rodent cell lines, and that longer repeats were much more sensitive to cleavage than shorter ones. Analysis of individual colonies arising after treatment revealed a spectrum of events consistent with ZFN-induced DSBs and dominated by repeat contractions. We also found that expressing a dominant-negative form of RAD51 in combination with a ZFN, dramatically reduced the effect of the nuclease, suggesting that DSB-induced repeat instability is mediated, in part, through homology directed repair. These studies identify a ZFN as a useful reagent for characterizing the effects of DSBs on CAG repeats in cells.
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Affiliation(s)
- David Mittelman
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology and
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030; and
| | - Christopher Moye
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology and
| | - Jason Morton
- Department of Biochemistry, University of Utah School of Medicine,Salt Lake City, UT 84112
| | - Kristen Sykoudis
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology and
| | - Yunfu Lin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology and
| | - Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine,Salt Lake City, UT 84112
| | - John H. Wilson
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology and
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030; and
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Morgan DH, Kristensen DM, Mittelman D, Lichtarge O. ET viewer: an application for predicting and visualizing functional sites in protein structures. Bioinformatics 2006; 22:2049-50. [PMID: 16809388 DOI: 10.1093/bioinformatics/btl285] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
SUMMARY The Evolutionary Trace Viewer (ETV) provides a one-stop environment in which to run, visualize and interpret Evolutionary Trace (ET) predictions of functional sites in protein structures. ETV is implemented using Java to run across different operating systems using Java Web Start technology. AVAILABILITY The ETV is available for download from our website at http://mammoth.bcm.tmc.edu/traceview/index.html. This webpage also links to sample trace results and a user manual that describes ET Viewer functions in detail.
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Affiliation(s)
- Daniel H Morgan
- Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
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31
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Abstract
PURPOSE To describe a form of acquired esotropia occurring in older adults, which here is termed age-related distance esotropia. METHODS A retrospective consecutive case series of 26 patients with this condition was reviewed. RESULTS The patients ranged in age from 62 to 91 years old with a median age of 77 years. The distance deviation varied from 4 prism diopters (PD) ET (esotropia) to 20 PD ET, with a median angle of 9 PD ET. At near fixation, the measurements ranged from 9 PD ET' to 10 PD X' (exophoria), with a median deviation of 3 PD ET'. Ductions and versions were full, with no evidence of lateral rectus paresis. None of these patients had an obvious underlying neurologic disorder, such as tumor or stroke. Treatment consisted of prescribing the minimum prismatic correction that eliminated distance diplopia, which was then incorporated into the patients' current spectacles. This treatment successfully eliminated the symptoms in all patients. No patient in this study required surgery. CONCLUSION A distinctive form of strabismus occurs in older adults that is characterized by esotropia greater at distance than near fixation. The etiology of this disorder is unknown, but it is likely secondary to anatomical changes in the orbit and/or muscles associated with aging. Most patients are readily corrected by prisms but, surgical correction might be required in some cases.
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Affiliation(s)
- David Mittelman
- Advocate Lutheran General Hospital/Advocate Lutheran General Children's Hospital, Park Ridge, Illinois, USA.
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32
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Gorbunova V, Seluanov A, Mittelman D, Wilson JH. Genome-wide demethylation destabilizes CTG.CAG trinucleotide repeats in mammalian cells. Hum Mol Genet 2004; 13:2979-89. [PMID: 15459182 DOI: 10.1093/hmg/ddh317] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many neurological diseases, including myotonic dystrophy, Huntington's disease and several spinocerebellar ataxias, result from intergenerational increases in the length of a CTG.CAG repeat tract. Although the basis for intergenerational repeat expansion is unclear, repeat tracts are especially unstable during germline development and production of gametes. Mammalian development is characterized by waves of genome-wide demethylation and remethylation. To test whether changes in methylation status might contribute to trinucleotide repeat instability, we examined the effects of DNA methyltransferase inhibitors on trinucleotide repeat stability in mammalian cells. Using a selectable genetic system for detection of repeat contractions in CHO cells, we showed that the rate of contractions increased >1000-fold upon treatment with the DNA methyltransferase inhibitor 5-aza-deoxycytidine (5-aza-CdR). The link between DNA demethylation and repeat instability was strengthened by similar results obtained with hydralazine treatment, which inhibits expression of DNA methyltransferase. In human cells from myotonic dystrophy patients, treatment with 5-aza-CdR strongly destabilized repeat tracts in the DMPK gene, with a clear bias toward expansion. The bias toward expansion events and changes in repeat length that occur in jumps, rather than by accumulation of small changes, are reminiscent of the intergenerational repeat instability observed in human patients. The dramatic destabilizing effect of DNA methyltransferase inhibitors supports the hypothesis that changes in methylation patterns during epigenetic reprogramming may trigger the intergenerational repeat expansions that lead to disease.
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Affiliation(s)
- Vera Gorbunova
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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Seluanov A, Mittelman D, Pereira-Smith OM, Wilson JH, Gorbunova V. DNA end joining becomes less efficient and more error-prone during cellular senescence. Proc Natl Acad Sci U S A 2004; 101:7624-9. [PMID: 15123826 PMCID: PMC419656 DOI: 10.1073/pnas.0400726101] [Citation(s) in RCA: 221] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2004] [Accepted: 03/29/2004] [Indexed: 12/29/2022] Open
Abstract
Accumulation of somatic mutations is thought to contribute to the aging process. Genomic instability has been shown to increase during aging, suggesting an aberrant function of DNA double-strand break (DSB) repair. Surprisingly, DSB repair has not been examined with respect to cellular senescence. Therefore, we have studied the ability of young, presenescent, and senescent normal human fibroblasts to repair DSBs in transfected DNA by using a fluorescent reporter substrate. We have found that the efficiency of end joining is reduced up to 4.5 fold in presenescent and senescent cells, relative to young cells. Sequence analysis of end junctions showed that the frequency of precise ligation was higher in young cells, whereas end joining in old cells was associated with extended deletions. These results indicate that end joining becomes inefficient and more error-prone during cellular senescence. Furthermore, the ability to use microhomologies for end joining was compromised in senescent cells, suggesting that young and senescent cells may use different end joining pathways. We hypothesize that inefficient and aberrant end joining is a likely mechanism underlying the age-related genomic instability and higher incidence of cancer in the elderly.
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Affiliation(s)
- Andrei Seluanov
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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Abstract
MOTIVATION The development of powerful automatic methods for the comparison of protein sequences has become increasingly important. Profile-to-profile comparisons allow for the use of broader information about protein families, resulting in more sensitive and accurate comparisons of distantly related sequences. A key part in the comparison of two profiles is the method for the calculation of scores for the position matches. A number of methods based on various theoretical considerations have been proposed. We implemented several previously reported scoring functions as well as our own functions, and compared them on the basis of their ability to produce accurate short ungapped alignments of a given length. RESULTS Our results suggest that the family of the probabilistic methods (log-odds based methods and prof_sim) may be the more appropriate choice for the generation of initial 'seeds' as the first step to produce local profile-profile alignments. The most effective scoring systems were the closely related modifications of functions previously implemented in the COMPASS and Picasso methods.
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Affiliation(s)
- David Mittelman
- Howard Hughes Medical Institute Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA
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Abstract
Amblyopia is a serious medical condition affecting tens of millions of individuals around the world. For the most part it is correctable, assuming that it is promptly recognized and vigorously treated. Amblyopia may result from form deprivation, anisometropia, or strabismus in infants and young children. Basic research in animal models has shown that the major pathologic changes in amblyopia occur in the visual cortex of the brain. The mainstay of treatment remains patching, although penalization has a role to play in the management of moderate degrees of amblyopia. Better methods for early identification of patients with amblyopia are being developed, along with newer novel methods of treatment.
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Affiliation(s)
- David Mittelman
- Department of Ophthalmology, University of Illinois at Chicago, UIC Eye Center, 1855 W. Taylor, Chicago, IL, USA.
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Abstract
ARROGANT (ARRay OrGANizing Tool) is a software tool developed to facilitate the identification, annotation and comparison of large collections of genes or clones. The objective is to enable users to compile gene/clone collections from different databases, allowing them to design experiments and analyze the collections as well as associated experimental data efficiently. ARROGANT can relate different sequence identifiers to their common reference sequence using the UniGene database, allowing for the comparison of data from two different microarray experiments. ARROGANT has been successfully used to analyze microarray expression data for colon cancer, to compile genes potentially related to cardiac diseases for subsequent resequencing (to identify single nucleotide polymorphisms, SNPs), to design a new comprehensive human cDNA microarray for cancer, to combine and compare expression data generated by different microarrays and to provide annotation for genes on custom and Affymetrix chips.
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Affiliation(s)
- Amit V Kulkarni
- Program in Biomedical Engineering, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
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Balog RP, de Souza YEP, Tang HM, DeMasellis GM, Gao B, Avila A, Gaban DJ, Mittelman D, Minna JD, Luebke KJ, Garner HR. Parallel assessment of CpG methylation by two-color hybridization with oligonucleotide arrays. Anal Biochem 2002; 309:301-10. [PMID: 12413464 PMCID: PMC3484840 DOI: 10.1016/s0003-2697(02)00294-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We have developed a method for the parallel analysis of multiple CpG sites in genomic DNA for their state of methylation. Hypermethylation of CpG islands within the promoters and 5' exons of genes has been found to be a mechanism of transcriptional inactivation associated with a variety of tumors. The method that we developed relies on the differential reactivity of methylated and unmethylated cytosines with sodium bisulfite, which exclusively converts unmethylated cytosines to deoxyuracils. The resulting sequence changes are determined with single-nucleotide resolution by hybridization to an oligonucleotide array. Cohybridization with a reference sample containing a different label provides an internal standard for assessment of methylation state. This method provides advantages in parallelism over existing methods of methylation analysis. We have demonstrated this technique with a region from the promoter of the tumor suppressor gene p16, which is hypermethylated in many cancers.
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Affiliation(s)
- Robert P. Balog
- Center for Biomedical Inventions, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8573, USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8591, USA
| | - Y. Emi Ponce de Souza
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8591, USA
| | - Hue M. Tang
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8591, USA
| | - Gina M. DeMasellis
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8591, USA
| | - Boning Gao
- The Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8593, USA
| | - Adrian Avila
- The Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8593, USA
| | - Desmond J. Gaban
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8591, USA
| | - David Mittelman
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8591, USA
| | - John D. Minna
- The Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8593, USA
| | - Kevin J. Luebke
- Center for Biomedical Inventions, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8573, USA
- Corresponding author. Fax: +1-214-648-4156. (K.J. Luebke)
| | - Harold R. Garner
- Center for Biomedical Inventions, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8573, USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8591, USA
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Cohn EJ, Gurd FRN, Surgenor DM, Barnes BA, Brown RK, Derouaux G, Gillespie JM, Kahnt FW, Lever WF, Liu CH, Mittelman D, Mouton RF, Schmid K, Uroma E. A System for the Separation of the Components of Human Blood: Quantitative Procedures for the Separation of the Protein Components of Human Plasma 1a,b,c. J Am Chem Soc 2002. [DOI: 10.1021/ja01157a122] [Citation(s) in RCA: 426] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pertsemlidis A, Pande A, Miller B, Schilling P, Wei MH, Lerman MI, Minna JD, Garner HR, Mittelman D. PANORAMA: an integrated Web-based sequence analysis tool and its role in gene discovery. Genomics 2000; 70:300-6. [PMID: 11161780 DOI: 10.1006/geno.2000.6359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As the exponential growth of DNA sequence information in databases continues, the task of converting this deposited information into knowledge becomes more dependent on integrative sequence analysis and visualization tools. PANORAMA is an Internet-accessible software package that performs a variety of informatics analyses on a given DNA sequence and returns a visual and interactive representation of the results. Its design is modular, so that further sequence analysis tools can be integrated with minimal effort. The utility of PANORAMA is demonstrated in the analysis of 650 kb of human genomic DNA from chromosome region 3p21.3, a region of potential tumor suppressor genes involved in lung cancer, breast cancer, and other forms of cancer. PANORAMA aided in the discovery of genes and alternate splice forms of known exons, in the demarcation of intron-exon boundaries, and in the identification of promoter regions and polymorphisms, all of which contributed to a better understanding of the region. PANORAMA is available on the World Wide Web at http://atlas.swmed.edu.
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Affiliation(s)
- A Pertsemlidis
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Affiliation(s)
- M S Ruttum
- Department of Ophthalmology, Medical College of Wisconsin, Milwaukee
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Roth SI, Mittelman D, Stock EL. Posterior amorphous corneal dystrophy. An ultrastructural study of a variant with histopathological features of an endothelial dystrophy. Cornea 1992; 11:165-72. [PMID: 1582220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Posterior amorphous corneal dystrophy (PACD) is a rare autosomal-dominant disease, generally classified with the pre-Descemet's dystrophies. It is characterized by deep stromal corneal opacification, flat corneas with low keratometry values, and central thinning. To our knowledge, only one previous ultrastructural study has been published on this disease. This 5-year-old white boy presented with best corrected vision (20/50 right and 20/60 -2 left). The corneas had dense opacities, bilaterally, deep in the corneal stroma. Keratometry was 39.50/40.50, bilaterally. The patient's father had 20/20 vision, bilaterally, with minimal opacifications in the deep corneal stroma. A penetrating keratoplasty was performed. In contrast to the previously reported case of PACD, in which the abnormalities were largely limited to the stroma, our patient had subepithelial deposits, only mild stromal abnormalities, and a thick collagenous layer posterior to Descemet's membrane, thus suggesting that this variant of PACD is a generalized corneal disease including endothelial and epithelial abnormalities, rather than a pure stromal dystrophy.
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Affiliation(s)
- S I Roth
- Department of Pathology, Northwestern University Medical School, Chicago, IL 60611
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42
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Abstract
Three patients with simulated Brown's superior oblique tendon sheath syndrome are presented. With the use of computed tomographic (CT) findings, the site of the pathology could be demonstrated. In all three patients, there were definite abnormal findings in the anterior sheath of the reflected tendon of the superior oblique. The abnormal findings in one case were confirmed at the time of surgery. Therapy in two of the cases was determined by the abnormal findings on the CT scan.
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Affiliation(s)
- E R Folk
- Department of Ophthalmology, University of Illinois, College of Medicine, Chicago 60612
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44
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Abstract
Four cases of isolated inferior rectus transection secondary to trauma are presented. The clinical and CT scan findings are illustrated. The CT scan findings are very useful in the surgical management and prognosis of these cases.
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45
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46
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Abstract
In order to investigate the role of retinal cryopexy in the management of accidental perforation of the globe during strabismus surgery, the retinas of 30 rabbit eyes were perforated with a needle simulating the clinical incident. Ten of these eyes received no further treatment, ten eyes were treated with moderate transscleral cryopexy of the surrounding retina, and the remaining ten eyes were treated with excessively heavy cryocoagulation. The incidence of secondary retinal detachment was identical in the first two groups of rabbits, while it was markedly increased in those rabbits treated with excessively heavy transscleral cryopexy (P less than .01). Based on these findings and a review of the literature, recommendations are made for the management of accidental perforation of the globe during strabismus surgery.
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Miller MT, Epstein RJ, Sugar J, Pinchoff BS, Sugar A, Gammon JA, Mittelman D, Dennis RF, Israel J. Anterior segment anomalies associated with the fetal alcohol syndrome. J Pediatr Ophthalmol Strabismus 1984; 21:8-18. [PMID: 6707858 DOI: 10.3928/0191-3913-19840101-04] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Anterior segment anomalies were noted in eight children diagnosed as having the fetal alcohol syndrome. Peters' and Axenfeld's anomalies were among the specific defects noted. Four children have maintained clear corneal grafts. A teratogenic action of alcohol during a critical period of development of anterior chamber structures is suggested as an etiologic factor. It is proposed that the varied types and severity of abnormalities noted might result from differences in blood alcohol levels, timing of the insult, and genetic background of the fetus. The observation of various types of malformations thought to share a similar pathogenesis lends additional support to the assumption that there is an interrelationship among these types of congenital segment pathology.
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Mittelman D, Cronin C. The relationship of blood transfusions to retrolental fibroplasia. Ann Ophthalmol 1983; 15:376-8. [PMID: 6689255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The medical records of 53 premature infants weighing less than 1,360 g at birth were examined. The retinas of 32 infants remained normal, while mild active retrolental fibroplasia developed in 17 babies, and severe active retrolental fibroplasia developed in four babies. The birth weight, duration of exposure of supplemental oxygen, and the amount of blood they received as transfusions were recorded. There was no significant difference in these values for those babies whose retinas remained normal and for those babies in whom mild retinopathy of prematurity developed. However, the infants in whom severe retrolental fibroplasia developed were significantly smaller in weight at birth and received more supplemental oxygen and transfused blood. There was a close correlation between the amount of blood transfused and days of exposure to supplemental oxygen. In addition, the ratio of transfused blood to days of supplemental oxygen exposure was greater in those infants in whom no retrolental fibroplasia developed and least in those infants in whom severe active retrolental fibroplasia developed.
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49
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Abstract
The medical records of 33 consecutive patients who developed secondary exotropia following surgery for esotropia were reviewed. Only six patients (18%) had normal medial rectus function. Lateral rectus recession proved to be an excellent procudure for correcting the deviation in these patients, provided the surgery was limited to the eye with the narrower palpebral fissure. Twenty-seven patients (82%) exhibited limitation of adduction secondary to medial rectus underaction. Of these patients, 75% were successfully corrected following a 12 mm advancement and resection of the underacting medial rectus muscle. The details of the surgical technique performed are discussed.
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Mittelman D, Kaban LB. Recurrent "non-Hodgkin's lymphoma presenting with gingival enlargement. Report of a case. Oral Surg Oral Med Oral Pathol 1976; 42:792-800. [PMID: 1069223 DOI: 10.1016/0030-4220(76)90102-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A 66-year-old white woman with recurrent "non-Hodgkin's lymphoma" is discussed. Her initial manifestation of recurrent disease was gingival enlargement. We reviewed the oral manifestations of lymphoma and discussed the course of this patient's disease, with particular attention to the local treatment of the gingival enlargement.
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