1
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Sheppard SK, Didelot X, Jolley KA, Darling AE, Pascoe B, Meric G, Kelly DJ, Cody A, Colles FM, Strachan NJC, Ogden ID, Forbes K, French NP, Carter P, Miller WG, McCarthy ND, Owen R, Litrup E, Egholm M, Affourtit JP, Bentley SD, Parkhill J, Maiden MCJ, Falush D. Progressive genome-wide introgression in agricultural Campylobacter coli. Mol Ecol 2012; 22:1051-64. [PMID: 23279096 PMCID: PMC3749442 DOI: 10.1111/mec.12162] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [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: 08/01/2012] [Revised: 10/16/2012] [Accepted: 10/21/2012] [Indexed: 01/24/2023]
Abstract
Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens Campylobacter coli and C. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. Using whole genome sequencing, we show that a single C. coli lineage, which has successfully colonized an agricultural niche, has been progressively accumulating C. jejuni DNA. Members of this lineage belong to two groups, the ST-828 and ST-1150 clonal complexes. The ST-1150 complex is less frequently isolated and has undergone a substantially greater amount of introgression leading to replacement of up to 23% of the C. coli core genome as well as import of novel DNA. By contrast, the more commonly isolated ST-828 complex bacteria have 10–11% introgressed DNA, and C. jejuni and nonagricultural C. coli lineages each have <2%. Thus, the C. coli that colonize agriculture, and consequently cause most human disease, have hybrid origin, but this cross-species exchange has so far not had a substantial impact on the gene pools of either C. jejuni or nonagricultural C. coli. These findings also indicate remarkable interchangeability of basic cellular machinery after a prolonged period of independent evolution.
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Affiliation(s)
- Samuel K Sheppard
- Department of Zoology, The Tinbergen Building, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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2
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Gianoulis TA, Griffin MA, Spakowicz DJ, Dunican BF, Alpha CJ, Sboner A, Sismour AM, Kodira C, Egholm M, Church GM, Gerstein MB, Strobel SA. Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. PLoS Genet 2012; 8:e1002558. [PMID: 22396667 PMCID: PMC3291568 DOI: 10.1371/journal.pgen.1002558] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [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: 10/07/2011] [Accepted: 01/12/2012] [Indexed: 11/19/2022] Open
Abstract
The microbial conversion of solid cellulosic biomass to liquid biofuels may provide a renewable energy source for transportation fuels. Endophytes represent a promising group of organisms, as they are a mostly untapped reservoir of metabolic diversity. They are often able to degrade cellulose, and they can produce an extraordinary diversity of metabolites. The filamentous fungal endophyte Ascocoryne sarcoides was shown to produce potential-biofuel metabolites when grown on a cellulose-based medium; however, the genetic pathways needed for this production are unknown and the lack of genetic tools makes traditional reverse genetics difficult. We present the genomic characterization of A. sarcoides and use transcriptomic and metabolomic data to describe the genes involved in cellulose degradation and to provide hypotheses for the biofuel production pathways. In total, almost 80 biosynthetic clusters were identified, including several previously found only in plants. Additionally, many transcriptionally active regions outside of genes showed condition-specific expression, offering more evidence for the role of long non-coding RNA in gene regulation. This is one of the highest quality fungal genomes and, to our knowledge, the only thoroughly annotated and transcriptionally profiled fungal endophyte genome currently available. The analyses and datasets contribute to the study of cellulose degradation and biofuel production and provide the genomic foundation for the study of a model endophyte system. A renewable source of energy is a pressing global need. The biological conversion of lignocellulose to biofuels by microorganisms presents a promising avenue, but few organisms have been studied thoroughly enough to develop the genetic tools necessary for rigorous experimentation. The filamentous-fungal endophyte A. sarcoides produces metabolites when grown on a cellulose-based medium that include eight-carbon volatile organic compounds, which are potential biofuel targets. Here we use broadly applicable methods including genomics, transcriptomics, and metabolomics to explore the biofuel production of A. sarcoides. These data were used to assemble the genome into 16 scaffolds, to thoroughly annotate the cellulose-degradation machinery, and to make predictions for the production pathway for the eight-carbon volatiles. Extremely high expression of the gene swollenin when grown on cellulose highlights the importance of accessory proteins in addition to the enzymes that catalyze the breakdown of the polymers. Correlation of the production of the eight-carbon biofuel-like metabolites with the expression of lipoxygenase pathway genes suggests the catabolism of linoleic acid as the mechanism of eight-carbon compound production. This is the first fungal genome to be sequenced in the family Helotiaceae, and A. sarcoides was isolated as an endophyte, making this work also potentially useful in fungal systematics and the study of plant–fungus relationships.
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Affiliation(s)
- Tara A. Gianoulis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Meghan A. Griffin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Daniel J. Spakowicz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Brian F. Dunican
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Cambria J. Alpha
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Andrea Sboner
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - A. Michael Sismour
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, United States of America
| | - Chinnappa Kodira
- Roche 454 Life Sciences, Branford, Connecticut, United States of America
| | - Michael Egholm
- Pall Corporation, Long Island City, New York, United States of America
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, United States of America
| | - Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- * E-mail: (MBG); (SAS)
| | - Scott A. Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- * E-mail: (MBG); (SAS)
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Borneman AR, Desany BA, Riches D, Affourtit JP, Forgan AH, Pretorius IS, Egholm M, Chambers PJ. The genome sequence of the wine yeast VIN7 reveals an allotriploid hybrid genome with Saccharomyces cerevisiae and Saccharomyces kudriavzevii origins. FEMS Yeast Res 2011; 12:88-96. [DOI: 10.1111/j.1567-1364.2011.00773.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 11/23/2011] [Accepted: 11/24/2011] [Indexed: 11/29/2022] Open
Affiliation(s)
| | | | - David Riches
- 454 Life Sciences; A Roche Company; Branford; CT; USA
| | | | - Angus H. Forgan
- The Australian Wine Research Institute; Adelaide; SA; Australia
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4
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Liao HX, Chen X, Munshaw S, Zhang R, Marshall DJ, Vandergrift N, Whitesides JF, Lu X, Yu JS, Hwang KK, Gao F, Markowitz M, Heath SL, Bar KJ, Goepfert PA, Montefiori DC, Shaw GC, Alam SM, Margolis DM, Denny TN, Boyd SD, Marshal E, Egholm M, Simen BB, Hanczaruk B, Fire AZ, Voss G, Kelsoe G, Tomaras GD, Moody MA, Kepler TB, Haynes BF. Initial antibodies binding to HIV-1 gp41 in acutely infected subjects are polyreactive and highly mutated. J Exp Med 2011; 208:2237-49. [PMID: 21987658 PMCID: PMC3201211 DOI: 10.1084/jem.20110363] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [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: 02/16/2011] [Accepted: 08/31/2011] [Indexed: 01/20/2023] Open
Abstract
The initial antibody response to HIV-1 is targeted to envelope (Env) gp41, and is nonneutralizing and ineffective in controlling viremia. To understand the origins and characteristics of gp41-binding antibodies produced shortly after HIV-1 transmission, we isolated and studied gp41-reactive plasma cells from subjects acutely infected with HIV-1. The frequencies of somatic mutations were relatively high in these gp41-reactive antibodies. Reverted unmutated ancestors of gp41-reactive antibodies derived from subjects acutely infected with HIV-1 frequently did not react with autologous HIV-1 Env; however, these antibodies were polyreactive and frequently bound to host or bacterial antigens. In one large clonal lineage of gp41-reactive antibodies, reactivity to HIV-1 Env was acquired only after somatic mutations. Polyreactive gp41-binding antibodies were also isolated from uninfected individuals. These data suggest that the majority of gp41-binding antibodies produced after acute HIV-1 infection are cross-reactive responses generated by stimulating memory B cells that have previously been activated by non-HIV-1 antigens.
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Affiliation(s)
- Hua-Xin Liao
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Xi Chen
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Supriya Munshaw
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Ruijun Zhang
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Dawn J. Marshall
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Nathan Vandergrift
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - John F. Whitesides
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Jae-Sung Yu
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Kwan-Ki Hwang
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Feng Gao
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | | | | | | | | | - David C. Montefiori
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | | | - S. Munir Alam
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | | | - Thomas N. Denny
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Scott D. Boyd
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305
| | - Eleanor Marshal
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305
| | | | | | | | - Andrew Z. Fire
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305
| | - Gerald Voss
- GlaxoSmithKline Biologicals, 1330 Rixensart, Belgium
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - M. Anthony Moody
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Thomas B. Kepler
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Department of Medicine, Department of Pediatrics, Department of Surgery, Department of Immunology, and Center for Computational Immunology, Duke University School of Medicine, Durham, NC 27710
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Palacios G, Lowenstine LJ, Cranfield MR, Gilardi KVK, Spelman L, Lukasik-Braum M, Kinani JF, Mudakikwa A, Nyirakaragire E, Bussetti AV, Savji N, Hutchison S, Egholm M, Lipkin WI. Human metapneumovirus infection in wild mountain gorillas, Rwanda. Emerg Infect Dis 2011; 17:711-3. [PMID: 21470468 PMCID: PMC3377396 DOI: 10.3201/eid1704.100883] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The genetic relatedness of mountain gorillas and humans has led to concerns about interspecies transmission of infectious agents. Human-to-gorilla transmission may explain human metapneumovirus in 2 wild mountain gorillas that died during a respiratory disease outbreak in Rwanda in 2009. Surveillance is needed to ensure survival of these critically endangered animals.
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Affiliation(s)
- Gustavo Palacios
- Center for Infection and Immunity, Columbia University, Rm 1709, 722 W 168th St, New York, NY 10032, USA.
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6
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Holcomb CL, Höglund B, Anderson MW, Blake LA, Böhme I, Egholm M, Ferriola D, Gabriel C, Gelber SE, Goodridge D, Hawbecker S, Klein R, Ladner M, Lind C, Monos D, Pando MJ, Pröll J, Sayer DC, Schmitz-Agheguian G, Simen BB, Thiele B, Trachtenberg EA, Tyan DB, Wassmuth R, White S, Erlich HA. A multi-site study using high-resolution HLA genotyping by next generation sequencing. ACTA ACUST UNITED AC 2011; 77:206-17. [PMID: 21299525 DOI: 10.1111/j.1399-0039.2010.01606.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The high degree of polymorphism at human leukocyte antigen (HLA) class I and class II loci makes high-resolution HLA typing challenging. Current typing methods, including Sanger sequencing, yield ambiguous typing results because of incomplete genomic coverage and inability to set phase for HLA allele determination. The 454 Life Sciences Genome Sequencer (GS FLX) next generation sequencing system coupled with conexio atf software can provide very high-resolution HLA genotyping. High-throughput genotyping can be achieved by use of primers with multiplex identifier (MID) tags to allow pooling of the amplicons generated from different individuals prior to sequencing. We have conducted a double-blind study in which eight laboratory sites performed amplicon sequencing using GS FLX standard chemistry and genotyped the same 20 samples for HLA-A, -B, -C, DPB1, DQA1, DQB1, DRB1, DRB3, DRB4, and DRB5 (DRB3/4/5) in a single sequencing run. The average sequence read length was 250 base pairs and the average number of sequence reads per amplicon was 672, providing confidence in the allele assignments. Of the 1280 genotypes considered, assignment was possible in 95% of the cases. Failure to assign genotypes was the result of researcher procedural error or the presence of a novel allele rather than a failure of sequencing technology. Concordance with known genotypes, in cases where assignment was possible, ranged from 95.3% to 99.4% for the eight sites, with overall concordance of 97.2%. We conclude that clonal pyrosequencing using the GS FLX platform and CONEXIO ATF software allows reliable identification of HLA genotypes at high resolution.
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Affiliation(s)
- C L Holcomb
- Roche Molecular Systems Inc. (RMS), Pleasanton, CA 94588, USA
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7
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Palacios G, Lowenstine LJ, Cranfield MR, Gilardi KVK, Spelman L, Lukasik-Braum M, Kinani JF, Mudakikwa A, Nyirakaragire E, Bussetti AV, Savji N, Hutchison S, Egholm M, Lipkin WI. Human metapneumovirus infection in wild mountain gorillas, Rwanda. Emerg Infect Dis 2011. [PMID: 21470468 DOI: 10.3201/eid1704100883] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The genetic relatedness of mountain gorillas and humans has led to concerns about interspecies transmission of infectious agents. Human-to-gorilla transmission may explain human metapneumovirus in 2 wild mountain gorillas that died during a respiratory disease outbreak in Rwanda in 2009. Surveillance is needed to ensure survival of these critically endangered animals.
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Affiliation(s)
- Gustavo Palacios
- Center for Infection and Immunity, Columbia University, Rm 1709, 722 W 168th St, New York, NY 10032, USA.
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8
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Borneman AR, Desany BA, Riches D, Affourtit JP, Forgan AH, Pretorius IS, Egholm M, Chambers PJ. Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae. PLoS Genet 2011; 7:e1001287. [PMID: 21304888 PMCID: PMC3033381 DOI: 10.1371/journal.pgen.1001287] [Citation(s) in RCA: 222] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 12/30/2010] [Indexed: 11/19/2022] Open
Abstract
Human intervention has subjected the yeast Saccharomyces cerevisiae to multiple rounds of independent domestication and thousands of generations of artificial selection. As a result, this species comprises a genetically diverse collection of natural isolates as well as domesticated strains that are used in specific industrial applications. However the scope of genetic diversity that was captured during the domesticated evolution of the industrial representatives of this important organism remains to be determined. To begin to address this, we have produced whole-genome assemblies of six commercial strains of S. cerevisiae (four wine and two brewing strains). These represent the first genome assemblies produced from S. cerevisiae strains in their industrially-used forms and the first high-quality assemblies for S. cerevisiae strains used in brewing. By comparing these sequences to six existing high-coverage S. cerevisiae genome assemblies, clear signatures were found that defined each industrial class of yeast. This genetic variation was comprised of both single nucleotide polymorphisms and large-scale insertions and deletions, with the latter often being associated with ORF heterogeneity between strains. This included the discovery of more than twenty probable genes that had not been identified previously in the S. cerevisiae genome. Comparison of this large number of S. cerevisiae strains also enabled the characterization of a cluster of five ORFs that have integrated into the genomes of the wine and bioethanol strains on multiple occasions and at diverse genomic locations via what appears to involve the resolution of a circular DNA intermediate. This work suggests that, despite the scrutiny that has been directed at the yeast genome, there remains a significant reservoir of ORFs and novel modes of genetic transmission that may have significant phenotypic impact in this important model and industrial species. The yeast S. cerevisiae has been associated with human activity for thousands of years in industries such as baking, brewing, and winemaking. During this time, humans have effectively domesticated this microorganism, with different industries selecting for specific desirable phenotypic traits. This has resulted in the species S. cerevisiae comprising a genetically diverse collection of individual strains that are often suited to very specific roles (e.g. wine strains produce wine but not beer and vice versa). In order to understand the genetic differences that underpin these diverse industrial characteristics, we have sequenced the genomes of six industrial strains of S. cerevisiae that comprise four strains used in commercial wine production and two strains used in beer brewing. By comparing these genome sequences to existing S. cerevisiae genome sequences from laboratory, pathogenic, bioethanol, and “natural” isolates, we were able to identify numerous genetic differences among these strains including the presence of novel open reading frames and genomic rearrangements, which may provide the basis for the phenotypic differences observed among these strains.
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9
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Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R. The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 2010; 42:833-9. [DOI: 10.1038/ng.654] [Citation(s) in RCA: 1538] [Impact Index Per Article: 109.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 08/03/2010] [Indexed: 11/09/2022]
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10
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Quan PL, Wagner TA, Briese T, Torgerson TR, Hornig M, Tashmukhamedova A, Firth C, Palacios G, Baisre-De-Leon A, Paddock CD, Hutchison SK, Egholm M, Zaki SR, Goldman JE, Ochs HD, Lipkin WI. Astrovirus encephalitis in boy with X-linked agammaglobulinemia. Emerg Infect Dis 2010; 16:918-25. [PMID: 20507741 PMCID: PMC4102142 DOI: 10.3201/eid1606.091536] [Citation(s) in RCA: 236] [Impact Index Per Article: 16.9] [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: 11/19/2022] Open
Abstract
Encephalitis is a major cause of death worldwide. Although >100 pathogens have been identified as causative agents, the pathogen is not determined for up to 75% of cases. This diagnostic failure impedes effective treatment and underscores the need for better tools and new approaches for detecting novel pathogens or determining new manifestations of known pathogens. Although astroviruses are commonly associated with gastroenteritis, they have not been associated with central nervous system disease. Using unbiased pyrosequencing, we detected an astrovirus as the causative agent for encephalitis in a 15-year-old boy with agammaglobulinemia; several laboratories had failed to identify the agent. Our findings expand the spectrum of causative agents associated with encephalitis and highlight unbiased molecular technology as a valuable tool for differential diagnosis of unexplained disease.
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11
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Palacios G, Lovoll M, Tengs T, Hornig M, Hutchison S, Hui J, Kongtorp RT, Savji N, Bussetti AV, Solovyov A, Kristoffersen AB, Celone C, Street C, Trifonov V, Hirschberg DL, Rabadan R, Egholm M, Rimstad E, Lipkin WI. Heart and skeletal muscle inflammation of farmed salmon is associated with infection with a novel reovirus. PLoS One 2010; 5:e11487. [PMID: 20634888 PMCID: PMC2901333 DOI: 10.1371/journal.pone.0011487] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [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: 04/19/2010] [Accepted: 06/04/2010] [Indexed: 11/19/2022] Open
Abstract
Atlantic salmon (Salmo salar L.) mariculture has been associated with epidemics of infectious diseases that threaten not only local production, but also wild fish coming into close proximity to marine pens and fish escaping from them. Heart and skeletal muscle inflammation (HSMI) is a frequently fatal disease of farmed Atlantic salmon. First recognized in one farm in Norway in 1999, HSMI was subsequently implicated in outbreaks in other farms in Norway and the United Kingdom. Although pathology and disease transmission studies indicated an infectious basis, efforts to identify an agent were unsuccessful. Here we provide evidence that HSMI is associated with infection with piscine reovirus (PRV). PRV is a novel reovirus identified by unbiased high throughput DNA sequencing and a bioinformatics program focused on nucleotide frequency as well as sequence alignment and motif analyses. Formal implication of PRV in HSMI will require isolation in cell culture and fulfillment of Koch's postulates, or prevention or modification of disease through use of specific drugs or vaccines. Nonetheless, as our data indicate that a causal relationship is plausible, measures must be taken to control PRV not only because it threatens domestic salmon production but also due to the potential for transmission to wild salmon populations.
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Affiliation(s)
- Gustavo Palacios
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | | | | | - Mady Hornig
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | | | - Jeffrey Hui
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | | | - Nazir Savji
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | - Ana V. Bussetti
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | - Alexander Solovyov
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | | | | | - Craig Street
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | - Vladimir Trifonov
- Department of Biomedical Informatics and Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
| | - David L. Hirschberg
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | - Raul Rabadan
- Department of Biomedical Informatics and Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
| | - Michael Egholm
- 454 Life Sciences, Branford, Connecticut, United States of America
| | - Espen Rimstad
- Norwegian School of Veterinary Science, Oslo, Norway
| | - W. Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
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12
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Lataillade M, Chiarella J, Yang R, Schnittman S, Wirtz V, Uy J, Seekins D, Krystal M, Mancini M, McGrath D, Simen B, Egholm M, Kozal M. Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naïve subjects in the CASTLE study. PLoS One 2010; 5:e10952. [PMID: 20532178 PMCID: PMC2880604 DOI: 10.1371/journal.pone.0010952] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 05/07/2010] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND CASTLE compared the efficacy of atazanavir/ritonavir with lopinavir/ritonavir, each in combination with tenofovir-emtricitabine in ARV-naïve subjects from 5 continents. OBJECTIVES Determine the baseline rate and clinical significance of TDR mutations using ultra-deep sequencing (UDS) in ARV-naïve subjects in CASTLE. METHODS A case control study was performed on baseline samples for all 53 subjects with virologic failures (VF) at Week 48 and 95 subjects with virologic successes (VS) randomly selected and matched by CD4 count and viral load. UDS was performed using 454 Life Sciences/Roche technology. RESULTS Of 148 samples, 141 had successful UDS (86 subtype B, 55 non-B subtypes). Overall, 30.5% of subjects had a TDR mutation at baseline; 15.6% only had TDR(s) at <20% of the viral population. There was no difference in the rate of TDRs by B (30.2%) or non-B subtypes (30.9%). VF (51) and VS (90) had similar rates of any TDRs (25.5% vs. 33.3%), NNRTI TDRs (11.1% vs.11.8%) and NRTI TDRs (24.4% vs. 25.5%). Of 9 (6.4%) subjects with M184V/I (7 at <20% levels), 6 experienced VF. 16 (11.3%) subjects had multiple TAMs, and 7 experienced VF. 3 (2.1%) subjects had both multiple TAMs+M184V, and all experienced VF. Of 14 (9.9%) subjects with PI TDRs (11 at <20% levels): only 1 experienced virologic failure. The majority of PI TDRs were found in isolation (e.g. 46I) at <20% levels, and had low resistance algorithm scores. CONCLUSION Among a representative sample of ARV-naïve subjects in CASTLE, TDR mutations were common (30.5%); B and non-B subtypes had similar rates of TDRs. Subjects with multiple PI TDRs were infrequent. Overall, TDRs did not affect virologic response for subjects on a boosted PI by week 48; however, a small subset of subjects with extensive NRTI backbone TDR patterns experienced virologic failure.
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Affiliation(s)
- Max Lataillade
- Global Development and Medical Affairs, Bristol-Myers Squibb, Wallingford, Connecticut, United States of America
- Yale University School of Medicine and Veterans Affairs Connecticut Healthcare System, New Haven, Connecticut, United States of America
| | - Jennifer Chiarella
- Yale University School of Medicine and Veterans Affairs Connecticut Healthcare System, New Haven, Connecticut, United States of America
| | - Rong Yang
- Global Development and Medical Affairs, Bristol-Myers Squibb, Wallingford, Connecticut, United States of America
| | - Steven Schnittman
- Global Development and Medical Affairs, Bristol-Myers Squibb, Wallingford, Connecticut, United States of America
| | - Victoria Wirtz
- Global Development and Medical Affairs, Bristol-Myers Squibb, Wallingford, Connecticut, United States of America
| | - Jonathan Uy
- Global Development and Medical Affairs, Bristol-Myers Squibb, Wallingford, Connecticut, United States of America
| | - Daniel Seekins
- Global Development and Medical Affairs, Bristol-Myers Squibb, Wallingford, Connecticut, United States of America
| | - Mark Krystal
- Global Development and Medical Affairs, Bristol-Myers Squibb, Wallingford, Connecticut, United States of America
| | - Marco Mancini
- Global Development and Medical Affairs, Bristol-Myers Squibb, Wallingford, Connecticut, United States of America
| | - Donnie McGrath
- Global Development and Medical Affairs, Bristol-Myers Squibb, Wallingford, Connecticut, United States of America
| | - Birgitte Simen
- 454 Life Sciences, a Roche company, Branford, Connecticut, United States of America
| | - Michael Egholm
- 454 Life Sciences, a Roche company, Branford, Connecticut, United States of America
| | - Michael Kozal
- Yale University School of Medicine and Veterans Affairs Connecticut Healthcare System, New Haven, Connecticut, United States of America
- * E-mail:
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13
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Boyd SD, Gaëta BA, Jackson KJ, Fire AZ, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Collins AM. Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements. J Immunol 2010; 184:6986-92. [PMID: 20495067 DOI: 10.4049/jimmunol.1000445] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Individual variation in the Ig germline gene repertoire leads to individual differences in the combinatorial diversity of the Ab repertoire, but the study of such variation has been problematic. The application of high-throughput DNA sequencing to the study of rearranged Ig genes now makes this possible. The sequencing of thousands of VDJ rearrangements from an individual, either from genomic DNA or expressed mRNA, should allow their germline IGHV, IGHD, and IGHJ repertoires to be inferred. In addition, where previously mere glimpses of diversity could be gained from sequencing studies, new large data sets should allow the rearrangement frequency of different genes and alleles to be seen with clarity. We analyzed the DNA of 108,210 human IgH chain rearrangements from 12 individuals and determined their individual IGH genotypes. The number of reportedly functional IGHV genes and allelic variants ranged from 45 to 60, principally because of variable levels of gene heterozygosity, and included 14 previously unreported IGHV polymorphisms. New polymorphisms of the IGHD3-16 and IGHJ6 genes were also seen. At heterozygous loci, remarkably different rearrangement frequencies were seen for the various IGHV alleles, and these frequencies were consistent between individuals. The specific alleles that make up an individual's Ig genotype may therefore be critical in shaping the combinatorial repertoire. The extent of genotypic variation between individuals is highlighted by an individual with aplastic anemia who appears to lack six contiguous IGHD genes on both chromosomes. These deletions significantly alter the potential expressed IGH repertoire, and possibly immune function, in this individual.
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Affiliation(s)
- Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
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14
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Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MHY, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome. Science 2010; 328:710-722. [PMID: 20448178 PMCID: PMC5100745 DOI: 10.1126/science.1188021] [Citation(s) in RCA: 2097] [Impact Index Per Article: 149.8] [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: 12/21/2022]
Abstract
Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
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Affiliation(s)
- Richard E. Green
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Johannes Krause
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Adrian W. Briggs
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Tomislav Maricic
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Udo Stenzel
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Martin Kircher
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heng Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Weiwei Zhai
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Markus Hsi-Yang Fritz
- European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Nancy F. Hansen
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric Y. Durand
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Anna-Sapfo Malaspinas
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey D. Jensen
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Tomas Marques-Bonet
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Institute of Evolutionary Biology (UPF-CSIC), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Can Alkan
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Hernán A. Burbano
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Jeffrey M. Good
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Rigo Schultz
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Anne Butthof
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Barbara Höber
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Barbara Höffner
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Madlen Siegemund
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Antje Weihmann
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Chad Nusbaum
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S. Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carsten Russ
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathaniel Novod
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Christine Verna
- Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Pavao Rudan
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | - Dejana Brajkovic
- Croatian Academy of Sciences and Arts, Institute for Quaternary Paleontology and Geology, Ante Kovacica 5, HR-10000 Zagreb, Croatia
| | - Željko Kucan
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | - Ivan Gušic
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | | | | | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marco de la Rasilla
- Área de Prehistoria Departamento de Historia Universidad de Oviedo, Oviedo, Spain
| | - Javier Fortea
- Área de Prehistoria Departamento de Historia Universidad de Oviedo, Oviedo, Spain
| | - Antonio Rosas
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Ralf W. Schmitz
- Der Landschaftverband Rheinlund–Landesmuseum Bonn, Bachstrasse 5-9, D-53115 Bonn, Germany
- Abteilung für Vor- und Frühgeschichtliche Archäologie, Universität Bonn, Germany
| | | | - Evan E. Eichler
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daniel Falush
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Ewan Birney
- European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - James C. Mullikin
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Michael Lachmann
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - David Reich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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15
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Baumeister E, Palacios G, Cisterna D, Solovyov A, Hui J, Savji N, Bussetti AV, Campos A, Pontoriero A, Jabado OJ, Street C, Hirschberg DL, Rabadan R, Alonio V, Molina V, Hutchison S, Egholm M, Lipkin WI. Molecular characterization of severe and mild cases of influenza A (H1N1) 2009 strain from Argentina. Medicina (B Aires) 2010; 70:518-523. [PMID: 21163739 PMCID: PMC4310694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
While worldwide pandemic influenza A(H1N1) pdm case fatality rate (CFR) was 0.4%, Argentina's was 4.5%. A total of 34 strains from mild and severe cases were analyzed. A full genome sequencing was carried out on 26 of these, and a partial sequencing on the remaining eight. We observed no evidence that the high CFR can be attributed to direct virus changes. No evidence of re-assortment, mutations associated with resistance to antiviral drugs, or genetic drift that might contribute to virulence was observed. Although the mutation D225G associated with severity in the latest reports from the Ukraine and Norway is not observed among the Argentine strains, an amino acid change in the area (S206T) surrounding the HA receptor binding domain was observed, the same previously established worldwide.
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Affiliation(s)
- Elsa Baumeister
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Dr. Carlos G. Malbrán, Buenos Aires, Argentina.
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16
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Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Fire AZ. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med 2009; 1:12ra23. [PMID: 20161664 PMCID: PMC2819115 DOI: 10.1126/scitranslmed.3000540] [Citation(s) in RCA: 310] [Impact Index Per Article: 20.7] [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: 09/23/2023]
Abstract
The complex repertoire of immune receptors generated by B and T cells enables recognition of diverse threats to the host organism. In this work, we show that massively parallel DNA sequencing of rearranged immune receptor loci can provide direct detection and tracking of immune diversity and expanded clonal lymphocyte populations in physiological and pathological contexts. DNA was isolated from blood and tissue samples, a series of redundant primers was used to amplify diverse DNA rearrangements, and the resulting mixtures of barcoded amplicons were sequenced using long-read ultra deep sequencing. Individual DNA molecules were then characterized on the basis of DNA segments that had been joined to make a functional (or nonfunctional) immune effector. Current experimental designs can accommodate up to 150 samples in a single sequence run, with the depth of sequencing sufficient to identify stable and dynamic aspects of the immune repertoire in both normal and diseased circumstances. These data provide a high-resolution picture of immune spectra in normal individuals and in patients with hematological malignancies, illuminating, in the latter case, both the initial behavior of clonal tumor populations and the later suppression or re-emergence of such populations after treatment.
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Affiliation(s)
- Scott D. Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Jason D. Merker
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Pediatrics-Medical Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jay M. Maniar
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lyndon N. Zhang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Bita Sahaf
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Carol D. Jones
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Khoa D. Nguyen
- Department of Pediatrics-Allergy and Clinical Immunology, Stanford University, Stanford, CA 94305, USA
| | - Kari C. Nadeau
- Department of Pediatrics-Allergy and Clinical Immunology, Stanford University, Stanford, CA 94305, USA
| | - Michael Egholm
- 454 Life Sciences, A Roche Company, Branford, CT 06405, USA
| | - David B. Miklos
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - James L. Zehnder
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Andrew Z. Fire
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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17
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Varghese V, Shahriar R, Rhee SY, Liu T, Simen BB, Egholm M, Hanczaruk B, Blake LA, Gharizadeh B, Babrzadeh F, Bachmann MH, Fessel WJ, Shafer RW. Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors. J Acquir Immune Defic Syndr 2009; 52:309-15. [PMID: 19734799 PMCID: PMC2809083 DOI: 10.1097/qai.0b013e3181bca669] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [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: 11/26/2022]
Abstract
OBJECTIVES K103N, the most common nonnucleoside reverse transcriptase inhibitor (NNRTI)-resistant mutation in patients with transmitted resistance and in patients receiving a failing NNRTI-containing regimen, is fully susceptible to the new NNRTI, etravirine. Therefore, we sought to determine how often NNRTI-resistant mutations other than K103N occur as minority variants in plasma samples for which standard genotypic resistance testing detects K103N alone. METHODS We performed ultradeep pyrosequencing (UDPS; 454 Life Sciences a Roche Company, Branford, CT) of plasma virus samples from 13 treatment-naive and 20 NNRTI-experienced patients in whom standard genotypic resistance testing revealed K103N but no other major NNRTI-resistance mutations. RESULTS Samples from 0 of 13 treatment-naive patients vs. 7 of 20 patients failing an NNRTI-containing regimen had minority variants with major etravirine-associated NNRTI-resistant mutations (P = 0.03, Fisher exact test): Y181C (7.0%), Y181C (3.6%) + G190A (3.2%), L100I (14%), L100I (32%) + 190A (5.4%), K101E (3.8%) + G190A (4.9%), K101E (4.0%) + G190S (4.8%), and G190S (3.1%). CONCLUSIONS In treatment-naive patients, UDPS did not detect additional major NNRTI-resistant mutations suggesting that etravirine may be effective in patients with transmitted K103N. In NNRTI-experienced patients, UDPS often detected additional major NNRTI-resistant mutations suggesting that etravirine may not be fully active in patients with acquired K103N.
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Affiliation(s)
- Vici Varghese
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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18
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Quan PL, Junglen S, Tashmukhamedova A, Conlan S, Hutchison SK, Kurth A, Ellerbrok H, Egholm M, Briese T, Leendertz FH, Lipkin WI. Moussa virus: a new member of the Rhabdoviridae family isolated from Culex decens mosquitoes in Côte d'Ivoire. Virus Res 2009; 147:17-24. [PMID: 19804801 DOI: 10.1016/j.virusres.2009.09.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 09/24/2009] [Accepted: 09/27/2009] [Indexed: 01/01/2023]
Abstract
Characterization of arboviruses at the interface of pristine habitats and anthropogenic landscapes is crucial to comprehensive emergent disease surveillance and forecasting efforts. In context of a surveillance campaign in and around a West African rainforest, particles morphologically consistent with rhabdoviruses were identified in cell cultures infected with homogenates of trapped mosquitoes. RNA recovered from these cultures was used to derive the first complete genome sequence of a rhabdovirus isolated from Culex decens mosquitoes in Côte d'Ivoire, tentatively named Moussa virus (MOUV). MOUV shows the classical genome organization of rhabdoviruses, with five open reading frames (ORF) in a linear order. However, sequences show only limited conservation (12-33% identity at amino acid level), and ORF2 and ORF3 have no significant similarity to sequences deposited in GenBank. Phylogenetic analysis indicates a potential new species with distant relationship to Tupaia and Tibrogargan virus.
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Affiliation(s)
- Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
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19
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Margeridon-Thermet S, Shulman NS, Ahmed A, Shahriar R, Liu T, Wang C, Holmes SP, Babrzadeh F, Gharizadeh B, Hanczaruk B, Simen BB, Egholm M, Shafer RW. Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients. J Infect Dis 2009; 199:1275-85. [PMID: 19301976 DOI: 10.1086/597808] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The dynamics of emerging nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI) resistance in hepatitis B virus (HBV) are not well understood because standard dideoxynucleotide direct polymerase chain reaction (PCR) sequencing assays detect drug-resistance mutations only after they have become dominant. To obtain insight into NRTI resistance, we used a new sequencing technology to characterize the spectrum of low-prevalence NRTI-resistance mutations in HBV obtained from 20 plasma samples from 11 NRTI-treated patients and 17 plasma samples from 17 NRTI-naive patients, by using standard direct PCR sequencing and ultra-deep pyrosequencing (UDPS). UDPS detected drug-resistance mutations that were not detected by PCR in 10 samples from 5 NRTI-treated patients, including the lamivudine-resistance mutation V173L (in 5 samples), the entecavir-resistance mutations T184S (in 2 samples) and S202G (in 1 sample), the adefovir-resistance mutation N236T (in 1 sample), and the lamivudine and adefovir-resistance mutations V173L, L180M, A181T, and M204V (in 1 sample). G-to-A hypermutation mediated by the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like family of cytidine deaminases was estimated to be present in 0.6% of reverse-transcriptase genes. Genotype A coinfection was detected by UDPS in each of 3 patients in whom genotype G virus was detected by direct PCR sequencing. UDPS detected low-prevalence HBV variants with NRTI-resistance mutations, G-to-A hypermutation, and low-level dual genotype infection with a sensitivity not previously possible.
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20
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Le T, Chiarella J, Simen BB, Hanczaruk B, Egholm M, Landry ML, Dieckhaus K, Rosen MI, Kozal MJ. Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use. PLoS One 2009; 4:e6079. [PMID: 19562031 PMCID: PMC2698118 DOI: 10.1371/journal.pone.0006079] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [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: 03/25/2009] [Accepted: 06/05/2009] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND It is largely unknown how frequently low-abundance HIV drug-resistant variants at levels under limit of detection of conventional genotyping (<20% of quasi-species) are present in antiretroviral-experienced persons experiencing virologic failure. Further, the clinical implications of low-abundance drug-resistant variants at time of virologic failure are unknown. METHODOLOGY/PRINCIPAL FINDINGS Plasma samples from 22 antiretroviral-experienced subjects collected at time of virologic failure (viral load 1380 to 304,000 copies/mL) were obtained from a specimen bank (from 2004-2007). The prevalence and profile of drug-resistant mutations were determined using Sanger sequencing and ultra-deep pyrosequencing. Genotypes were interpreted using Stanford HIV database algorithm. Antiretroviral treatment histories were obtained by chart review and correlated with drug-resistant mutations. Low-abundance drug-resistant mutations were detected in all 22 subjects by deep sequencing and only in 3 subjects by Sanger sequencing. In total they accounted for 90 of 247 mutations (36%) detected by deep sequencing; the majority of these (95%) were not detected by standard genotyping. A mean of 4 additional mutations per subject were detected by deep sequencing (p<0.0001, 95%CI: 2.85-5.53). The additional low-abundance drug-resistant mutations increased a subject's genotypic resistance to one or more antiretrovirals in 17 of 22 subjects (77%). When correlated with subjects' antiretroviral treatment histories, the additional low-abundance drug-resistant mutations correlated with the failing antiretroviral drugs in 21% subjects and correlated with historical antiretroviral use in 79% subjects (OR, 13.73; 95% CI, 2.5-74.3, p = 0.0016). CONCLUSIONS/SIGNIFICANCE Low-abundance HIV drug-resistant mutations in antiretroviral-experienced subjects at time of virologic failure can increase a subject's overall burden of resistance, yet commonly go unrecognized by conventional genotyping. The majority of unrecognized resistant mutations correlate with historical antiretroviral use. Ultra-deep sequencing can provide important historical resistance information for clinicians when planning subsequent antiretroviral regimens for highly treatment-experienced patients, particularly when their prior treatment histories and longitudinal genotypes are not available.
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Affiliation(s)
- Thuy Le
- Yale University School of Medicine, New Haven, CT, USA.
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21
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Cornman RS, Chen YP, Schatz MC, Street C, Zhao Y, Desany B, Egholm M, Hutchison S, Pettis JS, Lipkin WI, Evans JD. Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PLoS Pathog 2009; 5:e1000466. [PMID: 19503607 PMCID: PMC2685015 DOI: 10.1371/journal.ppat.1000466] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [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: 03/10/2009] [Accepted: 05/05/2009] [Indexed: 11/19/2022] Open
Abstract
Recent steep declines in honey bee health have severely impacted the beekeeping industry, presenting new risks for agricultural commodities that depend on insect pollination. Honey bee declines could reflect increased pressures from parasites and pathogens. The incidence of the microsporidian pathogen Nosema ceranae has increased significantly in the past decade. Here we present a draft assembly (7.86 MB) of the N. ceranae genome derived from pyrosequence data, including initial gene models and genomic comparisons with other members of this highly derived fungal lineage. N. ceranae has a strongly AT-biased genome (74% A+T) and a diversity of repetitive elements, complicating the assembly. Of 2,614 predicted protein-coding sequences, we conservatively estimate that 1,366 have homologs in the microsporidian Encephalitozoon cuniculi, the most closely related published genome sequence. We identify genes conserved among microsporidia that lack clear homology outside this group, which are of special interest as potential virulence factors in this group of obligate parasites. A substantial fraction of the diminutive N. ceranae proteome consists of novel and transposable-element proteins. For a majority of well-supported gene models, a conserved sense-strand motif can be found within 15 bases upstream of the start codon; a previously uncharacterized version of this motif is also present in E. cuniculi. These comparisons provide insight into the architecture, regulation, and evolution of microsporidian genomes, and will drive investigations into honey bee–Nosema interactions. Honey bee colonies are in decline in many parts of the world, in part due to pressures from a diverse assemblage of parasites and pathogens. The range and prevalence of the microsporidian pathogen Nosema ceranae has increased significantly in the past decade. Here we describe the N. ceranae genome, presenting genome traits, gene models and regulatory motifs. N. ceranae has an extremely reduced and AT-biased genome, yet one with substantial numbers of repetitive elements. We identify novel genes that appear to be conserved among microsporidia but undetected outside this phylum, which are of special interest as potential virulence factors for these obligate pathogens. A previously unrecognized motif is found upstream of many start codons and likely plays a role in gene regulation across the microsporidia. These and other comparisons provide insight into the architecture, regulation, and evolution of microsporidian genomes, and provide the first genetic tools for understanding how this pathogen interacts with honey bee hosts.
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Affiliation(s)
- R. Scott Cornman
- USDA-ARS Bee Research Lab, Beltsville, Maryland, United States of America
| | - Yan Ping Chen
- USDA-ARS Bee Research Lab, Beltsville, Maryland, United States of America
| | - Michael C. Schatz
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Craig Street
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Yan Zhao
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Brian Desany
- 454 Life Sciences/Roche Applied Sciences, Branford, Connecticut, United States of America
| | - Michael Egholm
- 454 Life Sciences/Roche Applied Sciences, Branford, Connecticut, United States of America
| | - Stephen Hutchison
- 454 Life Sciences/Roche Applied Sciences, Branford, Connecticut, United States of America
| | - Jeffery S. Pettis
- USDA-ARS Bee Research Lab, Beltsville, Maryland, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Jay D. Evans
- USDA-ARS Bee Research Lab, Beltsville, Maryland, United States of America
- * E-mail:
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22
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Briese T, Paweska JT, McMullan LK, Hutchison SK, Street C, Palacios G, Khristova ML, Weyer J, Swanepoel R, Egholm M, Nichol ST, Lipkin WI. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog 2009; 5:e1000455. [PMID: 19478873 PMCID: PMC2680969 DOI: 10.1371/journal.ppat.1000455] [Citation(s) in RCA: 325] [Impact Index Per Article: 21.7] [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: 02/23/2009] [Accepted: 04/28/2009] [Indexed: 12/13/2022] Open
Abstract
Lujo virus (LUJV), a new member of the family Arenaviridae and the first hemorrhagic fever–associated arenavirus from the Old World discovered in three decades, was isolated in South Africa during an outbreak of human disease characterized by nosocomial transmission and an unprecedented high case fatality rate of 80% (4/5 cases). Unbiased pyrosequencing of RNA extracts from serum and tissues of outbreak victims enabled identification and detailed phylogenetic characterization within 72 hours of sample receipt. Full genome analyses of LUJV showed it to be unique and branching off the ancestral node of the Old World arenaviruses. The virus G1 glycoprotein sequence was highly diverse and almost equidistant from that of other Old World and New World arenaviruses, consistent with a potential distinctive receptor tropism. LUJV is a novel, genetically distinct, highly pathogenic arenavirus. In September and October 2008, five cases of undiagnosed hemorrhagic fever, four of them fatal, were recognized in South Africa after air transfer of a critically ill index case from Zambia. Serum and tissue samples from victims were subjected to unbiased pyrosequencing, yielding within 72 hours of sample receipt, multiple discrete sequence fragments that represented approximately 50% of a prototypic arenavirus genome. Thereafter, full genome sequence was generated by PCR amplification of intervening fragments using specific primers complementary to sequence obtained by pyrosequencing and a universal primer targeting the conserved arenaviral termini. Phylogenetic analyses confirmed the presence of a new member of the family Arenaviridae, provisionally named Lujo virus (LUJV) in recognition of its geographic origin (Lusaka, Zambia, and Johannesburg, South Africa). Our findings enable the development of specific reagents to further investigate the reservoir, geographic distribution, and unusual pathogenicity of LUJV, and confirm the utility of unbiased high throughput pyrosequencing for pathogen discovery and public health.
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Affiliation(s)
- Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
- * E-mail: (TB); (WIL)
| | - Janusz T. Paweska
- Special Pathogens Unit, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, South Africa
| | - Laura K. McMullan
- Special Pathogens Branch, Division of Viral and Rickettsial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Craig Street
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Gustavo Palacios
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Marina L. Khristova
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jacqueline Weyer
- Special Pathogens Unit, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, South Africa
| | - Robert Swanepoel
- Special Pathogens Unit, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, South Africa
| | - Michael Egholm
- 454 Life Sciences, Branford, Connecticut, United States of America
| | - Stuart T. Nichol
- Special Pathogens Branch, Division of Viral and Rickettsial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
- * E-mail: (TB); (WIL)
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Abstract
Genome-wide association studies (GWASs) are regularly used to map genomic regions contributing to common human diseases, but they often do not identify the precise causative genes and sequence variants. To identify causative type 1 diabetes (T1D) variants, we resequenced exons and splice sites of 10 candidate genes in pools of DNA from 480 patients and 480 controls and tested their disease association in over 30,000 participants. We discovered four rare variants that lowered T1D risk independently of each other (odds ratio = 0.51 to 0.74; P = 1.3 x 10(-3) to 2.1 x 10(-16)) in IFIH1 (interferon induced with helicase C domain 1), a gene located in a region previously associated with T1D by GWASs. These variants are predicted to alter the expression and structure of IFIH1 [MDA5 (melanoma differentiation-associated protein 5)], a cytoplasmic helicase that mediates induction of interferon response to viral RNA. This finding firmly establishes the role of IFIH1 in T1D and demonstrates that resequencing studies can pinpoint disease-causing genes in genomic regions initially identified by GWASs.
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Affiliation(s)
- Sergey Nejentsev
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
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24
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Simen BB, Simons JF, Hullsiek KH, Novak RM, Macarthur RD, Baxter JD, Huang C, Lubeski C, Turenchalk GS, Braverman MS, Desany B, Rothberg JM, Egholm M, Kozal MJ. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 2009; 199:693-701. [PMID: 19210162 DOI: 10.1086/596736] [Citation(s) in RCA: 308] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Minor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important. OBJECTIVES To compare the prevalence of drug-resistant variants detected with standard and ultra-deep sequencing (detection down to 1% prevalence) and to determine the impact of minor resistant variants on virologic failure (VF). METHODS The Flexible Initial Retrovirus Suppressive Therapies (FIRST) Study (N = 1397) compared 3 initial antiretroviral therapy (ART) strategies. A random subset (n = 491) had baseline testing for drug-resistance mutations performed by use of standard sequencing methods. Ultra-deep sequencing was performed on samples that had sufficient viral content (N = 264). Proportional hazards models were used to compare rates of VF for those who did and did not have mutations identified. RESULTS Mutations were detected by standard and ultra-deep sequencing (in 14% and 28% of participants, respectively; P < .001). Among individuals who initiated treatment with an ART regimen that combined nucleoside and nonnucleoside reverse-transcriptase inhibitors (hereafter, "NNRTI strategy"), all individuals who had an NNRTI-resistance mutation identified by ultra-deep sequencing experienced VF. When these individuals were compared with individuals who initiated treatment with the NNRTI strategy but who had no NNRTI-resistance mutations, the risk of VF was higher for those who had an NNRTI-resistance mutation detected by both methods (hazard ratio [HR], 12.40 [95% confidence interval {CI}, 3.41-45.10]) and those who had mutation(s) detected only with ultra-deep sequencing (HR, 2.50 [95% CI, 1.17-5.36]). CONCLUSIONS Ultra-deep sequencing identified a significantly larger proportion of HIV-infected, treatment-naive persons as harboring drug-resistant viral variants. Among participants who initiated treatment with the NNRTI strategy, the risk of VF was significantly greater for participants who had low- and high-prevalence NNRTI-resistant variants.
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25
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Honkavuori KS, Shivaprasad HL, Williams BL, Quan PL, Hornig M, Street C, Palacios G, Hutchison SK, Franca M, Egholm M, Briese T, Lipkin WI. Novel borna virus in psittacine birds with proventricular dilatation disease. Emerg Infect Dis 2009; 14:1883-6. [PMID: 19046511 PMCID: PMC2634650 DOI: 10.3201/eid1412.080984] [Citation(s) in RCA: 175] [Impact Index Per Article: 11.7] [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: 11/19/2022] Open
Abstract
Pyrosequencing of cDNA from brains of parrots with proventricular dilatation disease (PDD), an unexplained fatal inflammatory central, autonomic, and peripheral nervous system disease, showed 2 strains of a novel Borna virus. Real-time PCR confirmed virus presence in brain, proventriculus, and adrenal gland of 3 birds with PDD but not in 4 unaffected birds.
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26
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PLF, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajković D, Kućan Z, Gusić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 2008; 134:416-26. [PMID: 18692465 DOI: 10.1016/j.cell.2008.06.021] [Citation(s) in RCA: 303] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 05/29/2008] [Accepted: 06/13/2008] [Indexed: 10/21/2022]
Abstract
A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from approximately 0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 +/- 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.
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Affiliation(s)
- Richard E Green
- Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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28
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Zito CI, Riches D, Kolmakova J, Simons J, Egholm M, Stern DF. Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer. Genes Chromosomes Cancer 2008; 47:633-8. [PMID: 18418848 DOI: 10.1002/gcc.20566] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Gene amplification is among the most common genetic abnormalities that cause cancer. One of the most clinically important gene amplifications in human cancer causes extensive reduplication of ERBB2. A variety of cancers also occasionally harbor somatic mutations in ERBB2. Gene amplification and activating mutations both have predictive value for clinical response to targeted inhibitors. Since the number of gene copies in an amplicon may exceed 100, and since amplicons may encompass multiple genes, high-resolution analysis of gene amplifications poses considerable technical challenges. We have overcome this obstacle by using emulsion-based resequencing to determine the sequence of many independently-amplified individual DNA molecules in parallel. We used this high throughput sequencing technology to analyze ERBB2 mutational status in five ERBB2 amplified cell lines (four breast, one ovarian) and two breast tumors. Genomic DNA was isolated and the 28 exons of ERBB2 were independently amplified. Amplicons were then pooled at equimolar ratios, subjected to emulsion PCR (emPCR) and finally to picotiter plate pyrosequencing. High-quality sequence data were obtained for all amplicons analyzed and no activating mutations within ERBB2 were identified. Although we did not find activating mutations within the multiple copies of ERBB2 in these samples, the results establish the utility of this technology as a feasible and cost-effective approach for high resolution analysis of amplified genes.
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Affiliation(s)
- Christina I Zito
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
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29
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Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008; 452:872-6. [PMID: 18421352 DOI: 10.1038/nature06884] [Citation(s) in RCA: 1151] [Impact Index Per Article: 71.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 03/04/2008] [Indexed: 12/13/2022]
Abstract
The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.
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Affiliation(s)
- David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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30
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Palacios G, Druce J, Du L, Tran T, Birch C, Briese T, Conlan S, Quan PL, Hui J, Marshall J, Simons JF, Egholm M, Paddock CD, Shieh WJ, Goldsmith CS, Zaki SR, Catton M, Lipkin WI. A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med 2008; 358:991-8. [PMID: 18256387 DOI: 10.1056/nejmoa073785] [Citation(s) in RCA: 473] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Three patients who received visceral-organ transplants from a single donor on the same day died of a febrile illness 4 to 6 weeks after transplantation. Culture, polymerase-chain-reaction (PCR) and serologic assays, and oligonucleotide microarray analysis for a wide range of infectious agents were not informative. METHODS We evaluated RNA obtained from the liver and kidney transplant recipients. Unbiased high-throughput sequencing was used to identify microbial sequences not found by means of other methods. The specificity of sequences for a new candidate pathogen was confirmed by means of culture and by means of PCR, immunohistochemical, and serologic analyses. RESULTS High-throughput sequencing yielded 103,632 sequences, of which 14 represented an Old World arenavirus. Additional sequence analysis showed that this new arenavirus was related to lymphocytic choriomeningitis viruses. Specific PCR assays based on a unique sequence confirmed the presence of the virus in the kidneys, liver, blood, and cerebrospinal fluid of the recipients. Immunohistochemical analysis revealed arenavirus antigen in the liver and kidney transplants in the recipients. IgM and IgG antiviral antibodies were detected in the serum of the donor. Seroconversion was evident in serum specimens obtained from one recipient at two time points. CONCLUSIONS Unbiased high-throughput sequencing is a powerful tool for the discovery of pathogens. The use of this method during an outbreak of disease facilitated the identification of a new arenavirus transmitted through solid-organ transplantation.
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Affiliation(s)
- Gustavo Palacios
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
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31
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Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders ACE, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M. Paired-end mapping reveals extensive structural variation in the human genome. Science 2007; 318:420-6. [PMID: 17901297 PMCID: PMC2674581 DOI: 10.1126/science.1149504] [Citation(s) in RCA: 900] [Impact Index Per Article: 52.9] [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: 01/02/2023]
Abstract
Structural variation of the genome involves kilobase- to megabase-sized deletions, duplications, insertions, inversions, and complex combinations of rearrangements. We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome-sequencing method to identify structural variants (SVs) approximately 3 kilobases (kb) or larger that combines the rescue and capture of paired ends of 3-kb fragments, massive 454 sequencing, and a computational approach to map DNA reads onto a reference genome. PEM was used to map SVs in an African and in a putatively European individual and identified shared and divergent SVs relative to the reference genome. Overall, we fine-mapped more than 1000 SVs and documented that the number of SVs among humans is much larger than initially hypothesized; many of the SVs potentially affect gene function. The breakpoint junction sequences of more than 200 SVs were determined with a novel pooling strategy and computational analysis. Our analysis provided insights into the mechanisms of SV formation in humans.
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Affiliation(s)
- Jan O Korbel
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
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32
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Toth AL, Varala K, Newman TC, Miguez FE, Hutchison SK, Willoughby DA, Simons JF, Egholm M, Hunt JH, Hudson ME, Robinson GE. Wasp Gene Expression Supports an Evolutionary Link Between Maternal Behavior and Eusociality. Science 2007; 318:441-4. [PMID: 17901299 DOI: 10.1126/science.1146647] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The presence of workers that forgo reproduction and care for their siblings is a defining feature of eusociality and a major challenge for evolutionary theory. It has been proposed that worker behavior evolved from maternal care behavior. We explored this idea by studying gene expression in the primitively eusocial wasp Polistes metricus. Because little genomic information existed for this species, we used 454 sequencing to generate 391,157 brain complementary DNA reads, resulting in robust hits to 3017 genes from the honey bee genome, from which we identified and assayed orthologs of 32 honey bee behaviorally related genes. Wasp brain gene expression in workers was more similar to that in foundresses, which show maternal care, than to that in queens and gynes, which do not. Insulin-related genes were among the differentially regulated genes, suggesting that the evolution of eusociality involved major nutritional and reproductive pathways.
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Affiliation(s)
- Amy L Toth
- Department of Entomology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, Quan PL, Briese T, Hornig M, Geiser DM, Martinson V, vanEngelsdorp D, Kalkstein AL, Drysdale A, Hui J, Zhai J, Cui L, Hutchison SK, Simons JF, Egholm M, Pettis JS, Lipkin WI. A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder. Science 2007; 318:283-7. [PMID: 17823314 DOI: 10.1126/science.1146498] [Citation(s) in RCA: 946] [Impact Index Per Article: 55.6] [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: 11/02/2022]
Abstract
In colony collapse disorder (CCD), honey bee colonies inexplicably lose their workers. CCD has resulted in a loss of 50 to 90% of colonies in beekeeping operations across the United States. The observation that irradiated combs from affected colonies can be repopulated with naive bees suggests that infection may contribute to CCD. We used an unbiased metagenomic approach to survey microflora in CCD hives, normal hives, and imported royal jelly. Candidate pathogens were screened for significance of association with CCD by the examination of samples collected from several sites over a period of 3 years. One organism, Israeli acute paralysis virus of bees, was strongly correlated with CCD.
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Affiliation(s)
- Diana L Cox-Foster
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
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Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, Du L, Egholm M, Rothberg JM, Paunovic M, Pääbo S. Analysis of one million base pairs of Neanderthal DNA. Nature 2006; 444:330-6. [PMID: 17108958 DOI: 10.1038/nature05336] [Citation(s) in RCA: 360] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 10/11/2006] [Indexed: 12/28/2022]
Abstract
Neanderthals are the extinct hominid group most closely related to contemporary humans, so their genome offers a unique opportunity to identify genetic changes specific to anatomically fully modern humans. We have identified a 38,000-year-old Neanderthal fossil that is exceptionally free of contamination from modern human DNA. Direct high-throughput sequencing of a DNA extract from this fossil has thus far yielded over one million base pairs of hominoid nuclear DNA sequences. Comparison with the human and chimpanzee genomes reveals that modern human and Neanderthal DNA sequences diverged on average about 500,000 years ago. Existing technology and fossil resources are now sufficient to initiate a Neanderthal genome-sequencing effort.
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Affiliation(s)
- Richard E Green
- Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.
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Thomas RK, Nickerson E, Simons JF, Jänne PA, Tengs T, Yuza Y, Garraway LA, LaFramboise T, Lee JC, Shah K, O'Neill K, Sasaki H, Lindeman N, Wong KK, Borras AM, Gutmann EJ, Dragnev KH, DeBiasi R, Chen TH, Glatt KA, Greulich H, Desany B, Lubeski CK, Brockman W, Alvarez P, Hutchison SK, Leamon JH, Ronan MT, Turenchalk GS, Egholm M, Sellers WR, Rothberg JM, Meyerson M. Erratum: Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat Med 2006. [DOI: 10.1038/nm1006-1220a] [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: 11/09/2022]
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36
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Stiller M, Green RE, Ronan M, Simons JF, Du L, He W, Egholm M, Rothberg JM, Keates SG, Keats SG, Ovodov ND, Antipina EE, Baryshnikov GF, Kuzmin YV, Vasilevski AA, Wuenschell GE, Termini J, Hofreiter M, Jaenicke-Després V, Pääbo S. Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc Natl Acad Sci U S A 2006; 103:13578-84. [PMID: 16938852 PMCID: PMC1564221 DOI: 10.1073/pnas.0605327103] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whereas evolutionary inferences derived from present-day DNA sequences are by necessity indirect, ancient DNA sequences provide a direct view of past genetic variants. However, base lesions that accumulate in DNA over time may cause nucleotide misincorporations when ancient DNA sequences are replicated. By repeated amplifications of mitochondrial DNA sequences from a large number of ancient wolf remains, we show that C/G-to-T/A transitions are the predominant type of such misincorporations. Using a massively parallel sequencing method that allows large numbers of single DNA strands to be sequenced, we show that modifications of C, as well as to a lesser extent of G, residues cause such misincorporations. Experiments where oligonucleotides containing modified bases are used as templates in amplification reactions suggest that both of these types of misincorporations can be caused by deamination of the template bases. New DNA sequencing methods in conjunction with knowledge of misincorporation processes have now, in principle, opened the way for the determination of complete genomes from organisms that became extinct during and after the last glaciation.
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Affiliation(s)
- M Stiller
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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Pinard R, de Winter A, Sarkis GJ, Gerstein MB, Tartaro KR, Plant RN, Egholm M, Rothberg JM, Leamon JH. Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics 2006; 7:216. [PMID: 16928277 PMCID: PMC1560136 DOI: 10.1186/1471-2164-7-216] [Citation(s) in RCA: 224] [Impact Index Per Article: 12.4] [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: 05/24/2006] [Accepted: 08/23/2006] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification-induced error and template bias generated by these methods have previously been addressed through either small scale (SNPs) or large scale (CGH array, FISH) methodologies. Here we utilized whole genome sequencing to assess amplification-induced bias in both coding and non-coding regions of two bacterial genomes. Halobacterium species NRC-1 DNA and Campylobacter jejuni were amplified by several common, commercially available protocols: multiple displacement amplification, primer extension pre-amplification and degenerate oligonucleotide primed PCR. The amplification-induced bias of each method was assessed by sequencing both genomes in their entirety using the 454 Sequencing System technology and comparing the results with those obtained from unamplified controls. RESULTS All amplification methodologies induced statistically significant bias relative to the unamplified control. For the Halobacterium species NRC-1 genome, assessed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 119 times greater than those from unamplified material, 164.0 times greater for Repli-G, 165.0 times greater for PEP-PCR and 252.0 times greater than the unamplified controls for DOP-PCR. For Campylobacter jejuni, also analyzed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 15 times greater than those from unamplified material, 19.8 times greater for Repli-G, 61.8 times greater for PEP-PCR and 220.5 times greater than the unamplified controls for DOP-PCR. CONCLUSION Of the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA.
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Affiliation(s)
- Robert Pinard
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
| | - Alex de Winter
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
| | - Gary J Sarkis
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
| | - Mark B Gerstein
- MB&B Department, Yale University, 266 Whitney Ave., New Haven CT 06520, USA
| | | | - Ramona N Plant
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
| | - Michael Egholm
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
| | | | - John H Leamon
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
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38
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Abstract
Three protocols in this issue highlight applications of emulsification procedures, which deliver high-throughput potential to the molecular biology laboratory, without the need for automation. These procedures have already generated interesting results and spurred the development of exciting new technologies, while requiring only readily available laboratory equipment.
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Affiliation(s)
- John H Leamon
- RainDance Technologies, Guilford, Connecticut 06437, USA
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39
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Thomas RK, Nickerson E, Simons JF, Jänne PA, Tengs T, Yuza Y, Garraway LA, LaFramboise T, Lee JC, Shah K, O'Neill K, Sasaki H, Lindeman N, Wong KK, Borras AM, Gutmann EJ, Dragnev KH, DeBiasi R, Chen TH, Glatt KA, Greulich H, Desany B, Lubeski CK, Brockman W, Alvarez P, Hutchison SK, Leamon JH, Ronan MT, Turenchalk GS, Egholm M, Sellers WR, Rothberg JM, Meyerson M. Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat Med 2006; 12:852-5. [PMID: 16799556 DOI: 10.1038/nm1437] [Citation(s) in RCA: 283] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Accepted: 05/16/2006] [Indexed: 01/29/2023]
Abstract
The sensitivity of conventional DNA sequencing in tumor biopsies is limited by stromal contamination and by genetic heterogeneity within the cancer. Here, we show that microreactor-based pyrosequencing can detect rare cancer-associated sequence variations by independent and parallel sampling of multiple representatives of a given DNA fragment. This technology can thereby facilitate accurate molecular diagnosis of heterogeneous cancer specimens and enable patient selection for targeted cancer therapies.
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Affiliation(s)
- Roman K Thomas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA
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40
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Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Goodwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437:376-80. [PMID: 16056220 PMCID: PMC1464427 DOI: 10.1038/nature03959] [Citation(s) in RCA: 4967] [Impact Index Per Article: 261.4] [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: 05/06/2005] [Accepted: 06/10/2005] [Indexed: 02/06/2023]
Abstract
The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.
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Affiliation(s)
- Marcel Margulies
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Michael Egholm
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | | | - Said Attiya
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Joel S. Bader
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Lisa A. Bemben
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Jan Berka
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | | | - Yi-Ju Chen
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Zhoutao Chen
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Scott B. Dewell
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Lei Du
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Joseph M. Fierro
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Xavier V. Gomes
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Brian C. Goodwin
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Wen He
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Scott Helgesen
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Chun He Ho
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Gerard P. Irzyk
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | | | | | - Thomas P. Jarvie
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Kshama B. Jirage
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Jong-Bum Kim
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - James R. Knight
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Janna R. Lanza
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - John H. Leamon
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | | | - Ming Lei
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Jing Li
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Kenton L. Lohman
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Hong Lu
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | | | - Keith E. McDade
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | | | | | | | - John R. Nobile
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Ramona Plant
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Bernard P. Puc
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Michael T. Ronan
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - George T. Roth
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Gary J. Sarkis
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | | | - John W. Simpson
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | | | | | - Alexander Tomasz
- Laboratory of Microbiology, The Rockefeller University, New York, NY 10021, USA
| | - Kari A. Vogt
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Greg A. Volkmer
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Shally H. Wang
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Yong Wang
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | - Michael P. Weiner
- The Rothberg Institute For Childhood Diseases, 530 Whitfield St., Guilford, CT 06437, USA
| | - Pengguang Yu
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
| | | | - Jonathan M. Rothberg
- 454 Life Sciences Corp., 20 Commercial St., Branford, CT 06405, USA
- Correspondence and requests for materials should be addressed to J. M. Rothberg (). Sequences for M. genitalium and S. pneumoniae were deposited at DDBJ/EMBL/GenBank under accession numbers AAGX01000000 and AAGY01000000 respectively
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41
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Thomas RK, Greulich H, Yuza Y, Lee JC, Tengs T, Feng W, Chen TH, Nickerson E, Simons J, Egholm M, Rothberg JM, Sellers WR, Meyerson ML. Detection of oncogenic mutations in the EGFR gene in lung adenocarcinoma with differential sensitivity to EGFR tyrosine kinase inhibitors. Cold Spring Harb Symp Quant Biol 2005; 70:73-81. [PMID: 16869740 DOI: 10.1101/sqb.2005.70.056] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The complete sequencing of the human genome and the development of molecularly targeted cancer therapy have promoted efforts to identify systematically the genetic alterations in human cancer. By high-throughput sequencing of tyrosine kinase genes in human non-small-cell lung cancer, we identified somatic mutations in the kinase domain of the epidermal growth factor receptor tyrosine kinase gene (EGFR) that are correlated with clinical response to EGFR tyrosine kinase inhibitors (TKIs). We have shown that these mutant forms of EGFR induce oncogenic transformation in different cellular systems. Cells whose growth depends on EGFR with mutations in exons 19 and 21 are sensitive to EGFR-TKIs, whereas cells expressing insertion mutations in exon 20 or the T790M point mutant, found in tumor biopsies from patients that relapsed after an initial response to EGFR-TKIs, are resistant. Furthermore, by applying a novel, massively parallel sequencing technology, we have shown that clinically relevant oncogene mutations can be detected in clinical specimens with very low tumor content, thereby enabling optimal patient selection for mutation-directed therapy. In summary, by applying high-throughput genomic resequencing, we have identified a novel therapeutic target, mutant EGFR, in lung cancer and evaluated its role in predicting response to targeted therapy.
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Affiliation(s)
- R K Thomas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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42
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Affiliation(s)
- Roger S Lasken
- Molecular Staging Inc., 300 George Street, New Haven, CT 06511, USA.
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43
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Alsmadi OA, Bornarth CJ, Song W, Wisniewski M, Du J, Brockman JP, Faruqi AF, Hosono S, Sun Z, Du Y, Wu X, Egholm M, Abarzúa P, Lasken RS, Driscoll MD. High accuracy genotyping directly from genomic DNA using a rolling circle amplification based assay. BMC Genomics 2003; 4:21. [PMID: 12777185 PMCID: PMC165428 DOI: 10.1186/1471-2164-4-21] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2003] [Accepted: 05/30/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rolling circle amplification of ligated probes is a simple and sensitive means for genotyping directly from genomic DNA. SNPs and mutations are interrogated with open circle probes (OCP) that can be circularized by DNA ligase when the probe matches the genotype. An amplified detection signal is generated by exponential rolling circle amplification (ERCA) of the circularized probe. The low cost and scalability of ligation/ERCA genotyping makes it ideally suited for automated, high throughput methods. RESULTS A retrospective study using human genomic DNA samples of known genotype was performed for four different clinically relevant mutations: Factor V Leiden, Factor II prothrombin, and two hemochromatosis mutations, C282Y and H63D. Greater than 99% accuracy was obtained genotyping genomic DNA samples from hundreds of different individuals. The combined process of ligation/ERCA was performed in a single tube and produced fluorescent signal directly from genomic DNA in less than an hour. In each assay, the probes for both normal and mutant alleles were combined in a single reaction. Multiple ERCA primers combined with a quenched-peptide nucleic acid (Q-PNA) fluorescent detection system greatly accellerated the appearance of signal. Probes designed with hairpin structures reduced misamplification. Genotyping accuracy was identical from either purified genomic DNA or genomic DNA generated using whole genome amplification (WGA). Fluorescent signal output was measured in real time and as an end point. CONCLUSIONS Combining the optimal elements for ligation/ERCA genotyping has resulted in a highly accurate single tube assay for genotyping directly from genomic DNA samples. Accuracy exceeded 99 % for four probe sets targeting clinically relevant mutations. No genotypes were called incorrectly using either genomic DNA or whole genome amplified sample.
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Affiliation(s)
- Osama A Alsmadi
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Carole J Bornarth
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Wanmin Song
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Michele Wisniewski
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Jing Du
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Joel P Brockman
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - A Fawad Faruqi
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Seiyu Hosono
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Zhenyu Sun
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Yuefen Du
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Xiaohong Wu
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Michael Egholm
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Patricio Abarzúa
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Roger S Lasken
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
| | - Mark D Driscoll
- Molecular Staging, Inc. 300 George Street, Suite 701, New Haven, CT 06511, USA
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44
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Hosono S, Faruqi AF, Dean FB, Du Y, Sun Z, Wu X, Du J, Kingsmore SF, Egholm M, Lasken RS. Unbiased whole-genome amplification directly from clinical samples. Genome Res 2003; 13:954-64. [PMID: 12695328 PMCID: PMC430878 DOI: 10.1101/gr.816903] [Citation(s) in RCA: 342] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Preparation of genomic DNA from clinical samples is a bottleneck in genotyping and DNA sequencing analysis and is frequently limited by the amount of specimen available. We use Multiple Displacement Amplification (MDA) to amplify the whole genome 10,000-fold directly from small amounts of whole blood, dried blood, buccal cells, cultured cells, and buffy coats specimens, generating large amounts of DNA for genetic testing. Genomic DNA was evenly amplified with complete coverage and consistent representation of all genes. All 47 loci analyzed from 44 individuals were represented in the amplified DNA at between 0.5- and 3.0-fold of the copy number in the starting genomic DNA template. A high-fidelity DNA polymerase ensures accurate representation of the DNA sequence. The amplified DNA was indistinguishable from the original genomic DNA template in 5 SNP and 10 microsatellite DNA assays on three different clinical sample types for 20 individuals. Amplification of genomic DNA directly from cells is highly reproducible, eliminates the need for DNA template purification, and allows genetic testing from small clinical samples. The low amplification bias of MDA represents a dramatic technical improvement in the ability to amplify a whole genome compared with older, PCR-based methods.
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Affiliation(s)
- Seiyu Hosono
- Molecular Staging, Inc., New Haven, Connecticut 06511, USA
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45
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Abstract
Site-specific DNA binding molecules offer the potential for genetic manipulation of mammalian cells. Peptide nucleic acids (PNAs) are a DNA mimic in which the purine and pyrimidine bases are attached to a polyamide backbone. PNAs bind with high affinity to single-stranded DNA via Watson-Crick base pairing and can form triple helices via Hoogsteen binding to DNAPNA duplexes. Dimeric bis-PNAs capable of both strand invasion and triplex formation can form clamp structures on target DNAs. As a strategy to promote site-directed recombination, a bis-PNA was coupled to a 40-nt donor DNA fragment homologous to an adjacent region in the target gene. The PNA-DNA conjugate was found to mediate site-directed recombination with a plasmid substrate in human cell-free extracts, resulting in correction of a mutation in a reporter gene at a frequency at least 60-fold above background. Induced site-specific recombination was also seen when the bis-PNA and the donor DNA were co-mixed without covalent linkage. In addition, the bis-PNA and the bis-PNA-DNA conjugate were found to induce DNA repair specifically in the target plasmid. Both the PNA-induced recombination and the PNA-induced repair were found to be dependent on the nucleotide excision repair factor, XPA (xeroderma pigmentosum complementation group A protein). These results suggest that the formation of a PNA clamp on duplex DNA creates a helical distortion that strongly provokes DNA repair and thereby sensitizes the target site to recombination. The ability to promote recombination in a site-directed manner using PNA-DNA conjugates may provide a useful strategy to achieve targeted correction of defective genes.
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Affiliation(s)
- Faye A Rogers
- Departments of Therapeutic Radiology and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
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Hyrup B, Egholm M, Nielsen PE, Wittung P, Norden B, Buchardt O. Structure-Activity Studies of the Binding of Modified Peptide Nucleic Acids (PNAs) to DNA. J Am Chem Soc 2002. [DOI: 10.1021/ja00097a002] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Dueholm KL, Egholm M, Behrens C, Christensen L, Hansen HF, Vulpius T, Petersen KH, Berg RH, Nielsen PE, Buchardt O. Synthesis of Peptide Nucleic Acid Monomers Containing the Four Natural Nucleobases: Thymine, Cytosine, Adenine, and Guanine and Their Oligomerization. J Org Chem 2002. [DOI: 10.1021/jo00098a042] [Citation(s) in RCA: 249] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kim SK, Nielsen PE, Egholm M, Buchardt O, Berg RH, Norden B. Right-handed triplex formed between peptide nucleic acid PNA-T8 and poly(dA) shown by linear and circular dichroism spectroscopy. J Am Chem Soc 2002. [DOI: 10.1021/ja00068a001] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Egholm M, Buchardt O, Nielsen PE, Berg RH. Peptide nucleic acids (PNA). Oligonucleotide analogs with an achiral peptide backbone. J Am Chem Soc 2002. [DOI: 10.1021/ja00031a062] [Citation(s) in RCA: 582] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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