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Bruce SA, Schiraldi NJ, Kamath PL, Easterday WR, Turner WC. A classification framework for Bacillus anthracis defined by global genomic structure. Evol Appl 2020; 13:935-944. [PMID: 32431744 PMCID: PMC7232756 DOI: 10.1111/eva.12911] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/18/2019] [Accepted: 11/14/2019] [Indexed: 12/22/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax, is a considerable global health threat affecting wildlife, livestock, and the general public. In this study, whole-genome sequence analysis of over 350 B. anthracis isolates was used to establish a new high-resolution global genotyping framework that is both biogeographically informative and compatible with multiple genomic assays. The data presented in this study shed new light on the diverse global dissemination of this species and indicate that many lineages may be uniquely suited to the geographic regions in which they are found. In addition, we demonstrate that plasmid genomic structure for this species is largely consistent with chromosomal population structure, suggesting vertical inheritance in this bacterium has contributed to its evolutionary persistence. This classification methodology is the first based on population genomic structure for this species and has potential use for local and broader institutions seeking to understand both disease outbreak origins and recent introductions. In addition, we provide access to a newly developed genotyping script as well as the full whole-genome sequence analyses output for this study, allowing future studies to rapidly employ and append their data in the context of this global collection. This framework may act as a powerful tool for public health agencies, wildlife disease laboratories, and researchers seeking to utilize and expand this classification scheme for further investigations into B. anthracis evolution.
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Affiliation(s)
- Spencer A. Bruce
- Department of Biological SciencesUniversity at Albany – State University of New YorkAlbanyNYUSA
| | - Nicholas J. Schiraldi
- Department of Information Technology ServicesUniversity at Albany – State University of New YorkAlbanyNYUSA
| | | | - W. Ryan Easterday
- Centre for Ecological and Evolutionary SynthesisDepartment of BiosciencesUniversity of OsloOsloNorway
| | - Wendy C. Turner
- Department of Biological SciencesUniversity at Albany – State University of New YorkAlbanyNYUSA
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2
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Abstract
From the investigation of disease-associated loci in humans, to monitoring the changing genomes of pathogenic viruses and bacteria, sequencing is a powerful and versatile tool. A new generation of sequencing technologies will increase the speed and lower the cost of sequencing, and promises to expand the utility of sequencing in drug discovery and development.:
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3
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Vanhomwegen J, Berthet N, Mazuet C, Guigon G, Vallaeys T, Stamboliyska R, Dubois P, Kennedy GC, Cole ST, Caro V, Manuguerra JC, Popoff MR. Application of high-density DNA resequencing microarray for detection and characterization of botulinum neurotoxin-producing clostridia. PLoS One 2013; 8:e67510. [PMID: 23818983 PMCID: PMC3688605 DOI: 10.1371/journal.pone.0067510] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 05/22/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Clostridium botulinum and related clostridia express extremely potent toxins known as botulinum neurotoxins (BoNTs) that cause severe, potentially lethal intoxications in humans. These BoNT-producing bacteria are categorized in seven major toxinotypes (A through G) and several subtypes. The high diversity in nucleotide sequence and genetic organization of the gene cluster encoding the BoNT components poses a great challenge for the screening and characterization of BoNT-producing strains. METHODOLOGY/PRINCIPAL FINDINGS In the present study, we designed and evaluated the performances of a resequencing microarray (RMA), the PathogenId v2.0, combined with an automated data approach for the simultaneous detection and characterization of BoNT-producing clostridia. The unique design of the PathogenID v2.0 array allows the simultaneous detection and characterization of 48 sequences targeting the BoNT gene cluster components. This approach allowed successful identification and typing of representative strains of the different toxinotypes and subtypes, as well as the neurotoxin-producing C. botulinum strain in a naturally contaminated food sample. Moreover, the method allowed fine characterization of the different neurotoxin gene cluster components of all studied strains, including genomic regions exhibiting up to 24.65% divergence with the sequences tiled on the arrays. CONCLUSIONS/SIGNIFICANCE The severity of the disease demands rapid and accurate means for performing risk assessments of BoNT-producing clostridia and for tracing potentials sources of contamination in outbreak situations. The RMA approach constitutes an essential higher echelon component in a diagnostics and surveillance pipeline. In addition, it is an important asset to characterise potential outbreak related strains, but also environment isolates, in order to obtain a better picture of the molecular epidemiology of BoNT-producing clostridia.
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Affiliation(s)
- Jessica Vanhomwegen
- Institut Pasteur, Laboratory for Urgent Responses to Biological Threats, Paris, France
| | - Nicolas Berthet
- Institut Pasteur, Epidemiology and Pathophysiology of Oncogenic Viruses, Paris, France
- CNRS, UMR3569, Paris, France
| | | | - Ghislaine Guigon
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | - Tatiana Vallaeys
- CNRS – CC093 Université Montpellier II, UMR5119 Ecosystèmes lagunaires, Montpellier, France
| | - Rayna Stamboliyska
- Department of Biology II, University of Munich (LMU), Planegg-Martinsried, Germany
| | - Philippe Dubois
- Institut Pasteur, Laboratory for Urgent Responses to Biological Threats, Paris, France
| | - Giulia C. Kennedy
- Department of Research and Development, Veracyte, Inc., South San Francisco, California, United States of America
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Valérie Caro
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
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4
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Ono N, Suzuki S, Furusawa C, Shimizu H, Yomo T. Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays. PLoS One 2013; 8:e54571. [PMID: 23382915 PMCID: PMC3557292 DOI: 10.1371/journal.pone.0054571] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/12/2012] [Indexed: 11/18/2022] Open
Abstract
High-density DNA microarrays are useful tools for analyzing sequence changes in DNA samples. Although microarray analysis provides informative signals from a large number of probes, the analysis and interpretation of these signals have certain inherent limitations, namely, complex dependency of signals on the probe sequences and the existence of false signals arising from non-specific binding between probe and target. In this study, we have developed a novel algorithm to detect the single-base substitutions by using microarray data based on a thermodynamic model of hybridization. We modified the thermodynamic model by introducing a penalty for mismatches that represent the effects of substitutions on hybridization affinity. This penalty results in significantly higher detection accuracy than other methods, indicating that the incorporation of hybridization free energy can improve the analysis of sequence variants by using microarray data.
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Affiliation(s)
- Naoaki Ono
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Shingo Suzuki
- Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
| | - Chikara Furusawa
- Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
- * E-mail:
| | - Hiroshi Shimizu
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Tetsuya Yomo
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- ERATO, JST, Suita, Osaka, Japan
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5
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Steinberg KM, Ramachandran D, Patel VC, Shetty AC, Cutler DJ, Zwick ME. Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder. Mol Autism 2012; 3:8. [PMID: 23020841 PMCID: PMC3492087 DOI: 10.1186/2040-2392-3-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 09/14/2012] [Indexed: 01/03/2023] Open
Abstract
UNLABELLED BACKGROUND Autism spectrum disorder (ASD) is highly heritable, but the genetic risk factors for it remain largely unknown. Although structural variants with large effect sizes may explain up to 15% ASD, genome-wide association studies have failed to uncover common single nucleotide variants with large effects on phenotype. The focus within ASD genetics is now shifting to the examination of rare sequence variants of modest effect, which is most often achieved via exome selection and sequencing. This strategy has indeed identified some rare candidate variants; however, the approach does not capture the full spectrum of genetic variation that might contribute to the phenotype. METHODS We surveyed two loci with known rare variants that contribute to ASD, the X-linked neuroligin genes by performing massively parallel Illumina sequencing of the coding and noncoding regions from these genes in males from families with multiplex autism. We annotated all variant sites and functionally tested a subset to identify other rare mutations contributing to ASD susceptibility. RESULTS We found seven rare variants at evolutionary conserved sites in our study population. Functional analyses of the three 3' UTR variants did not show statistically significant effects on the expression of NLGN3 and NLGN4X. In addition, we identified two NLGN3 intronic variants located within conserved transcription factor binding sites that could potentially affect gene regulation. CONCLUSIONS These data demonstrate the power of massively parallel, targeted sequencing studies of affected individuals for identifying rare, potentially disease-contributing variation. However, they also point out the challenges and limitations of current methods of direct functional testing of rare variants and the difficulties of identifying alleles with modest effects.
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Affiliation(s)
- Karyn Meltz Steinberg
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA
- Graduate Program in Population Biology, Ecology and Evolution, Emory University, 1510 Clifton Road, Atlanta, 30322, GA, USA
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195, WA, USA
| | - Dhanya Ramachandran
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA
| | - Viren C Patel
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA
| | - Amol C Shetty
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA
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6
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Leski TA, Lin B, Malanoski AP, Stenger DA. Application of resequencing microarrays in microbial detection and characterization. Future Microbiol 2012; 7:625-37. [PMID: 22568717 DOI: 10.2217/fmb.12.30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Microarrays are powerful, highly parallel assays that are transforming microbiological diagnostics and research. The adaptation of microarray-based resequencing technology for microbial detection and characterization resulted in the development of a number assays that have unique advantages over other existing technologies. This technological platform seems to be especially useful for sensitive and high-resolution multiplexed diagnostics for clinical syndromes with similar symptoms, screening environmental samples for biothreat agents, as well as genotyping and whole-genome analysis of single pathogens.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, SW, Washington, DC 20375, USA.
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7
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Mondal K, Ramachandran D, Patel VC, Hagen KR, Bose P, Cutler DJ, Zwick ME. Excess variants in AFF2 detected by massively parallel sequencing of males with autism spectrum disorder. Hum Mol Genet 2012; 21:4356-64. [PMID: 22773736 DOI: 10.1093/hmg/dds267] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Autism spectrum disorder (ASD) is a heterogeneous disorder with substantial heritability, most of which is unexplained. ASD has a population prevalence of one percent and affects four times as many males as females. Patients with fragile X E (FRAXE) intellectual disability, which is caused by a silencing of the X-linked gene AFF2, display a number of ASD-like phenotypes. Duplications and deletions at the AFF2 locus have also been reported in cases with moderate intellectual disability and ASD. We hypothesized that other rare X-linked sequence variants at the AFF2 locus might contribute to ASD. We sequenced the AFF2 genomic region in 202 male ASD probands and found that 2.5% of males sequenced had missense mutations at highly conserved evolutionary sites. When compared with the frequency of missense mutations in 5545 X chromosomes from unaffected controls, we saw a statistically significant enrichment in patients with ASD (OR: 4.9; P < 0.014). In addition, we identified rare AFF2 3' UTR variants at conserved sites which alter gene expression in a luciferase assay. These data suggest that rare variation in AFF2 may be a previously unrecognized ASD susceptibility locus and may help explain some of the male excess of ASD.
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Affiliation(s)
- Kajari Mondal
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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8
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Zwick ME, Joseph SJ, Didelot X, Chen PE, Bishop-Lilly KA, Stewart AC, Willner K, Nolan N, Lentz S, Thomason MK, Sozhamannan S, Mateczun AJ, Du L, Read TD. Genomic characterization of the Bacillus cereus sensu lato species: backdrop to the evolution of Bacillus anthracis. Genome Res 2012; 22:1512-24. [PMID: 22645259 PMCID: PMC3409264 DOI: 10.1101/gr.134437.111] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The key genes required for Bacillus anthracis to cause anthrax have been acquired recently by horizontal gene transfer. To understand the genetic background for the evolution of B. anthracis virulence, we obtained high-redundancy genome sequences of 45 strains of the Bacillus cereus sensu lato (s.l.) species that were chosen for their genetic diversity within the species based on the existing multilocus sequence typing scheme. From the resulting data, we called more than 324,000 new genes representing more than 12,333 new gene families for this group. The core genome size for the B. cereus s.l. group was ∼1750 genes, with another 2150 genes found in almost every genome constituting the extended core. There was a paucity of genes specific and conserved in any clade. We found no evidence of recent large-scale gene loss in B. anthracis or for unusual accumulation of nonsynonymous DNA substitutions in the chromosome; however, several B. cereus genomes isolated from soil and not previously associated with human disease were degraded to various degrees. Although B. anthracis has undergone an ecological shift within the species, its chromosome does not appear to be exceptional on a macroscopic scale compared with close relatives.
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Affiliation(s)
- Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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9
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Golubchik T, Brueggemann AB, Street T, Gertz RE, Spencer CCA, Ho T, Giannoulatou E, Link-Gelles R, Harding RM, Beall B, Peto TEA, Moore MR, Donnelly P, Crook DW, Bowden R. Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event. Nat Genet 2012; 44:352-5. [PMID: 22286217 PMCID: PMC3303117 DOI: 10.1038/ng.1072] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 12/12/2011] [Indexed: 12/31/2022]
Abstract
Streptococcus pneumoniae ('pneumococcus') causes an estimated 14.5 million cases of serious disease and 826,000 deaths annually in children under 5 years of age(1). The highly effective introduction of the PCV7 pneumococcal vaccine in 2000 in the United States(2,3) provided an unprecedented opportunity to investigate the response of an important pathogen to widespread, vaccine-induced selective pressure. Here, we use array-based sequencing of 62 isolates from a US national monitoring program to study five independent instances of vaccine escape recombination(4), showing the simultaneous transfer of multiple and often large (up to at least 44 kb) DNA fragments. We show that one such new strain quickly became established, spreading from east to west across the United States. These observations clarify the roles of recombination and selection in the population genomics of pneumococcus and provide proof of principle of the considerable value of combining genomic and epidemiological information in the surveillance and enhanced understanding of infectious diseases.
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Affiliation(s)
| | | | - Teresa Street
- Department of Statistics, University of Oxford, Oxford, UK
| | - Robert E. Gertz
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Thien Ho
- Department of Statistics, University of Oxford, Oxford, UK
| | - Eleni Giannoulatou
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ruth Link-Gelles
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Bernard Beall
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tim E. A. Peto
- Oxford Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew R. Moore
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Peter Donnelly
- Department of Statistics, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Derrick W. Crook
- Oxford Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rory Bowden
- Department of Statistics, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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10
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Genetic variation and linkage disequilibrium in Bacillus anthracis. Sci Rep 2011; 1:169. [PMID: 22355684 PMCID: PMC3240990 DOI: 10.1038/srep00169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 11/03/2011] [Indexed: 12/27/2022] Open
Abstract
We performed whole-genome amplification followed by hybridization of custom-designed resequencing arrays to resequence 303 kb of genomic sequence from a worldwide panel of 39 Bacillus anthracis strains. We used an efficient algorithm contained within a custom software program, UniqueMER, to identify and mask repetitive sequences on the resequencing array to reduce false-positive identification of genetic variation, which can arise from cross-hybridization. We discovered a total of 240 single nucleotide variants (SNVs) and showed that B. anthracis strains have an average of 2.25 differences per 10,000 bases in the region we resequenced. Common SNVs in this region are found to be in complete linkage disequilibrium. These patterns of variation suggest there has been little if any historical recombination among B. anthracis strains since the origin of the pathogen. This pattern of common genetic variation suggests a framework for recognizing new or genetically engineered strains.
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11
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Didelot X, Bowden R, Street T, Golubchik T, Spencer C, McVean G, Sangal V, Anjum MF, Achtman M, Falush D, Donnelly P. Recombination and population structure in Salmonella enterica. PLoS Genet 2011; 7:e1002191. [PMID: 21829375 PMCID: PMC3145606 DOI: 10.1371/journal.pgen.1002191] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 06/04/2011] [Indexed: 01/22/2023] Open
Abstract
Salmonella enterica is a bacterial pathogen that causes enteric fever and gastroenteritis in humans and animals. Although its population structure was long described as clonal, based on high linkage disequilibrium between loci typed by enzyme electrophoresis, recent examination of gene sequences has revealed that recombination plays an important evolutionary role. We sequenced around 10% of the core genome of 114 isolates of enterica using a resequencing microarray. Application of two different analysis methods (Structure and ClonalFrame) to our genomic data allowed us to define five clear lineages within S. enterica subspecies enterica, one of which is five times older than the other four and two thirds of the age of the whole subspecies. We show that some of these lineages display more evidence of recombination than others. We also demonstrate that some level of sexual isolation exists between the lineages, so that recombination has occurred predominantly between members of the same lineage. This pattern of recombination is compatible with expectations from the previously described ecological structuring of the enterica population as well as mechanistic barriers to recombination observed in laboratory experiments. In spite of their relatively low level of genetic differentiation, these lineages might therefore represent incipient species.
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Affiliation(s)
- Xavier Didelot
- Department of Statistics, Oxford University, Oxford, United Kingdom
| | - Rory Bowden
- Department of Statistics, Oxford University, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom
| | - Teresa Street
- Department of Statistics, Oxford University, Oxford, United Kingdom
| | - Tanya Golubchik
- Department of Statistics, Oxford University, Oxford, United Kingdom
| | - Chris Spencer
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom
| | - Gil McVean
- Department of Statistics, Oxford University, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom
| | - Vartul Sangal
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Muna F. Anjum
- Veterinary Laboratories Agency, Addlestone, United Kingdom
| | - Mark Achtman
- Environmental Research Institute and Department of Microbiology, University College Cork, Cork, Ireland
| | - Daniel Falush
- Environmental Research Institute and Department of Microbiology, University College Cork, Cork, Ireland
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Peter Donnelly
- Department of Statistics, Oxford University, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom
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12
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Gowrisankar S, Lerner-Ellis JP, Cox S, White ET, Manion M, LeVan K, Liu J, Farwell LM, Iartchouk O, Rehm HL, Funke BH. Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications. J Mol Diagn 2010; 12:818-27. [PMID: 20864638 DOI: 10.2353/jmoldx.2010.100014] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Medical sequencing for diseases with locus and allelic heterogeneities has been limited by the high cost and low throughput of traditional sequencing technologies. "Second-generation" sequencing (SGS) technologies allow the parallel processing of a large number of genes and, therefore, offer great promise for medical sequencing; however, their use in clinical laboratories is still in its infancy. Our laboratory offers clinical resequencing for dilated cardiomyopathy (DCM) using an array-based platform that interrogates 19 of more than 30 genes known to cause DCM. We explored both the feasibility and cost effectiveness of using PCR amplification followed by SGS technology for sequencing these 19 genes in a set of five samples enriched for known sequence alterations (109 unique substitutions and 27 insertions and deletions). While the analytical sensitivity for substitutions was comparable to that of the DCM array (98%), SGS technology performed better than the DCM array for insertions and deletions (90.6% versus 58%). Overall, SGS performed substantially better than did the current array-based testing platform; however, the operational cost and projected turnaround time do not meet our current standards. Therefore, efficient capture methods and/or sample pooling strategies that shorten the turnaround time and decrease reagent and labor costs are needed before implementing this platform into routine clinical applications.
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Affiliation(s)
- Sivakumar Gowrisankar
- Laboratory for Molecular Medicine, Partners HealthCare Center for Personalized Genetic Medicine, 65 Landsdowne St., Cambridge, MA 02139, USA
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13
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Abstract
PURPOSE Genetic tests for the most commonly mutated genes in dilated cardiomyopathy (DCM) can confirm a clinical diagnosis in the proband and inform family management. Presymptomatic family members can be identified, allowing for targeted clinical monitoring to minimize adverse outcomes. However, the marked locus and allelic heterogeneity associated with DCM have made clinical genetic testing challenging. Novel sequencing platforms have now opened up avenues for more comprehensive diagnostic testing while simultaneously decreasing test cost and turn around time. METHODS By using a custom design based on triplicate resequencing and separate genotyping of known disease-causing variants, we developed the DCM CardioChip for efficient analysis of 19 genes previously implicated in causing DCM. RESULTS The chip's analytical sensitivity for known and novel substitution variants is 100% and 98%, respectively. In screening 73 previously tested DCM patients who did not carry clinically significant variants in 10 genes, 7 variants of likely clinical significance were identified in the remaining 9 genes included on the chip. Compared with traditional Sanger-based sequencing, test cost and turn around time were reduced by approximately 50%. CONCLUSIONS The DCM CardioChip is a highly efficient screening test with a projected clinical sensitivity of 26-29%.
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14
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Mulle JG, Patel VC, Warren ST, Hegde MR, Cutler DJ, Zwick ME. Empirical evaluation of oligonucleotide probe selection for DNA microarrays. PLoS One 2010; 5:e9921. [PMID: 20360966 PMCID: PMC2847945 DOI: 10.1371/journal.pone.0009921] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 12/04/2009] [Indexed: 12/04/2022] Open
Abstract
DNA-based microarrays are increasingly central to biomedical research. Selecting oligonucleotide sequences that will behave consistently across experiments is essential to the design, production and performance of DNA microarrays. Here our aim was to improve on probe design parameters by empirically and systematically evaluating probe performance in a multivariate context. We used experimental data from 19 array CGH hybridizations to assess the probe performance of 385,474 probes tiled in the Duchenne muscular dystrophy (DMD) region of the X chromosome. Our results demonstrate that probe melting temperature, single nucleotide polymorphisms (SNPs), and homocytosine motifs all have a strong effect on probe behavior. These findings, when incorporated into future microarray probe selection algorithms, may improve microarray performance for a wide variety of applications.
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Affiliation(s)
- Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America.
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15
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Chen PE, Cook C, Stewart AC, Nagarajan N, Sommer DD, Pop M, Thomason B, Thomason MPK, Lentz S, Nolan N, Sozhamannan S, Sulakvelidze A, Mateczun A, Du L, Zwick ME, Read TD. Genomic characterization of the Yersinia genus. Genome Biol 2010; 11:R1. [PMID: 20047673 PMCID: PMC2847712 DOI: 10.1186/gb-2010-11-1-r1] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2009] [Revised: 10/07/2009] [Accepted: 01/04/2010] [Indexed: 01/18/2023] Open
Abstract
Comparative Yersinia genomics identifies features responsible for the colonization of specific host habitats and the horizontal transfer of virulence determinants. Background New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. Prior to this study, three species of the enterobacterial genus Yersinia that cause invasive human diseases (Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica) had been sequenced. However, there were no genomic data on the Yersinia species with more limited virulence potential, frequently found in soil and water environments. Results We used high-throughput sequencing-by-synthesis instruments to obtain 25- to 42-fold average redundancy, whole-genome shotgun data from the type strains of eight species: Y. aldovae, Y. bercovieri, Y. frederiksenii, Y. kristensenii, Y. intermedia, Y. mollaretii, Y. rohdei, and Y. ruckeri. The deepest branching species in the genus, Y. ruckeri, causative agent of red mouth disease in fish, has the smallest genome (3.7 Mb), although it shares the same core set of approximately 2,500 genes as the other members of the species, whose genomes range in size from 4.3 to 4.8 Mb. Yersinia genomes had a similar global partition of protein functions, as measured by the distribution of Cluster of Orthologous Groups families. Genome to genome variation in islands with genes encoding functions such as ureases, hydrogeneases and B-12 cofactor metabolite reactions may reflect adaptations to colonizing specific host habitats. Conclusions Rapid high-quality draft sequencing was used successfully to compare pathogenic and non-pathogenic members of the Yersinia genus. This work underscores the importance of the acquisition of horizontally transferred genes in the evolution of Y. pestis and points to virulence determinants that have been gained and lost on multiple occasions in the history of the genus.
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Affiliation(s)
- Peter E Chen
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, USA.
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16
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Abstract
The emergence of massively parallel DNA sequencing platforms has made resequencing an affordable approach to study genetic variation. However, the cost of whole genome resequencing remains too high to apply to large numbers of human samples. Genomic partitioning methods allow enrichment for regions of interest at a scale that is matched to the throughput of the new sequencing platforms. We review general categories of methods for genomic partitioning including multiplex PCR, capture-by-circularization, and capture-by-hybridization. Parameters that are relevant to the performance of any given method include multiplexity, specificity, uniformity, input requirements, scalability, and cost. The successful development of genomic partitioning strategies will be key to taking full advantage of massively parallel sequencing, at least until resequencing of complete mammalian genomes becomes widely affordable.
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Affiliation(s)
- Emily H Turner
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065, USA.
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Uttamchandani M, Neo JL, Ong BNZ, Moochhala S. Applications of microarrays in pathogen detection and biodefence. Trends Biotechnol 2008; 27:53-61. [PMID: 19008003 PMCID: PMC7114317 DOI: 10.1016/j.tibtech.2008.09.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 09/03/2008] [Accepted: 09/22/2008] [Indexed: 11/28/2022]
Abstract
The microarray is a platform with wide-ranging potential in biodefence. Owing to the high level of throughput attainable through miniaturization, microarrays have accelerated the ability to respond in an epidemic or crisis. Extending beyond diagnostics, recent studies have applied microarrays as a research tool towards understanding the etiology and pathogenicity of dangerous pathogens, as well as in vaccine development. The original emphasis was on DNA microarrays, but the range now includes protein, antibody and carbohydrate microarrays, and research groups have exploited this diversity to further extend microarray applications in the area of biodefence. Here, we discuss the impact and contributions of the growing range of microarrays and emphasize the concepts that might shape the future of biodefence research.
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Affiliation(s)
- Mahesh Uttamchandani
- Defence Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, 117510, Singapore.
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18
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Zwick ME, Kiley MP, Stewart AC, Mateczun A, Read TD. Genotyping of Bacillus cereus strains by microarray-based resequencing. PLoS One 2008; 3:e2513. [PMID: 18596941 PMCID: PMC2438477 DOI: 10.1371/journal.pone.0002513] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 05/18/2008] [Indexed: 11/20/2022] Open
Abstract
The ability to distinguish microbial pathogens from closely related but nonpathogenic strains is key to understanding the population biology of these organisms. In this regard, Bacillus anthracis, the bacterium that causes inhalational anthrax, is of interest because it is closely related and often difficult to distinguish from other members of the B. cereus group that can cause diverse diseases. We employed custom-designed resequencing arrays (RAs) based on the genome sequence of Bacillus anthracis to generate 422 kb of genomic sequence from a panel of 41 Bacillus cereus sensu lato strains. Here we show that RAs represent a “one reaction” genotyping technology with the ability to discriminate between highly similar B. anthracis isolates and more divergent strains of the B. cereus s.l. Clade 1. Our data show that RAs can be an efficient genotyping technology for pre-screening the genetic diversity of large strain collections to selected the best candidates for whole genome sequencing.
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Affiliation(s)
- Michael E Zwick
- Biological Defense Research Directorate, Naval Medical Research Center, Silver Spring, Maryland, United States of America. Michael E. Zwick
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19
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Steinberg KM, Okou DT, Zwick ME. Applying rapid genome sequencing technologies to characterize pathogen genomes. Anal Chem 2008; 80:520-8. [PMID: 18320606 DOI: 10.1021/ac086027z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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20
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Mandel MJ, Stabb EV, Ruby EG. Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: focus on point miscalls and artefactual expansions. BMC Genomics 2008; 9:138. [PMID: 18366731 PMCID: PMC2330054 DOI: 10.1186/1471-2164-9-138] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Accepted: 03/25/2008] [Indexed: 01/19/2023] Open
Abstract
Background Sequence closure often represents the end-point of a genome project, without a system in place for subsequent improvement and refinement. Building on the genome project of Vibrio fischeri ES114, we used a comparative approach to identify and investigate genes that had a high likelihood of sequence error. Results Comparison of the V. fischeri ES114 genome with that of conspecific strain MJ11 identified 82 target loci in ES114 as containing likely errors, and thus of high-priority for resequencing. Analysis of the targets identified 75 loci in which an error had occurred, resulting in the correction of 10,457 base pairs to generate the new ES114 genomic sequence. A majority of the inaccurate loci involved frameshift errors, correction of which fused adjacent ORFs. Although insertions/deletions are thought to be rare in microbial genome assemblies, fourteen of the loci contained extraneous sequence of over 300 bp, likely due to imperfect contig ends that were misassembled in tandem rather than as overlapping segments. Additionally we updated the entire genome annotation with 113 new features including previously uncalled protein-coding genes, regulatory RNA genes and operon leader peptides, and we analyzed the transcriptional apparatus encoded by ES114. Conclusion We demonstrate that errors in microbial genome sequences, thought to largely be confined to point mutations, may also consist of other prevalent large-scale rearrangements such as insertions. Ongoing genome quality control and annotation programs are necessary to accompany technological advancements in data generation. These updates further advance V. fischeri as an important model for understanding intercellular communication and colonization of animal tissue.
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Affiliation(s)
- Mark J Mandel
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, 1550 Linden Drive, Madison WI 53706-1521, USA.
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21
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Berthet N, Dickinson P, Filliol I, Reinhardt AK, Batejat C, Vallaeys T, Kong KA, Davies C, Lee W, Zhang S, Turpaz Y, Heym B, Coralie G, Dacheux L, Burguière AM, Bourhy H, Old IG, Manuguerra J, Cole ST, Kennedy GC. Massively parallel pathogen identification using high-density microarrays. Microb Biotechnol 2008; 1:79-86. [PMID: 21261824 PMCID: PMC3864434 DOI: 10.1111/j.1751-7915.2007.00012.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 09/28/2007] [Indexed: 11/29/2022] Open
Abstract
Identification of microbial pathogens in clinical specimens is still performed by phenotypic methods that are often slow and cumbersome, despite the availability of more comprehensive genotyping technologies. We present an approach based on whole-genome amplification and resequencing microarrays for unbiased pathogen detection. This 10 h process identifies a broad spectrum of bacterial and viral species and predicts antibiotic resistance and pathogenicity and virulence profiles. We successfully identify a variety of bacteria and viruses, both in isolation and in complex mixtures, and the high specificity of the microarray distinguishes between different pathogens that cause diseases with overlapping symptoms. The resequencing approach also allows identification of organisms whose sequences are not tiled on the array, greatly expanding the repertoire of identifiable organisms and their variants. We identify organisms by hybridization of their DNA in as little as 1-4 h. Using this method, we identified Monkeypox virus and drug-resistant Staphylococcus aureus in a skin lesion taken from a child suspected of an orthopoxvirus infection, despite poor transport conditions of the sample, and a vast excess of human DNA. Our results suggest this technology could be applied in a clinical setting to test for numerous pathogens in a rapid, sensitive and unbiased manner.
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Affiliation(s)
- Nicolas Berthet
- Genotyping of Pathogens and Public Health Technological Platform
| | | | - Ingrid Filliol
- Genotyping of Pathogens and Public Health Technological Platform
| | | | | | | | | | | | - Walter Lee
- Affymetrix, 3420 Central Expressway, Santa Clara, CA, USA
| | - Shenglan Zhang
- Affymetrix, 3420 Central Expressway, Santa Clara, CA, USA
| | - Yaron Turpaz
- Affymetrix, 3420 Central Expressway, Santa Clara, CA, USA
| | - Beate Heym
- Ambroise‐Paré Hospital, Boulogne‐Billancourt, France
| | | | | | | | | | | | | | - Stewart T. Cole
- Bacterial Molecular Genetics Unit, Institut Pasteur, Paris, France
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22
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Abstract
Fast-sequencing throughput methods have increased the number of completely sequenced bacterial genomes to about 400 by December 2006, with the number increasing rapidly. These include several strains. In silico methods of comparative genomics are of use in categorizing and phylogenetically sorting these bacteria. Various word-based tools have been used for quantifying the similarities and differences between entire genomes. The simple di-nucleotide frequency comparison, codon specificity and k-mer repeat detection are among some of the well-known methods. In this paper, we show that the Mutual Information function, which is a measure of correlations and a concept from Information Theory, is very effective in determining the similarities and differences among genome sequences of various strains of bacteria such as the plant pathogen Xylella fastidiosa, marine Cyanobacteria Prochlorococcus marinus or animal and human pathogens such as species of Ehrlichia and Legionella. The short-range three-base periodicity, small sequence repeats and long-range correlations taken together constitute a genome signature that can be used as a technique for identifying new bacterial strains with the help of strains already catalogued in the database. There have been several applications of using the Mutual Information function as a measure of correlations in genomics but this is the first whole genome analysis done to detect strain similarities and differences.
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Affiliation(s)
- D Swati
- Department of Physics, MMV, Banaras Hindu University, Varanasi 221005, India.
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23
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Pandya GA, Holmes MH, Sunkara S, Sparks A, Bai Y, Verratti K, Saeed K, Venepally P, Jarrahi B, Fleischmann RD, Peterson SN. A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform. Nucleic Acids Res 2007; 35:e148. [PMID: 18006572 PMCID: PMC2175352 DOI: 10.1093/nar/gkm918] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA resequencing arrays enable rapid acquisition of high-quality sequence data. This technology represents a promising platform for rapid high-resolution genotyping of microorganisms. Traditional array-based resequencing methods have relied on the use of specific PCR-amplified fragments from the query samples as hybridization targets. While this specificity in the target DNA population reduces the potential for artifacts caused by cross-hybridization, the subsampling of the query genome limits the sequence coverage that can be obtained and therefore reduces the technique's resolution as a genotyping method. We have developed and validated an Affymetrix Inc. GeneChip® array-based, whole-genome resequencing platform for Francisella tularensis, the causative agent of tularemia. A set of bioinformatic filters that targeted systematic base-calling errors caused by cross-hybridization between the whole-genome sample and the array probes and by deletions in the sample DNA relative to the chip reference sequence were developed. Our approach eliminated 91% of the false-positive single-nucleotide polymorphism calls identified in the SCHU S4 query sample, at the cost of 10.7% of the true positives, yielding a total base-calling accuracy of 99.992%.
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Affiliation(s)
- Gagan A Pandya
- Pathogen Functional Genomics Resource Center, The Institute for Genomic Research at the J. Craig Venter Institute, Rockville, MD 20850, USA
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24
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Microarray-based genomic selection for high-throughput resequencing. Nat Methods 2007; 4:907-9. [PMID: 17934469 DOI: 10.1038/nmeth1109] [Citation(s) in RCA: 277] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 09/20/2007] [Indexed: 11/08/2022]
Abstract
We developed a general method, microarray-based genomic selection (MGS), capable of selecting and enriching targeted sequences from complex eukaryotic genomes without the repeat blocking steps necessary for bacterial artificial chromosome (BAC)-based genomic selection. We demonstrate that large human genomic regions, on the order of hundreds of kilobases, can be enriched and resequenced with resequencing arrays. MGS, when combined with a next-generation resequencing technology, can enable large-scale resequencing in single-investigator laboratories.
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25
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Weng Z, Barthelson R, Gowda S, Hilf ME, Dawson WO, Galbraith DW, Xiong Z. Persistent infection and promiscuous recombination of multiple genotypes of an RNA virus within a single host generate extensive diversity. PLoS One 2007; 2:e917. [PMID: 17878952 PMCID: PMC1975466 DOI: 10.1371/journal.pone.0000917] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 08/20/2007] [Indexed: 11/19/2022] Open
Abstract
Recombination and reassortment of viral genomes are major processes contributing to the creation of new, emerging viruses. These processes are especially significant in long-term persistent infections where multiple viral genotypes co-replicate in a single host, generating abundant genotypic variants, some of which may possess novel host-colonizing and pathogenicity traits. In some plants, successive vegetative propagation of infected tissues and introduction of new genotypes of a virus by vector transmission allows for viral populations to increase in complexity for hundreds of years allowing co-replication and subsequent recombination of the multiple viral genotypes. Using a resequencing microarray, we examined a persistent infection by a Citrus tristeza virus (CTV) complex in citrus, a vegetatively propagated, globally important fruit crop, and found that the complex comprised three major and a number of minor genotypes. Subsequent deep sequencing analysis of the viral population confirmed the presence of the three major CTV genotypes and, in addition, revealed that the minor genotypes consisted of an extraordinarily large number of genetic variants generated by promiscuous recombination between the major genotypes. Further analysis provided evidence that some of the recombinants underwent subsequent divergence, further increasing the genotypic complexity. These data demonstrate that persistent infection of multiple viral genotypes within a host organism is sufficient to drive the large-scale production of viral genetic variants that may evolve into new and emerging viruses.
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Affiliation(s)
- Ziming Weng
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Roger Barthelson
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Siddarame Gowda
- Citrus Research and Education Center, University of Florida, Lake Alfred, Florida, United States of America
| | - Mark E. Hilf
- United States Department of Agriculture-Agricultural Research Service-United States Horticulture Research Laboratory, Fort Pierce, Florida, United States of America
| | - William O. Dawson
- Citrus Research and Education Center, University of Florida, Lake Alfred, Florida, United States of America
| | - David W. Galbraith
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Zhongguo Xiong
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
- * To whom correspondence should be addressed. E-mail:
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26
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Herring CD, Palsson BØ. An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes. BMC Genomics 2007; 8:274. [PMID: 17697331 PMCID: PMC2072959 DOI: 10.1186/1471-2164-8-274] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Accepted: 08/14/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the development of new technology, it has recently become practical to resequence the genome of a bacterium after experimental manipulation. It is critical though to know the accuracy of the technique used, and to establish confidence that all of the mutations were detected. RESULTS In order to evaluate the accuracy of genome resequencing using the microarray-based Comparative Genome Sequencing service provided by Nimblegen Systems Inc., we resequenced the E. coli strain W3110 Kohara using MG1655 as a reference, both of which have been completely sequenced using traditional sequencing methods. CGS detected 7 of 8 small sequence differences, one large deletion, and 9 of 12 IS element insertions present in W3110, but did not detect a large chromosomal inversion. In addition, we confirmed that CGS also detected 2 SNPs, one deletion and 7 IS element insertions that are not present in the genome sequence, which we attribute to changes that occurred after the creation of the W3110 lambda clone library. The false positive rate for SNPs was one per 244 Kb of genome sequence. CONCLUSION CGS is an effective way to detect multiple mutations present in one bacterium relative to another, and while highly cost-effective, is prone to certain errors. Mutations occurring in repeated sequences or in sequences with a high degree of secondary structure may go undetected. It is also critical to follow up on regions of interest in which SNPs were not called because they often indicate deletions or IS element insertions.
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Affiliation(s)
- Christopher D Herring
- Department of Bioengineering, University of California San Diego, La Jolla, USA
- Mascoma Corporation, 16 Cavendish Court, Lebanon, NH 03766, USA
| | - Bernhard Ø Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, USA
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27
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Bergman NH, Passalacqua KD, Hanna PC, Qin ZS. Operon prediction for sequenced bacterial genomes without experimental information. Appl Environ Microbiol 2007; 73:846-54. [PMID: 17122389 PMCID: PMC1800777 DOI: 10.1128/aem.01686-06] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 11/04/2006] [Indexed: 11/20/2022] Open
Abstract
Various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes. In this study, we explored the possibility of using phylogenetic information to aid in operon prediction, and we constructed a Bayesian hidden Markov model that incorporates comparative genomic data with traditional predictors, such as intergenic distances. The prediction algorithm performs as well as the best previously reported method, with several significant advantages. It uses fewer data sources and so it is easier to implement, and the method is more broadly applicable than previous methods--it can be applied to essentially every gene in any sequenced bacterial genome. Furthermore, we show that near-optimal performance is easily reached with a generic set of comparative genomes and does not depend on a specific relationship between the subject genome and the comparative set. We applied the algorithm to the Bacillus anthracis genome and found that it successfully predicted all previously verified B. anthracis operons. To further test its performance, we chose a predicted operon (BA1489-92) containing several genes with little apparent functional relatedness and tested their cotranscriptional nature. Experimental evidence shows that these genes are cotranscribed, and the data have interesting implications for B. anthracis biology. Overall, our findings show that this algorithm is capable of highly sensitive and accurate operon prediction in a wide range of bacterial genomes and that these predictions can lead to the rapid discovery of new functional relationships among genes.
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Affiliation(s)
- Nicholas H Bergman
- University of Michigan Medical School, Bioinformatics Program and Department of Microbiology & Immunology, 6605H Medical Sciences Bldg. II, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-0620, USA.
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28
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Chapter 5 The 454 Life Sciences Picoliter Sequencing System. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/s1871-0069(06)02005-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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29
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Ziebolz B, Droege M. Toward a new era in sequencing. ACTA ACUST UNITED AC 2007; 13:1-26. [PMID: 17875471 DOI: 10.1016/s1387-2656(07)13001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Sequencing is a powerful tool that helps scientists in gaining new insights in many areas of medicine and biology. The electrophoresis-based Sanger method is currently the most popular sequencing technology and was the foundation stone of the human genome project. With the Sanger technique it became possible to sequence not only complete genomes, but also fragments of genomes. Nowadays, this standard method is very close to reach its limits.
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30
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Sulaiman IM, Tang K, Osborne J, Sammons S, Wohlhueter RM. GeneChip resequencing of the smallpox virus genome can identify novel strains: a biodefense application. J Clin Microbiol 2006; 45:358-63. [PMID: 17182757 PMCID: PMC1829075 DOI: 10.1128/jcm.01848-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We developed a set of seven resequencing GeneChips, based on the complete genome sequences of 24 strains of smallpox virus (variola virus), for rapid characterization of this human-pathogenic virus. Each GeneChip was designed to analyze a divergent segment of approximately 30,000 bases of the smallpox virus genome. This study includes the hybridization results of 14 smallpox virus strains. Of the 14 smallpox virus strains hybridized, only 7 had sequence information included in the design of the smallpox virus resequencing GeneChips; similar information for the remaining strains was not tiled as a reference in these GeneChips. By use of variola virus-specific primers and long-range PCR, 22 overlapping amplicons were amplified to cover nearly the complete genome and hybridized with the smallpox virus resequencing GeneChip set. These GeneChips were successful in generating nucleotide sequences for all 14 of the smallpox virus strains hybridized. Analysis of the data indicated that the GeneChip resequencing by hybridization was fast and reproducible and that the smallpox virus resequencing GeneChips could differentiate the 14 smallpox virus strains characterized. This study also suggests that high-density resequencing GeneChips have potential biodefense applications and may be used as an alternate tool for rapid identification of smallpox virus in the future.
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Affiliation(s)
- Irshad M Sulaiman
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Preparedness, Detection, and Control of Infectious Diseases, Atlanta, GA 30333, USA.
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31
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Abstract
Over 120 inherited primary immunodeficiency diseases (PIDs) are known to exist. The genes responsible for many of these diseases have also been identified. Recent advances in diagnostic procedures have enabled these to be identified earlier and appropriately treated. While a number of approaches are available to identify mutations, direct sequencing remains the gold standard. This approach identifies the exact genetic change with substantial precision. We suggest that a sensitive and economical approach to mutation detection could be the direct sequencing of cDNA followed by the confirmatory sequencing of the corresponding exon. While screening techniques such as single-stranded conformation polymorphism (SSCP), heteroduplex analysis (HA), denaturing gradient gel electrophoresis (DGGE), and denaturing high-performance liquid chromatography (dHPLC) have proven useful, each has inherent advantages and disadvantages. We discuss these advantages and disadvantages and also discuss the potential of future sequencing technologies such as pyrosequencing, combinatorial sequencing-by-hybridization, multiplex polymerase colony (polony), and resequencing arrays as tools for future mutation detection. In addition we briefly discuss several high-throughput SNP detection technologies.
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Affiliation(s)
- Maurizio Costabile
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia.
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32
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Bailly X, Béna G, Lenief V, de Lajudie P, Avarre JC. Development of a lab-made microarray for analyzing the genetic diversity of nitrogen fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae. J Microbiol Methods 2006; 67:114-24. [PMID: 16626823 DOI: 10.1016/j.mimet.2006.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 03/09/2006] [Accepted: 03/09/2006] [Indexed: 11/20/2022]
Abstract
Some bacterial species, like nitrogen-fixing Sinorhizobium that interact with Medicago plants, are prone to frequent horizontal gene transfers. Investigation of their genetic structure requires to study polymorphism patterns at many loci. Although DNA microarrays represent a method of choice for high throughput analysis of polymorphisms, this technology yet remains an expensive and heavy approach, thus depriving most of research groups from this powerful tool. In an attempt to overcome this limitation, we have developed a simple genotyping procedure by DNA microarrays, and have evaluated its ability to characterize a Sinorhizobium population. Thirty 18- to 24-mer oligonucleotide probes were designed to target the most frequent mutations in three polymorphic loci of Sinorhizobium meliloti and S. medicae. Probe hybridization efficiency was compared on two spotting surfaces: nylon membranes and epoxy-coated glass slides. Epoxy-coated glass slides revealed more sensitive than nylon membranes and allowed discrimination of single mismatches. Using this procedure, an uncharacterized population consisting of 33 S. meliloti/S. medicae isolates was successfully genotyped.
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Affiliation(s)
- Xavier Bailly
- Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR113 IRD/INRA/CIRAD/UM2/Agro-M, Campus International de Baillarguet, Montpellier F34398, France
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33
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Malanoski AP, Lin B, Wang Z, Schnur JM, Stenger DA. Automated identification of multiple micro-organisms from resequencing DNA microarrays. Nucleic Acids Res 2006; 34:5300-11. [PMID: 17012284 PMCID: PMC1636417 DOI: 10.1093/nar/gkl565] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
There is an increasing recognition that detailed nucleic acid sequence information will be useful and even required in the diagnosis, treatment and surveillance of many significant pathogens. Because generating detailed information about pathogens leads to significantly larger amounts of data, it is necessary to develop automated analysis methods to reduce analysis time and to standardize identification criteria. This is especially important for multiple pathogen assays designed to reduce assay time and costs. In this paper, we present a successful algorithm for detecting pathogens and reporting the maximum level of detail possible using multi-pathogen resequencing microarrays. The algorithm filters the sequence of base calls from the microarray and finds entries in genetic databases that most closely match. Taxonomic databases are then used to relate these entries to each other so that the microorganism can be identified. Although developed using a resequencing microarray, the approach is applicable to any assay method that produces base call sequence information. The success and continued development of this approach means that a non-expert can now perform unassisted analysis of the results obtained from partial sequence data.
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Affiliation(s)
- Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, Code 6900, Naval Research Laboratory, Washington, DC 20375, USA.
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34
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Abstract
AIM Anthrax is caused by the bacterium Bacillus anthracis. Although primarily a disease of animals, it can also infect man, sometimes with fatal consequences. As a result of concerns over the illicit use of this organism, considerable effort is focussed on the development of therapies capable of conferring protection against anthrax. This brief review will describe the efforts being made to address these issues. METHODS AND RESULTS A review of the literature and the proceedings of the sixth international conference on anthrax, held in Santa Fe, USA in 2005 shows intense activity, but there has been as yet no real progress. While effective antibiotics, antitoxins and vaccines are available, concerns over their toxicity and the emergence of resistant strains have driven the development of second-generation products. The principal target for vaccine development is Protective Antigen (PA), the nontoxic cell-binding component of anthrax lethal toxin. While the recombinant products currently undergoing human clinical trials will offer considerable advantages in terms of reduced side effects and ease of production, they would still require multiple, needle-based dosing, and the inclusion of the adjuvant alum makes them expensive to administer and stockpile. To address these issues, researchers are developing vaccine formulations, which stimulate rapid protection following needle-free injection (nasal, oral or transcutaneous), and are stable at room temperature to facilitate stockpiling and mass vaccination programs. CONCLUSIONS An array of medical countermeasures targeting B. anthracis will become available over the next 5-10 years. SIGNIFICANCE AND IMPACT OF THE STUDY The huge investment of research dollars is expected to dramatically expand the knowledge base. A better understanding of basic issues, such as survival in nature and pathogenesis in humans, will facilitate the development of new modalities to eliminate the threat posed by this organism.
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Affiliation(s)
- L W J Baillie
- Biodefence Initiative, Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, 21201, USA.
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Lindroos H, Vinnere O, Mira A, Repsilber D, Näslund K, Andersson SGE. Genome rearrangements, deletions, and amplifications in the natural population of Bartonella henselae. J Bacteriol 2006; 188:7426-39. [PMID: 16936024 PMCID: PMC1636255 DOI: 10.1128/jb.00472-06] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cats are the natural host for Bartonella henselae, an opportunistic human pathogen and the agent of cat scratch disease. Here, we have analyzed the natural variation in gene content and genome structure of 38 Bartonella henselae strains isolated from cats and humans by comparative genome hybridizations to microarrays and probe hybridizations to pulsed-field gel electrophoresis (PFGE) blots. The variation in gene content was modest and confined to the prophage and the genomic islands, whereas the PFGE analyses indicated extensive rearrangements across the terminus of replication with breakpoints in areas of the genomic islands. We observed no difference in gene content or structure between feline and human strains. Rather, the results suggest multiple sources of human infection from feline B. henselae strains of diverse genotypes. Additionally, the microarray hybridizations revealed DNA amplification in some strains in the so-called chromosome II-like region. The amplified segments were centered at a position corresponding to a putative phage replication initiation site and increased in size with the duration of cultivation. We hypothesize that the variable gene pool in the B. henselae population plays an important role in the establishment of long-term persistent infection in the natural host by promoting antigenic variation and escape from the host immune response.
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Affiliation(s)
- Hillevi Lindroos
- Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, Norbyvägen 18C, S-752 36 Uppsala, Sweden
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Morse SA, Budowle B. Microbial forensics: application to bioterrorism preparedness and response. Infect Dis Clin North Am 2006; 20:455-73, xi. [PMID: 16762747 DOI: 10.1016/j.idc.2006.03.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Stephen A Morse
- Bioterrorism Preparedness and Response Program, Centers for Disease Control and Prevention, 1600 Clifton Road, MS C-12, Atlanta, GA 30333, USA.
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Wang Z, Daum LT, Vora GJ, Metzgar D, Walter EA, Canas LC, Malanoski AP, Lin B, Stenger DA. Identifying influenza viruses with resequencing microarrays. Emerg Infect Dis 2006; 12:638-46. [PMID: 16704813 PMCID: PMC3294710 DOI: 10.3201/eid1204.051441] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Resequencing microarrays rapidly identify influenza viruses. Identification of genetic variations of influenza viruses is essential for epidemic and pandemic outbreak surveillance and determination of vaccine strain selection. In this study, we combined a random amplification strategy with high-density resequencing microarray technology to demonstrate simultaneous detection and sequence-based typing of 25 geographically distributed human influenza virus strains collected in 2004 and 2005. In addition to identification, this method provided primary sequence information, which suggested that distinct lineages of influenza viruses co-circulated during the 2004–2005 season, and simultaneously identified and typed all component strains of the trivalent FluMist intranasal vaccine. The results demonstrate a novel, timely, and unbiased method for the molecular epidemiologic surveillance of influenza viruses.
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Affiliation(s)
- Zheng Wang
- Naval Research Laboratory, Washington, DC, USA
- NOVA Research Inc., Alexandria, Virginia, USA
| | - Luke T. Daum
- Air Force Institute for Operational Health, Brooks City Base, San Antonio, Texas, USA
| | | | - David Metzgar
- Naval Health Research Center, San Diego, California, USA
| | | | - Linda C. Canas
- Air Force Institute for Operational Health, Brooks City Base, San Antonio, Texas, USA
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Ragoussis J, Elvidge G. Affymetrix GeneChip system: moving from research to the clinic. Expert Rev Mol Diagn 2006; 6:145-52. [PMID: 16512775 DOI: 10.1586/14737159.6.2.145] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Affymetrix Inc.'s GeneChip technology has become the industry standard in microarray-based research. Due to the high density of content per array that can be achieved today (an industry leading 6.5 million features) the GeneChips can be used for high-throughput mutation detection, single nucleotide polymorphism genotyping, expression profiling and detection of chromosomal aberrations. This in turn opens the way for clinical applications in genetics, cytogenetics, pharmacogenetics, oncology and pathogen recognition. Establishing standards is a central issue in improving data quality and, in combination with automatic, easy-to-interpret reports, will form the basis of the clinical applicability. Future pricing policies and the resolving of ethical considerations will also dictate the technology's full translation from research into clinical laboratories.
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Affiliation(s)
- Jiannis Ragoussis
- Genomics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK.
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39
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Stratilo CW, Lewis CT, Bryden L, Mulvey MR, Bader D. Single-nucleotide repeat analysis for subtyping Bacillus anthracis isolates. J Clin Microbiol 2006; 44:777-82. [PMID: 16517854 PMCID: PMC1393151 DOI: 10.1128/jcm.44.3.777-782.2006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Single-nucleotide repeats (SNRs) are variable-number tandem repeats that display very high mutation rates. In an outbreak situation, the use of a marker system that exploits regions with very high mutation rates, such as SNRs, allows the differentiation of isolates with extremely low levels of genetic diversity. This report describes the identification and analysis of SNR loci of Bacillus anthracis. SNR loci were selected in silico, and the loci with the highest diversity were used to design and test locus-specific primers against a number of B. anthracis strains with the same multilocus variable-number tandem repeat analysis (MLVA) genotype. SNR markers that allowed strains with the same MLVA genotype to be differentiated from each other were identified. The resulting SNR marker system can be used as a molecular epidemiological tool in a natural outbreak or bioterrorism event, offering the best chance of distinguishing very closely related isolates.
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Affiliation(s)
- Chad W Stratilo
- Chemical and Biological Defence Section, Defence R&D Canada--Suffield Medicine Hat, AB, CBDS, P.O. Box 4000, Station Main, Medicine Hat, Alberta T1A 8K6, Canada.
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40
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Zhang W, Qi W, Albert TJ, Motiwala AS, Alland D, Hyytia-Trees EK, Ribot EM, Fields PI, Whittam TS, Swaminathan B. Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms. Genome Res 2006; 16:757-67. [PMID: 16606700 PMCID: PMC1473186 DOI: 10.1101/gr.4759706] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the two complete STEC O157 genomes (Sakai and EDL933) revealed a strikingly high level of sequence identity in orthologous protein-coding genes, limiting the use of nucleotide sequences to study the evolution and epidemiology of this bacterial pathogen. To systematically examine single nucleotide polymorphisms (SNPs) at a genome scale, we designed comparative genome sequencing microarrays and analyzed 1199 chromosomal genes (a total of 1,167,948 bp) and 92,721 bp of the large virulence plasmid (pO157) of eleven outbreak-associated STEC O157 strains. We discovered 906 SNPs in 523 chromosomal genes and observed a high level of DNA polymorphisms among the pO157 plasmids. Based on a uniform rate of synonymous substitution for Escherichia coli and Salmonella enterica (4.7x10(-9) per site per year), we estimate that the most recent common ancestor of the contemporary beta-glucuronidase-negative, non-sorbitolfermenting STEC O157 strains existed ca. 40 thousand years ago. The phylogeny of the STEC O157 strains based on the informative synonymous SNPs was compared to the maximum parsimony trees inferred from pulsed-field gel electrophoresis and multilocus variable numbers of tandem repeats analysis. The topological discrepancies indicate that, in contrast to the synonymous mutations, parts of STEC O157 genomes have evolved through different mechanisms with highly variable divergence rates. The SNP loci reported here will provide useful genetic markers for developing high-throughput methods for fine-resolution genotyping of STEC O157. Functional characterization of nucleotide polymorphisms should shed new insights on the evolution, epidemiology, and pathogenesis of STEC O157 and related pathogens.
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Affiliation(s)
- Wei Zhang
- Foodborne and Diarrheal Diseases Branch, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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41
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Budowle B, Johnson MD, Fraser CM, Leighton TJ, Murch RS, Chakraborty R. Genetic analysis and attribution of microbial forensics evidence. Crit Rev Microbiol 2006; 31:233-54. [PMID: 16417203 DOI: 10.1080/10408410500304082] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Because of the availability of pathogenic microorganisms and the relatively low cost of preparing and disseminating bioweapons, there is a continuing threat of biocrime and bioterrorism. Thus, enhanced capabilities are needed that enable the full and robust forensic exploitation and interpretation of microbial evidence from acts of bioterrorism or biocrimes. To respond to the need, greater resources and efforts are being applied to the burgeoning field of microbial forensics. Microbial forensics focuses on the characterization, analysis and interpretation of evidence for attributional purposes from a bioterrorism act, biocrime, hoax or inadvertent agent release. To enhance attribution capabilities, a major component of microbial forensics is the analysis of nucleic acids to associate or eliminate putative samples. The degree that attribution can be addressed depends on the context of the case, the available knowledge of the genetics, phylogeny, and ecology of the target microorganism, and technologies applied. The types of genetic markers and features that can impact statistical inferences of microbial forensic evidence include: single nucleotide polymorphisms, repetitive sequences, insertions and deletions, mobile elements, pathogenicity islands, virulence and resistance genes, house keeping genes, structural genes, whole genome sequences, asexual and sexual reproduction, horizontal gene transfer, conjugation, transduction, lysogeny, gene conversion, recombination, gene duplication, rearrangements, and mutational hotspots. Nucleic acid based typing technologies include: PCR, real-time PCR, MLST, MLVA, whole genome sequencing, and microarrays.
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42
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Sulaiman IM, Liu X, Frace M, Sulaiman N, Olsen-Rasmussen M, Neuhaus E, Rota PA, Wohlhueter RM. Evaluation of affymetrix severe acute respiratory syndrome resequencing GeneChips in characterization of the genomes of two strains of coronavirus infecting humans. Appl Environ Microbiol 2006; 72:207-11. [PMID: 16391044 PMCID: PMC1352236 DOI: 10.1128/aem.72.1.207-211.2006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome (SARS) was discovered during a recent global outbreak of atypical pneumonia. A number of immunologic and molecular studies of the clinical samples led to the conclusion that a novel coronavirus (SARS-CoV) was associated with the outbreak. Later, a SARS resequencing GeneChip was developed by Affymetrix to characterize the complete genome of SARS-CoV on a single GeneChip. The present study was carried out to evaluate the performance of SARS resequencing GeneChips. Two human SARS-CoV strains (CDC#200301157 and Urbani) were resequenced by the SARS GeneChips. Five overlapping PCR amplicons were generated for each strain and hybridized with these GeneChips. The successfully hybridized GeneChips generated nucleotide sequences of nearly complete genomes for the two SARS-CoV strains with an average call rate of 94.6%. Multiple alignments of nucleotide sequences obtained from SARS GeneChips and conventional sequencing revealed full concordance. Furthermore, the GeneChip-based analysis revealed no additional polymorphic sites. The results of this study suggest that GeneChip-based genome characterization is fast and reproducible. Thus, SARS resequencing GeneChips may be employed as an alternate tool to obtain genome sequences of SARS-CoV strains pathogenic for humans in order to further understand the transmission dynamics of these viruses.
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Affiliation(s)
- Irshad M Sulaiman
- Biotechnology Core Facility Branch, Scientific Resources Program, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Mailstop G-36, 1600 Clifton Road, Atlanta, GA 30333, USA.
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43
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Wirtenberger M, Hemminki K, Burwinkel B. Identification of frequent chromosome copy-number polymorphisms by use of high-resolution single-nucleotide-polymorphism arrays. Am J Hum Genet 2006; 78:520-2. [PMID: 16572511 PMCID: PMC1380295 DOI: 10.1086/500793] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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44
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Dorrell N, Hinchliffe SJ, Wren BW. Comparative phylogenomics of pathogenic bacteria by microarray analysis. Curr Opin Microbiol 2006; 8:620-6. [PMID: 16125441 PMCID: PMC7108221 DOI: 10.1016/j.mib.2005.08.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 08/15/2005] [Indexed: 10/31/2022]
Abstract
DNA microarrays represent a powerful technology that enables whole-scale comparison of bacterial genomes. This, coupled with new methods to model DNA microarray data, is facilitating the development of robust comparative phylogenomics analyses. Such studies have dramatically increased our ability to differentiate between bacteria, highlighting previously undetected genetic differences and population structures and providing new insight into virulence and evolution of bacterial pathogens. Recent results from such studies have generated insights into the evolution of bacterial pathogens, the levels of diversity and plasticity in the genome of a species, as well as the differences in virulence amongst pathogenic bacteria.
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45
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Tezak Z, Ranamukhaarachchi D, Russek-Cohen E, Gutman SI. FDA perspectives on potential microarray-based clinical diagnostics. Hum Genomics 2006; 2:236-43. [PMID: 16460648 PMCID: PMC3525154 DOI: 10.1186/1479-7364-2-4-236] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Accepted: 09/02/2005] [Indexed: 11/10/2022] Open
Abstract
The US Food and Drug Administration (FDA) encourages the development of new technologies such as microarrays which may improve and streamline assessments of safety and the effectiveness of medical products for the benefit of public health. The FDA anticipates that these new technologies may offer the potential for more effective approaches to medical treatment and disease prevention and management. This paper discusses issues associated with the translation of nucleic acid microarray-based devices from basic research and target discovery to in vitro clinical diagnostic use, which the Office of In Vitro Diagnostic Device Evaluation and Safety in the Center for Devices and Radiological Health foresees will be important for assurance of safety and effectiveness of these types of devices. General technological points, assessment of potential concerns for transitioning microarrays into clinical diagnostic use and approaches for evaluating the performance of these types of devices will be discussed.
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Affiliation(s)
- Zivana Tezak
- Office of In Vitro Diagnostic Device Evaluation and Safety, Center for Devices and Radiological Health, US Food and Drug Administration, Rockville, MD 20850, USA.
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46
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Polissi A, Soria MR. Functional genomics of bacterial pathogens: from post-genomics to therapeutic targets. Mol Microbiol 2005; 57:307-12. [PMID: 15978065 DOI: 10.1111/j.1365-2958.2005.04480.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A wealth of new data have become available to the scientific community as a result of the sequencing of many pathogen genomes. A recent meeting devoted to functional genomics of pathogenic microorganisms confirmed the notion that bacterial genomes are not static, because large blocks of genes can be acquired or deleted. Less complex environments usually result in reduction in genome size, while genome expansion is usually associated with environmental change and complexity. During the meeting, pathogenicity and evolutionary aspects were illustrated for enteric pathogens, as well as the microevolution of the plague bacillus Yersinia pestis. New clues for evolution and pathogenicity were derived from comparative genomics of Listeria species. The genomic organization of Bartonellae, an emerging human pathogen, was also discussed in an evolutionary context. Population and functional genomics of Anthrax-causing bacteria highlighted current scientific interest in this potential biothreat.
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Abstract
Bacillus anthracis is a pathogen of animals which rarely infects humans. Its use as a bioweapon has stimulated efforts to develop genetic typing methods and therapeutics to respond to an attack. Of particular concern is the transfer of virulence genes from B. anthracis to other closely related strains of bacillus.
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Affiliation(s)
- L W J Baillie
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201, USA.
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48
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Macdonald SJ, Pastinen T, Genissel A, Cornforth TW, Long AD. A low-cost open-source SNP genotyping platform for association mapping applications. Genome Biol 2005; 6:R105. [PMID: 16356268 PMCID: PMC1414086 DOI: 10.1186/gb-2005-6-12-r105] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 07/20/2005] [Accepted: 10/21/2005] [Indexed: 02/27/2023] Open
Abstract
Association mapping aimed at identifying DNA polymorphisms that contribute to variation in complex traits entails genotyping a large number of single-nucleotide polymorphisms (SNPs) in a very large panel of individuals. Few technologies, however, provide inexpensive high-throughput genotyping. Here, we present an efficient approach developed specifically for genotyping large fixed panels of diploid individuals. The cost-effective, open-source nature of our methodology may make it particularly attractive to those working in nonmodel systems.
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Affiliation(s)
- Stuart J Macdonald
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697-2525, USA
| | - Tomi Pastinen
- McGill University and Genome Québec Innovation Centre, 740 Docteur Penfield Avenue, Montreal, Québec H3A 1A4, Canada
| | - Anne Genissel
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697-2525, USA
- Section of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
| | - Theodore W Cornforth
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697-2525, USA
- Institute of Neuroscience, 1254 University of Oregon, Eugene, Oregon 97403-1254, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697-2525, USA
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49
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Rasko DA, Altherr MR, Han CS, Ravel J. Genomics of theBacillus cereusgroup of organisms. FEMS Microbiol Rev 2005. [DOI: 10.1016/j.fmrre.2004.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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