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Gao W, Li C, Wang F, Yang Y, Zhang L, Wang Z, Chen X, Tan M, Cao G, Zong G. An efflux pump in genomic island GI-M202a mediates the transfer of polymyxin B resistance in Pandoraea pnomenusa M202. Int Microbiol 2024; 27:277-290. [PMID: 37316617 PMCID: PMC10266961 DOI: 10.1007/s10123-023-00384-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/19/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Polymyxin B is considered a last-line therapeutic option against multidrug-resistant gram-negative bacteria, especially in COVID-19 coinfections or other serious infections. However, the risk of antimicrobial resistance and its spread to the environment should be brought to the forefront. METHODS Pandoraea pnomenusa M202 was isolated under selection with 8 mg/L polymyxin B from hospital sewage and then was sequenced by the PacBio RS II and Illumina HiSeq 4000 platforms. Mating experiments were performed to evaluate the transfer of the major facilitator superfamily (MFS) transporter in genomic islands (GIs) to Escherichia coli 25DN. The recombinant E. coli strain Mrc-3 harboring MFS transporter encoding gene FKQ53_RS21695 was also constructed. The influence of efflux pump inhibitors (EPIs) on MICs was determined. The mechanism of polymyxin B excretion mediated by FKQ53_RS21695 was investigated by Discovery Studio 2.0 based on homology modeling. RESULTS The MIC of polymyxin B for the multidrug-resistant bacterial strain P. pnomenusa M202, isolated from hospital sewage, was 96 mg/L. GI-M202a, harboring an MFS transporter-encoding gene and conjugative transfer protein-encoding genes of the type IV secretion system, was identified in P. pnomenusa M202. The mating experiment between M202 and E. coli 25DN reflected the transferability of polymyxin B resistance via GI-M202a. EPI and heterogeneous expression assays also suggested that the MFS transporter gene FKQ53_RS21695 in GI-M202a was responsible for polymyxin B resistance. Molecular docking revealed that the polymyxin B fatty acyl group inserts into the hydrophobic region of the transmembrane core with Pi-alkyl and unfavorable bump interactions, and then polymyxin B rotates around Tyr43 to externally display the peptide group during the efflux process, accompanied by an inward-to-outward conformational change in the MFS transporter. Additionally, verapamil and CCCP exhibited significant inhibition via competition for binding sites. CONCLUSIONS These findings demonstrated that GI-M202a along with the MFS transporter FKQ53_RS21695 in P. pnomenusa M202 could mediate the transmission of polymyxin B resistance.
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Affiliation(s)
- Wenhui Gao
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China
| | - Congcong Li
- Shandong Quancheng Test & Technology Limited Company, Ji'nan, 250101, China
| | - Fengtian Wang
- Jinan Municipal Minzu Hospital, Ji'nan, 250012, China
| | - Yilin Yang
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China
| | - Lu Zhang
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China
| | - Zhongxue Wang
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Xi Chen
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Meixia Tan
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Guangxiang Cao
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China.
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China.
| | - Gongli Zong
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China.
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China.
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Tedersoo L, Albertsen M, Anslan S, Callahan B. Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology. Appl Environ Microbiol 2021; 87:e0062621. [PMID: 34132589 PMCID: PMC8357291 DOI: 10.1128/aem.00626-21] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example, by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities, such as rapid molecular diagnostics and direct RNA sequencing, and both Pacific Biosciences (PacBio) and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long-read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Sten Anslan
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Benjamin Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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Dagher F, Nickzad A, Zheng J, Hoffmann M, Déziel E. Characterization of the biocontrol activity of three bacterial isolates against the phytopathogen Erwinia amylovora. Microbiologyopen 2021; 10:e1202. [PMID: 34180603 PMCID: PMC8182272 DOI: 10.1002/mbo3.1202] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 01/21/2023] Open
Abstract
Antibiotics are sprayed on apple and pear orchards to control, among other pathogens, the bacterium Erwinia amylovora, the causative agent of fire blight. As with many other pathogens, we observe the emergence of antibiotic-resistant strains of E. amylovora. Consequently, growers are looking for alternative solutions to combat fire blight. To find alternatives to antibiotics against this pathogen, we have previously isolated three bacterial strains with antagonistic and extracellular activity against E. amylovora, both in vitro and in planta, corresponding to three different bacterial genera: Here, we identified the inhibitory mode of action of each of the three isolates against E. amylovora. Isolate Bacillus amyloliquefaciens subsp. plantarum (now B. velezensis) FL50S produces several secondary metabolites including surfactins, iturins, and fengycins. Specifically, we identified oxydifficidin as the most active against E. amylovora S435. Pseudomonas poae FL10F produces an active extracellular compound against E. amylovora S435 that can be attributed to white-line-inducing principle (WLIP), a cyclic lipopeptide belonging to the viscosin subfamily (massetolide E, F, L, or viscosin). Pantoea agglomerans NY60 has a direct cell-to-cell antagonistic effect against E. amylovora S435. By screening mutants of this strain generated by random transposon insertion with decreased antagonist activity against strain S435, we identified several defective transposants. Of particular interest was a mutant in a gene coding for a Major Facilitator Superfamily (MFS) transporter corresponding to a transmembrane protein predicted to be involved in the extracytoplasmic localization of griseoluteic acid, an intermediate in the biosynthesis of the broad-spectrum phenazine antibiotic D-alanylgriseoluteic acid.
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Affiliation(s)
- Fadi Dagher
- Centre Armand‐Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS)LavalQuébecH7V 1B7Canada
| | - Arvin Nickzad
- Centre Armand‐Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS)LavalQuébecH7V 1B7Canada
| | - Jie Zheng
- US Food and Drug Administration Regulatory Science Center for Food Safety and Applied NutritionCollege ParkMarylandUSA
| | - Maria Hoffmann
- US Food and Drug Administration Regulatory Science Center for Food Safety and Applied NutritionCollege ParkMarylandUSA
| | - Eric Déziel
- Centre Armand‐Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS)LavalQuébecH7V 1B7Canada
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Haghshenas E, Hach F, Sahinalp SC, Chauve C. CoLoRMap: Correcting Long Reads by Mapping short reads. Bioinformatics 2017; 32:i545-i551. [PMID: 27587673 DOI: 10.1093/bioinformatics/btw463] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
MOTIVATION Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are characterized by a high error rate, and assembling from long reads require a high depth of coverage. This motivates the development of hybrid approaches that leverage the high quality of short reads to correct errors in long reads. RESULTS We introduce CoLoRMap, a hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology, using high-quality Illumina paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algorithm to find a sequence of overlapping short reads that minimizes the edit score to a long read and extending corrected regions by local assembly of unmapped mates of mapped short reads. Our results on bacterial, fungal and insect data sets show that CoLoRMap compares well with existing hybrid correction methods. AVAILABILITY AND IMPLEMENTATION The source code of CoLoRMap is freely available for non-commercial use at https://github.com/sfu-compbio/colormap CONTACT ehaghshe@sfu.ca or cedric.chauve@sfu.ca SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ehsan Haghshenas
- School of Computing Sciences MADD-Gen Graduate Program, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Faraz Hach
- School of Computing Sciences Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - S Cenk Sahinalp
- School of Computing Sciences Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada, School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Cedric Chauve
- Department of Mathematics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Complete Genome Sequence of Bacillus subtilis J-5, a Potential Biocontrol Agent. GENOME ANNOUNCEMENTS 2017; 5:5/23/e00275-17. [PMID: 28596389 PMCID: PMC5465608 DOI: 10.1128/genomea.00275-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacillus subtilis J-5 was isolated from tomato rhizosphere soil and exhibited strong inhibitory activity against Botrytis cinerea. To shed light on the molecular mechanism underlying the biological control on phytopathogens, the whole genome of this strain was sequenced. Genes encoding antimicrobial compounds and the regulatory systems were identified in the genome.
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Ee R, Lim YL, Yin WF, See-Too WS, Roberts RJ, Chan KG. Novel Methyltransferase Recognition Motif Identified in Chania multitudinisentens RB-25(T) gen. nov., sp. nov. Front Microbiol 2016; 7:1362. [PMID: 27630623 PMCID: PMC5005818 DOI: 10.3389/fmicb.2016.01362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/17/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Robson Ee
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | | | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
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Lim YL, Ee R, How KY, Lee SK, Yong D, Tee KK, Yin WF, Chan KG. Complete genome sequencing of Pandoraea pnomenusa RB38 and Molecular Characterization of Its N-acyl homoserine lactone synthase gene ppnI. PeerJ 2015; 3:e1225. [PMID: 26336650 PMCID: PMC4556143 DOI: 10.7717/peerj.1225] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 08/11/2015] [Indexed: 01/05/2023] Open
Abstract
In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1. An additional orphan luxR homolog, ppnR2, was also discovered. Multiple sequence alignment and phylogenetic analysis revealed that ppnI is an N-acyl homoserine lactone (AHL) synthase gene that is distinct from those of the nearest phylogenetic neighbor viz. Burkholderia spp. High resolution tandem mass spectrometry (LC-MS/MS) analysis showed that Escherichia coli BL21 harboring ppnI produced a similar AHL profile (N-octanoylhomoserine lactone, C8-HSL) as P. pnomenusa RB38, the wild-type donor strain, confirming that PpnI directed the synthesis of AHL in P. pnomenusa RB38. To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea.
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Affiliation(s)
- Yan-Lue Lim
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Kah-Yan How
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Siew-Kim Lee
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Delicia Yong
- Department of Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Kok Keng Tee
- Department of Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
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Draft Genome Sequence of a Natural Root Isolate, Bacillus subtilis UD1022, a Potential Plant Growth-Promoting Biocontrol Agent. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00696-15. [PMID: 26159522 PMCID: PMC4490843 DOI: 10.1128/genomea.00696-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Bacillus subtilis, which belongs to the phylum Firmicutes, is the most widely studied Gram-positive model organism. It is found in a wide variety of environments and is particularly abundant in soils and in the gastrointestinal tracts of ruminants and humans. Here, we present the complete genome sequence of the newly described B. subtilis strain UD1022. The UD1022 genome consists of a 4.025-Mbp chromosome, and other major findings from our analysis will provide insights into the genomic basis of it being a plant growth-promoting rhizobacterium (PGPR) with biocontrol potential.
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Insights on Quorum-Quenching Properties of Lysinibacillus fusiformis Strain RB21, a Malaysian Municipal Solid-Waste Landfill Soil Isolate, via Complete Genome Sequence Analysis. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00409-15. [PMID: 25953192 PMCID: PMC4424308 DOI: 10.1128/genomea.00409-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lysinibacillus fusiformis strain RB21 is a quorum-quenching bacterium that is able to degrade quorum-sensing signaling molecules. Here, we present the first complete genome sequence of L. fusiformis strain RB21. The finished genome is 4.8 Mbp in size, and the quorum-quenching gene was identified.
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Genome Sequences of Two Pandoraea pnomenusa Isolates Recovered 11 Months Apart from a Cystic Fibrosis Patient. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01389-14. [PMID: 25657265 PMCID: PMC4319598 DOI: 10.1128/genomea.01389-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pandoraea is an emerging respiratory pathogen capable of causing chronic lung infections in people with cystic fibrosis (CF), but the clinical significance of this infection is ambiguous. We have sequenced and annotated the genomes of two multidrug-resistant Pandoraea pnomenusa isolates recovered 11 months apart from the same CF patient.
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Bahassi EM, Stambrook PJ. Next-generation sequencing technologies: breaking the sound barrier of human genetics. Mutagenesis 2014; 29:303-10. [PMID: 25150023 PMCID: PMC7318892 DOI: 10.1093/mutage/geu031] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Demand for new technologies that deliver fast, inexpensive and accurate genome information has never been greater. This challenge has catalysed the rapid development of advances in next-generation sequencing (NGS). The generation of large volumes of sequence data and the speed of data acquisition are the primary advantages over previous, more standard methods. In 2013, the Food and Drug Administration granted marketing authorisation for the first high-throughput NG sequencer, Illumina's MiSeqDx, which allowed the development and use of a large number of new genome-based tests. Here, we present a review of template preparation, nucleic acid sequencing and imaging, genome assembly and alignment approaches as well as recent advances in current and near-term commercially available NGS instruments. We also outline the broad range of applications for NGS technologies and provide guidelines for platform selection to best address biological questions of interest. DNA sequencing has revolutionised biological and medical research, and is poised to have a similar impact on the practice of medicine. This tool is but one of an increasing arsenal of developing tools that enhance our capabilities to identify, quantify and functionally characterise the components of biological networks that keep us healthy or make us sick. Despite advances in other 'omic' technologies, DNA sequencing and analysis, in many respects, have played the leading role to date. The new technologies provide a bridge between genotype and phenotype, both in man and model organisms, and have revolutionised how risk of developing a complex human disease may be assessed. The generation of large DNA sequence data sets is producing a wealth of medically relevant information on a large number of individuals and populations that will potentially form the basis of truly individualised medical care in the future.
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Affiliation(s)
- El Mustapha Bahassi
- Department of Internal Medicine, Division of Hematology/Oncology, UC Brain Tumor Center, University of Cincinnati, 3125 Eden Avenue, Cincinnati, OH 45267-0508, USA, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, 3125 Eden Avenue, Cincinnati, OH 45267-0508, USA
| | - Peter J Stambrook
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, 3125 Eden Avenue, Cincinnati, OH 45267-0508, USA
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