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Abstract
The invention of the Polymerase Chain Reaction (PCR) has revolutionized molecular biology enabling gene isolation and characterization in hours rather than days. Scientists working in transplant diagnostics have proven to be pioneers in adapting this molecular technique to the clinical needs of histocompatibility testing. This chapter describes a number of novel genotyping technologies which have been used to address the challenges posed by genetic diversity seen in the extensive polymorphism in HLA genes. These novel approaches include single-stranded and duplex conformational analyses, real-time PCR, microarray hybridization, RNA-based sequencing, and the present day Next Generation Sequencing. The chapter concludes with a brief look at a possible next, Next Generation Sequencing system.
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Zhang GL, Keskin DB, Lin HN, Lin HH, DeLuca DS, Leppanen S, Milford EL, Reinherz EL, Brusic V. Human leukocyte antigen typing using a knowledge base coupled with a high-throughput oligonucleotide probe array analysis. Front Immunol 2014; 5:597. [PMID: 25505899 PMCID: PMC4245923 DOI: 10.3389/fimmu.2014.00597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 11/06/2014] [Indexed: 01/11/2023] Open
Abstract
Human leukocyte antigens (HLA) are important biomarkers because multiple diseases, drug toxicity, and vaccine responses reveal strong HLA associations. Current clinical HLA typing is an elimination process requiring serial testing. We present an alternative in situ synthesized DNA-based microarray method that contains hundreds of thousands of probes representing a complete overlapping set covering 1,610 clinically relevant HLA class I alleles accompanied by computational tools for assigning HLA type to 4-digit resolution. Our proof-of-concept experiment included 21 blood samples, 18 cell lines, and multiple controls. The method is accurate, robust, and amenable to automation. Typing errors were restricted to homozygous samples or those with very closely related alleles from the same locus, but readily resolved by targeted DNA sequencing validation of flagged samples. High-throughput HLA typing technologies that are effective, yet inexpensive, can be used to analyze the world's populations, benefiting both global public health and personalized health care.
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Affiliation(s)
- Guang Lan Zhang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Computer Science, Metropolitan College, Boston University , Boston, MA , USA
| | - Derin B Keskin
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA ; Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, MA , USA
| | - Hsin-Nan Lin
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Institute of Information Science, Academia Sinica , Taipei , Taiwan
| | - Hong Huang Lin
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Boston University School of Medicine , Boston, MA , USA
| | - David S DeLuca
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA
| | | | - Edgar L Milford
- Department of Medicine, Harvard Medical School , Boston, MA , USA ; Histocompatibility and Tissue Typing Laboratory, Brigham and Women's Hospital , Boston, MA , USA
| | - Ellis L Reinherz
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA ; Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, MA , USA
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Computer Science, Metropolitan College, Boston University , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA
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Rue-Albrecht K, Magee DA, Killick KE, Nalpas NC, Gordon SV, MacHugh DE. Comparative functional genomics and the bovine macrophage response to strains of the mycobacterium genus. Front Immunol 2014; 5:536. [PMID: 25414700 PMCID: PMC4220711 DOI: 10.3389/fimmu.2014.00536] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/10/2014] [Indexed: 02/06/2023] Open
Abstract
Mycobacterial infections are major causes of morbidity and mortality in cattle and are also potential zoonotic agents with implications for human health. Despite the implementation of comprehensive animal surveillance programs, many mycobacterial diseases have remained recalcitrant to eradication in several industrialized countries. Two major mycobacterial pathogens of cattle are Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis (MAP), the causative agents of bovine tuberculosis (BTB) and Johne's disease (JD), respectively. BTB is a chronic, granulomatous disease of the respiratory tract that is spread via aerosol transmission, while JD is a chronic granulomatous disease of the intestines that is transmitted via the fecal-oral route. Although these diseases exhibit differential tissue tropism and distinct complex etiologies, both M. bovis and MAP infect, reside, and replicate in host macrophages - the key host innate immune cell that encounters mycobacterial pathogens after initial exposure and mediates the subsequent immune response. The persistence of M. bovis and MAP in macrophages relies on a diverse series of immunomodulatory mechanisms, including the inhibition of phagosome maturation and apoptosis, generation of cytokine-induced necrosis enabling dissemination of infection through the host, local pathology, and ultimately shedding of the pathogen. Here, we review the bovine macrophage response to infection with M. bovis and MAP. In particular, we describe how recent advances in functional genomics are shedding light on the host macrophage-pathogen interactions that underlie different mycobacterial diseases. To illustrate this, we present new analyses of previously published bovine macrophage transcriptomics data following in vitro infection with virulent M. bovis, the attenuated vaccine strain M. bovis BCG, and MAP, and discuss our findings with respect to the differing etiologies of BTB and JD.
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Affiliation(s)
- Kévin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - David A. Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Kate E. Killick
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Nicolas C. Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - David E. MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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Menegatti E, Berardi D, Messina M, Ferrante I, Giachino O, Spagnolo B, Restagno G, Cognolato L, Roccatello D. Lab-on-a-chip: emerging analytical platforms for immune-mediated diseases. Autoimmun Rev 2012; 12:814-20. [PMID: 23219952 DOI: 10.1016/j.autrev.2012.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Miniaturization of analytical procedures has a significant impact on diagnostic testing since it provides several advantages such as: reduced sample and reagent consumption, shorter analysis time and less sample handling. Lab-on-a-chip (LoC), usually silicon, glass, or silicon-glass, or polymer disposable cartridges, which are produced using techniques inherited from the microelectronics industry, could perform and integrate the operations needed to carry out biochemical analysis through the mechanical realization of a dedicated instrument. Analytical devices based on miniaturized platforms like LoC may provide an important contribution to the diagnosis of high prevalence and rare diseases. In this paper we review some of the uses of Lab-on-a-chip in the clinical diagnostics of immune-mediated diseases and we provide an overview of how specific applications of these technologies could improve and simplify several complex diagnostic procedures.
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Affiliation(s)
- Elisa Menegatti
- Department of Medicine and Experimental Oncology, Section of Clinical Pathology, University of Turin, Turin, Italy.
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Dunn PPJ. Human leucocyte antigen typing: techniques and technology, a critical appraisal. Int J Immunogenet 2012; 38:463-73. [PMID: 22059555 DOI: 10.1111/j.1744-313x.2011.01040.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Methods for the identification of Human Leukocyte Antigens (HLA) have changed significantly since this group of polymorphic proteins were first characterized by serological reagents in the 1960s and 1970s. The invention and development of the Polymerase Chain Reaction (PCR) has been key in the progress of methods for HLA genotyping. As the complexity of HLA polymorphism has unravelled so it has exposed the weaknesses in techniques such as PCR - Restriction Fragment Length Polymorphism (RFLP) and Reference Strand Mediated Conformation Analysis (RSCA), which are no longer in use today. Methods which have been considered routine laboratory tools in recent years, such as Sequence-Specific Primer - PCR and Sequencing Based Typing (SBT) are now also threatened with extinction, not only because of the depth of HLA variation but also because of the rapid development of Next Generation Sequencing and technologies which will follow this. This review describes the merits and disadvantages of current technologies available to HLA Typing laboratories, future trends and the problems posed by new alleles.
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Affiliation(s)
- P P J Dunn
- Tissue Typing Laboratory, New Zealand Blood Service, Auckland, New Zealand.
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Neumann T, Bonham AJ, Dame G, Berchtold B, Brandstetter T, Rühe J. Temperature and Time-Resolved Total Internal Reflectance Fluorescence Analysis of Reusable DNA Hydrogel Chips. Anal Chem 2010; 82:6124-31. [DOI: 10.1021/ac1008578] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thorsten Neumann
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
| | - Andrew J. Bonham
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
| | - Gregory Dame
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
| | - Bernd Berchtold
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
| | - Thomas Brandstetter
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
| | - Jürgen Rühe
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
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Feng C, Putonti C, Zhang M, Eggers R, Mitra R, Hogan M, Jayaraman K, Fofanov Y. Ultraspecific probes for high throughput HLA typing. BMC Genomics 2009; 10:85. [PMID: 19232123 PMCID: PMC2661095 DOI: 10.1186/1471-2164-10-85] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 02/20/2009] [Indexed: 11/23/2022] Open
Abstract
Background The variations within an individual's HLA (Human Leukocyte Antigen) genes have been linked to many immunological events, e.g. susceptibility to disease, response to vaccines, and the success of blood, tissue, and organ transplants. Although the microarray format has the potential to achieve high-resolution typing, this has yet to be attained due to inefficiencies of current probe design strategies. Results We present a novel three-step approach for the design of high-throughput microarray assays for HLA typing. This approach first selects sequences containing the SNPs present in all alleles of the locus of interest and next calculates the number of base changes necessary to convert a candidate probe sequences to the closest subsequence within the set of sequences that are likely to be present in the sample including the remainder of the human genome in order to identify those candidate probes which are "ultraspecific" for the allele of interest. Due to the high specificity of these sequences, it is possible that preliminary steps such as PCR amplification are no longer necessary. Lastly, the minimum number of these ultraspecific probes is selected such that the highest resolution typing can be achieved for the minimal cost of production. As an example, an array was designed and in silico results were obtained for typing of the HLA-B locus. Conclusion The assay presented here provides a higher resolution than has previously been developed and includes more alleles than previously considered. Based upon the in silico and preliminary experimental results, we believe that the proposed approach can be readily applied to any highly polymorphic gene system.
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Affiliation(s)
- Chen Feng
- Department of Computer Science, University of Houston, Houston, TX, USA.
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Rouillard JM, Gulari E. OligoArrayDb: pangenomic oligonucleotide microarray probe sets database. Nucleic Acids Res 2008; 37:D938-41. [PMID: 18948290 PMCID: PMC2686523 DOI: 10.1093/nar/gkn761] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OligoArrayDb is a comprehensive database containing pangenomic oligonucleotide microarray probe sets designed for most of the sequenced genomes that are not covered by commercial catalog arrays. The availability of probe sequences, associated with custom microarray fabrication services offered by many companies and cores presents the unequalled possibility to perform microarray experiments on most of the sequenced organisms. OligoArrayDb contains more than 2.8 probes per gene in average for more than 600 organisms, mostly archaea and bacteria strains available from public database. On average, 98% of the annotated genes have at least one probe which is predicted to be specific to its intended target in >94% of the cases. OligoArrayDb is weekly updated as new sequenced genomes become available. Probe sequences, in addition to a comprehensive set of annotations can be downloaded from this database. OligoArrayDb is publicly accessible online at http://berry.engin.umich.edu/oligoarraydb.
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Affiliation(s)
- Jean-Marie Rouillard
- Chemical Engineering Department, University of Michigan, 2300 Hayward Street, Ann Arbor, MI 48109, USA.
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Kim YR, Min J, Lee IH, Kim S, Kim AG, Kim K, Namkoong K, Ko C. Nanopore sensor for fast label-free detection of short double-stranded DNAs. Biosens Bioelectron 2007; 22:2926-31. [PMID: 17218091 DOI: 10.1016/j.bios.2006.12.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 11/27/2006] [Accepted: 12/01/2006] [Indexed: 11/16/2022]
Abstract
Functionalizing surface enhanced the molecular sensing ability of a fabricated nanopore by increasing the translocation duration time for a short double-stranded DNA. The surface of nanopore was derivatized with gamma-aminopropyltriethoxysilane and the positively charged surface attracted DNA molecules when they were in the vicinity of nanopore. The translocation duration time of DNA increased due to the strong electrostatic interaction and it enabled us to detect a short double-stranded DNA (<1 kbp) that is under the size limit of a conventional solid state nanopore sensor. Both 539 and 910 bp double-stranded DNAs were analyzed with the surface functionalized nanopore and their translocation kinetics are presented in this work. The new feature of the surface modified nanopore that can detect short double-stranded DNA molecules could readily be applied for a rapid label-free diagnostic analysis in a Lab-On-a-Chip type DNA sensor.
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Affiliation(s)
- Young-Rok Kim
- Bio Device Research Laboratory, Samsung Advanced Institute of Technology, Mt. 14-1, Nongseo-Dong, Giheung-Gu, Yongin-Si 449-712, South Korea
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